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    Evolutionary adaptation of anaerobic and aerobic metabolism to high sulfide and hypoxic hydrothermal vent crab, Xenograpsus testudinatus

    AbstractThe vent crab, Xenograpsus testudinatus (xtcrab), is adapted to inhabit shallow-water, high sulfide and hypoxic hydrothermal vent. Our previous study revealed sulfide tolerance of vent xtcrabs which sulfide: quinone oxidoreductase (xtSQR) paralogs aid in sulfide detoxification. However, the mechanisms of how xtcrab adapts to high sulfide-hypoxic conditions in the vent area remain to be explored. In the present study, we tested the tolerance of xtcrab to sulfide-induced hypoxia, and investigated their aerobic and anaerobic responses in situ and in the laboratory. Comparisons were made to a non-vent, intertidal species, Thranita danae (tdcrab). We analyzed the several factors related to aerobic metabolism (SQR, cytochrome c [CYTC], complex IV [COXIV]), the product of anaerobic metabolism (hemolymph lactate levels) and glucose levels. Our results showed a higher survival tolerance to hypoxia of xtcrabs than tdcrabs. Hemolymph lactate levels increased more rapidly in xtcrabs than tdcrabs exposed to experimental hypoxia, revealing a rapid induction of anaerobic metabolism in hypoxic xtcrabs. Lactate measurement in xtcrabs returned from aquaria to original capture sites (vent habitats), further assessed the remarkable ability of xtcrabs to rapidly switch on and off their anaerobic metabolism. To assess aerobic metabolism, long-term exposure of xtcrabs to hydrothermal vent habitat increased gill xtCYTC transcripts and protein levels together with steadily enzymatic activity of COXIV. This revealed ability of xtcrabs to maintain functional capacity of aerobic respiration in hypoxia. Phylogenetic analysis showed that xtSQR paralogs in xtcrabs were more distant compared to tdSQR paralogs in tdcrabs. The increase of transcripts and enzymatic activity of gill xtSQR, and co-localization of xtSQR and xtCYTC also contribute to maintain aerobic metabolism by preventing sulfide toxicity on mitochondrial respiratory function. Overall, our study suggests that multiple strategies including detoxification of sulfide by gill xtSQR, and a quick/dynamic switch between aerobic and anaerobic metabolisms may play important roles in the metabolic adaptations of xtcrabs to extreme hydrothermal vent environment.

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    The original data are available from Chi Chen and Ching-Fong Chang upon requests.
    ReferencesWannamaker, C. M. & Rice, J. A. Effects of hypoxia on movements and behavior of selected estuarine organisms from the southeastern united States. J. Exp. Mar. Biol. Ecol. 249 (2), 145–163. https://doi.org/10.1016/s0022-0981(00)00160-x (2000).
    Google Scholar 
    Giomi, F. & Beltramini, M. The molecular heterogeneity of hemocyanin: its role in the adaptive plasticity of crustacea. Gene 398 (1–2), 192–201. https://doi.org/10.1016/j.gene.2007.02.039 (2007).
    Google Scholar 
    McMahon, B. R. Respiratory and circulatory compensation to hypoxia in crustaceans. Respir Physiol. 128 (3), 349–364. https://doi.org/10.1016/S0034-5687(01)00311-5 (2001).
    Google Scholar 
    de Lima, T. M., Geihs, M. A., Nery, L. E. M. & Maciel, F. E. Air exposure behavior of the semiterrestrial crab Neohelice granulata allows tolerance to severe hypoxia but not prevent oxidative damage due to hypoxia–reoxygenation cycle. Physiol. Behav. 151, 97–101. https://doi.org/10.1016/j.physbeh.2015.07.013 (2015).
    Google Scholar 
    de Lima, T. M. et al. Emersion behavior of the semi-terrestrial crab Neohelice granulata during hypoxic conditions: Lactate as a trigger. Comp Biochem Physiol A Mol Integr Physiol, 252, 110835. (2021). https://doi.org/10.1016/j.cbpa.2020.110835 (2021).Hirota, S. et al. Structural basis of the lactate-dependent allosteric regulation of oxygen binding in arthropod Hemocyanin. J. Biol. Chem. 285 (25), 19338–19345 (2010).
    Google Scholar 
    Van Dover, C. L. The Ecology of deep-sea Hydrothermal Vents (Princeton University Press, 2000). https://doi.org/10.1515/9780691239477Powell, M. & Somero, G. Adaptations to sulfide by hydrothermal vent animals: sites and mechanisms of detoxification and metabolism. Biol. Bull. 171 (1), 274–290 (1986).
    Google Scholar 
    Chiu, L. et al. Shallow-water hydrothermal vent system as an extreme proxy for discovery of Microbiome significance in a crustacean holobiont. Front. Mar. Sci. 1670. https://doi.org/10.3389/fmars.2022.976255 (2022).Sun, Y. et al. Adaption to hydrogen sulfide-rich environments: strategies for active detoxification in deep-sea symbiotic mussels, Gigantidas platifrons. Sci. Total Environ. 804, 150054. https://doi.org/10.1016/j.scitotenv.2021.150054 (2022).
    Google Scholar 
    Mickel, T. J. & Childress, J. J. Effects of temperature, pressure, and oxygen concentration on the oxygen consumption rate of the hydrothermal vent crab bythograea thermydron (Brachyura). Physiol. Zool. 55 (2), 199–207 (1982).
    Google Scholar 
    Sanders, N. & Childress, J. Specific effects of thiosulphate and L-lactate on hemocyanin-O2 affinity in a brachyuran hydrothermal vent crab. Mar. Biol. 113 (2), 175–180. https://doi.org/10.1007/BF00347269 (1992).
    Google Scholar 
    Jeng, M. S., Ng, N. & Ng, P. Hydrothermal vent crabs feast on sea ‘snow’. Nature 432 (7020), 969–969. https://doi.org/10.1038/432969a (2004).
    Google Scholar 
    Chen, C. et al. Duplicated paralog of sulfide: Quinone oxidoreductase contributes to the adaptation to hydrogen sulfide-rich environment in the hydrothermal vent crab, xenograpsus testudinatus. Sci. Total Environ. 890, 164257. https://doi.org/10.1016/j.scitotenv.2023.164257 (2023).
    Google Scholar 
    Corrigan, E., Chen, C. J., Wang, B. S., Dufour, S. & Chang, C. F. Robustness of gametogenesis in the scleractinian coral, Tubastraea aurea, in the shallow-water hydrothermal vent field off Kueishan Island, Northeastern Taiwan. Sci. Total Environ. 992, 179901. https://doi.org/10.1016/j.scitotenv.2025.179901 (2025).
    Google Scholar 
    Chan, B. K. K. et al. Community structure of macrobiota and environmental parameters in shallow water hydrothermal vents off Kueishan Island, Taiwan. PLoS One. 11 (2), e0148675. https://doi.org/10.1371/journal.pone.0148675 (2016).
    Google Scholar 
    Mei, K. et al. Transformation, fluxes and impacts of dissolved metals from shallow water hydrothermal vents on nearby ecosystem offshore of Kueishantao (NE Taiwan). Sustainability 14 (3), 1754. https://doi.org/10.3390/su14031754 (2022).
    Google Scholar 
    Wang, Y. G. et al. Copepods as indicators of different water masses during the Northeast monsoon prevailing period in the Northeast Taiwan. Biology 11 (9), 1357. https://doi.org/10.3390/biology11091357 (2022).
    Google Scholar 
    Chiu, L., Wang, M. C., Wei, C. L., Lin, T. H. & Tseng, Y. C. A two-year physicochemical and acoustic observation reveals Spatiotemporal effects of earthquake‐induced shallow‐water hydrothermal venting on the surrounding environments. Limnol. Oceanogr. Lett. 9 (4), 423–432. https://doi.org/10.1002/lol2.10412 (2024).
    Google Scholar 
    Davidson, A. M., Tseng, L. C., Wang, Y. G. & Hwang, J. S. Mortality of mesozooplankton in an acidified ocean: investigating the impact of shallow hydrothermal vents across multiple monsoonal periods. Mar. Pollut Bull. 205, 116547. https://doi.org/10.1016/j.marpolbul.2024.116547 (2024).
    Google Scholar 
    Huang, Y. H. & Shih, H. T. Diversity of the swimming crabs (Crustacea: brachyura: Portunidae) from Dongsha Island, with a new record from Taiwan. J. Taiwan. Mus. 76 (3&4), 37–102. https://doi.org/10.6532/JNTM.202312_76(3_4).04 (2023).
    Google Scholar 
    Jansen, S. et al. Functioning of intertidal flats inferred from Temporal and Spatial dynamics of O2, H2S and pH in their surface sediment. Ocean. Dyn. 59 (2), 317–332 (2009).
    Google Scholar 
    Nicholls, P. & Kim, J. K. Sulphide as an inhibitor and electron donor for the cytochrome c oxidase system. Can. J. Biochem. 60 (6), 613–623. https://doi.org/10.1139/o82-076 (1982).
    Google Scholar 
    Khan, A. et al. Effects of hydrogen sulfide exposure on lung mitochondrial respiratory chain enzymes in rats. Toxicol. Appl. Pharmacol. 103 (3), 482–490. https://doi.org/10.1016/0041-008x(90)90321-k (1990).
    Google Scholar 
    Searcy, D. G. Metabolic integration during the evolutionary origin of mitochondria. Cell. Res. 13 (4), 229–238. https://doi.org/10.1038/sj.cr.7290168 (2003).
    Google Scholar 
    Vitvitsky, V. et al. Cytochrome c reduction by H2S potentiates sulfide signaling. ACS Chem. Biol. 13 (8), 2300–2307. https://doi.org/10.1021/acschembio.8b00463 (2018).
    Google Scholar 
    Morrison, B. R. S. An investigation into the effects of the piscicide antimycin A on the fish and invertebrates of a Scottish stream. Aquac Res. 10 (3), 111–122. https://doi.org/10.1111/j.1365-2109.1979.tb00262.x (1979).
    Google Scholar 
    Han, Y. H., Kim, S. H., Kim, S. Z. & Park, W. H. Antimycin A as a mitochondrial electron transport inhibitor prevents the growth of human lung cancer A549 cells. Oncol. Rep. 20 (3), 689–693. https://doi.org/10.3892/or_00000061 (2008).
    Google Scholar 
    29. Shahak, Y & Hauska, G. Sulfide Oxidation from Cyanobacteria to Humans: Sulfide–Quinone Oxidoreductase (SQR) in Sulfur Metabolism in Phototrophic Organisms. Advances in Photosynthesis and Respiration (ed. Hell, R., Dahl, C., Knaff, D & Leustek, T.) vol 27. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6863-8_16(2008).
    Google Scholar 
    Marcia, M., Ermler, U., Peng, G. & Michel, H. A new structure-based classification of sulfide: Quinone oxidoreductases. Proteins 78 (5), 1073–1083. https://doi.org/10.1002/prot.22665 (2010).
    Google Scholar 
    Hu, M. Y. et al. Strong ion regulatory abilities enable the crab xenograpsus testudinatus to inhabit highly acidified marine vent systems. Front. Physiol. 7, 14. https://doi.org/10.3389/fphys.2016.00014 (2016).
    Google Scholar 
    Diaz, R. J. & Rosenberg, R. Spreading dead zones and consequences for marine ecosystems. Science 321 (5891), 926–929. https://doi.org/10.1126/science.1156401 (2008).
    Google Scholar 
    Isensee, K. et al. The ocean is losing its breath. In Ocean and Climate Scientific Notes. Vol. 2. 20–32 (2016). (2016).Arp, A. J. & Childress, J. J. Functional characteristics of the blood of the deep-sea hydrothermal vent brachyuran crab. Science 214 (4520), 559–561. https://doi.org/10.1126/science.214.4520.559 (1981).
    Google Scholar 
    Fredricks, K. T., Hubert, T. D., Amberg, J. J., Cupp, A. R. & Dawson, V. K. Chemical controls for an integrated pest management program. N Am. J. Fish. Manag. 41 (2), 289–300. https://doi.org/10.1002/nafm.10339 (2021).
    Google Scholar 
    Ott, K. C. & Antimycin A brief review of it’s chemistry, environmental fate, and toxicology. Biochem. Et Biophys. Acta. 1185, 1–9 (1994).
    Google Scholar 
    Saari, G. N. Antimycin-A species sensitivity distribution: perspectives for non-indigenous fish control. Manag Biol Invasions. 14(3). https://doi.org/%2010.3391/mbi.14.3.09 (2023). (2023).Thorpe, K. E., Taylor, A. C. & Huntingford, F. A. How costly is fighting? Physiological effects of sustained exercise and fighting in swimming crabs, Necora puber (L.)(Brachyura, Portunidae). Anim. Behav. 50 (6), 1657–1666. https://doi.org/10.1016/0003-3472(95)80019-0 (1995).
    Google Scholar 
    Cota-Ruiz, K., Peregrino-Uriarte, A. B., Felix-Portillo, M., Martnez-Quintana, J. A. & Yepiz-Plascencia, G. Expression of Fructose 1, 6-bisphosphatase and phosphofructokinase is induced in hepatopancreas of the white shrimp Litopenaeus vannamei by hypoxia. Mar. Environ. Res. 106, 1–9. https://doi.org/10.1016/j.marenvres.2015.02.003 (2015).
    Google Scholar 
    Reyes-Ramos, C. A. et al. Phosphoenolpyruvate Carboxykinase cytosolic and mitochondrial isoforms are expressed and active during hypoxia in the white shrimp Litopenaeus vannamei. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 226, 1–9. https://doi.org/10.1016/j.cbpb.2018.08.001 (2018).
    Google Scholar 
    Bao, J., Li, X., Yu, H. & Jiang, H. Respiratory metabolism responses of Chinese mitten crab, eriocheir sinensis and Chinese grass shrimp, palaemonetes sinensis, subjected to environmental hypoxia stress. Front. Physiol. 9, 1559. https://doi.org/10.3389/fphys.2018.01559 (2018).
    Google Scholar 
    Opie, L. H. & Lopaschuk, G. D. Fuels: Aerobic and Anaerobic metabolism. Heart Physiology: from Cell To Circulation 4th edn, 306–354 (Lippincott, Williams and Wilkins, 2004).Hervant, F., Garin, D., Mathieu, J. & Freminet, A. Lactate metabolism and glucose turnover in the subterranean crustacean niphargus virei during post-hypoxic recovery. J. Exp. Biol. 202 (5), 579–592. https://doi.org/10.1242/jeb.202.5.579 (1999).
    Google Scholar 
    Kabil, O. & Banerjee, R. Redox biochemistry of hydrogen sulfide. J. Biol. Chem. 285 (29), 21903–21907. https://doi.org/10.1074/jbc.R110.128363 (2010).
    Google Scholar 
    Kelly, J. L. et al. Mechanisms underlying adaptation to life in Hydroten sulfide-rich environments. Mol. Biol. Evol. 33 (6), 1419–1434. https://doi.org/10.1093/molbev/msw020 (2016).
    Google Scholar 
    Henry, R. P., Lucu, C., Onken, H. & Weihrauch, D. Multiple functions of the crustacean gill: osmotic/ionic regulation, acid-base balance, ammonia excretion, and bioaccumulation of toxic metals. Front. Physiol. 3, 431. https://doi.org/10.3389/fphys.2012.00431 (2012).
    Google Scholar 
    Ogunbona, O. B. & Claypool, S. M. Emerging roles in the biogenesis of cytochrome c oxidase for members of the mitochondrial carrier family. Front. Cell. Dev. Biol. 7, 3. https://doi.org/10.3389/fcell.2019.00003 (2019).
    Google Scholar 
    Herzig, R. P., Scacco, S. & Scarpulla, R. C. Sequential serum-dependent activation of CREB and NRF-1 leads to enhanced mitochondrial respiration through the induction of cytochrome c. J. Biol. Chem. 275 (17), 13134–13141. https://doi.org/10.1074/jbc.275.17.13134 (2000).
    Google Scholar 
    Jimenez-Gutierrez, L. R., Uribe-Carvajal, S., Sanchez-Paz, A., Chimeo, C. & Muhlia-Almazan, A. The cytochrome c oxidase and its mitochondrial function in the whiteleg shrimp Litopenaeus vannamei during hypoxia. J. Bioenerg Biomembr. 46, 189–196. https://doi.org/10.1007/s10863-013-9537-5 (2014).
    Google Scholar 
    Pfenninger, M. et al. Parallel evolution of Cox genes in H2S-tolerant fish as key adaptation to a toxic environment. Nat. Commun. 5 (1), 3873. https://doi.org/10.1038/ncomms4873 (2014).
    Google Scholar 
    Mellado, M., de Ana, A. M., Moreno, M. C., Martı́nez-A, C. & Rodrıguez-Frade, J. M. A potential immune escape mechanism by melanoma cells through the activation of chemokine-induced T cell death. Curr. Biol. 11 (9), 691–696. https://doi.org/10.1016/s0960-9822(01)00199-3 (2001).
    Google Scholar 
    Shi, Y. et al. Effects of salinity on survival, growth, haemolymph osmolality, gill Na+-K+‐ATPase activity, respiration and excretion of the sword Prawn Parapenaeopsis hardwickii. Aquac Res. 53 (2), 603–611. https://doi.org/10.1111/are.15604 (2022).
    Google Scholar 
    Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33 (7), 1870–1874. https://doi.org/10.1093/molbev/msw054 (2016).
    Google Scholar 
    Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta delta C(T)) method. Methods 25 (4), 402–408. https://doi.org/10.1006/meth.2001.1262 (2001).
    Google Scholar 
    Download referencesAcknowledgementsThis work was supported by the Center of Excellence for the Oceans, NTOU from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), Taiwan, the Yushan Scholar Program (Sylvie Dufour), MOE, Taiwan (MOE-113-YSFAG-0012-001-P2), and the National Science and Technology Council (NSTC 112-2313-B-019-008; 113-2313-B-019-014). We thank to captain Dai-Shiu Lan, SCUBA diving coach Jen-Wei Lu, and Jen-sheng Lu for xtcrabs collection. We thank the staff of Yung-Che Tseng’s laboratory at Academia Sinica for xtcrabs collection. We thank Ying-Syuan Lyu of Ching-Fong Chang’s laboratory at NTOU for xtcrabs collection. We thank Emily Corrigan for the English correction. Thanks to Jie-Lin Guo of Ching-Fong Chang’s laboratory at NTOU for tdcrabs collection.FundingThis work was supported by the Center of Excellence for the Oceans, NTOU from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), Taiwan, the Yushan Scholar Program (Sylvie Dufour), MOE, Taiwan (MOE-113-YSFAG-0012-001-P2), and the National Science and Technology Council (NSTC 112-2313-B-019-008; 113-2313-B-019-014).Author informationAuthors and AffiliationsDepartment of Aquaculture, National Taiwan Ocean University, Keelung, TaiwanChi Chen, Guan-Chung Wu & Ching-Fong ChangCenter of Excellence for the Oceans, National Taiwan Ocean University, Keelung, TaiwanChi Chen, Guan-Chung Wu, Sylvie Dufour & Ching-Fong ChangInstitute of Cellular and Organismic Biology, Academia Sinica, Taipei, TaiwanYung-Che TsengBiology of Aquatic Organisms and Ecosystems (BOREA), Muséum National d’Histoire Naturelle, Sorbonne Université, CNRS, IRD, Paris, FranceSylvie DufourAuthorsChi ChenView author publicationsSearch author on:PubMed Google ScholarGuan-Chung WuView author publicationsSearch author on:PubMed Google ScholarYung-Che TsengView author publicationsSearch author on:PubMed Google ScholarSylvie DufourView author publicationsSearch author on:PubMed Google ScholarChing-Fong ChangView author publicationsSearch author on:PubMed Google ScholarContributionsChi Chen: conducted the sample collection, developed the methodologies in *xt* crab and *td* crab performed the experiments, data curation and analyses of data, and wrote the original draft. Guan-Chung Wu, Yung-Che Tseng and Ching-Fong Chang: developed the concept of the study, guided the experiments, and evaluated the data. Ching-Fong Chang: acquired funding, wrote, reviewed, and edited the paper. Sylvie Dufour: gave important input into conceptual and mechanistic insights, reviewed and edited the paper. All authors approved the paper.Corresponding authorsCorrespondence to
    Chi Chen, Guan-Chung Wu or Ching-Fong Chang.Ethics declarations

    Competing interests
    The authors declare no competing interests.

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    Reprints and permissionsAbout this articleCite this articleChen, C., Wu, GC., Tseng, YC. et al. Evolutionary adaptation of anaerobic and aerobic metabolism to high sulfide and hypoxic hydrothermal vent crab, Xenograpsus testudinatus.
    Sci Rep (2025). https://doi.org/10.1038/s41598-025-31968-1Download citationReceived: 04 September 2025Accepted: 05 December 2025Published: 15 December 2025DOI: https://doi.org/10.1038/s41598-025-31968-1Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    KeywordsAerobic respiration; anaerobic respirationHydrogen sulfideCellular energyExtreme environmentAdaptation More

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    Integrating microbial siderophores into concepts of plant iron nutrition

    AbstractIron is a crucial micronutrient for plants, but its availability in soil is often limited. Iron deficiency compromises plant growth, and low iron content in crops contributes substantially to the ‘hidden hunger’ that affects human health globally. The elucidation of Strategy I (reduction-based) and Strategy II (phytosiderophore-based) for iron acquisition was a milestone in plant biology and enabled the development of biofortification concepts. However, recent genetic evidence reveals that the boundary between the two strategies is blurred, with many plants possessing elements of both. Here we show that plant iron uptake mechanisms are more complex and diverse than the classical dichotomy suggests. We review evidence for this integrative view and highlight the critical role of microbial siderophores. We explain how plants access iron from microbial siderophores not only indirectly through Strategy I and II pathways but also via the direct uptake of iron–siderophore complexes, an overlooked mechanism that we introduce as Strategy III. We propose three potential routes for this direct uptake and conclude that harnessing Strategy III holds great potential for novel agricultural interventions to enhance iron biofortification and improve human health.

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    Fig. 1: Milestones in the discovery of molecular and physiological mechanisms underlying plant iron absorption.Fig. 2: Strategy I and II iron uptake mechanisms in plants and their partial co-occurrence in select species.Fig. 3: Phylogenetic distribution and functional traits of plant iron-promoting microorganisms.Fig. 4: Proposed mechanisms of how plants can use microbial siderophores for iron acquisition, including the emerging Strategy III.

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    ReferencesAndrews, S. C., Robinson, A. K. & Rodríguez-Quiñones, F. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215–237 (2003).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ponka, P., Tenenbein, M. & Eaton, J. W. in Handbook on the Toxicology of Metals (eds Nordberg G. F. et al.) 879–902 (Elsevier, 2015).Lauderdale, J. M., Braakman, R., Forget, G., Dutkiewicz, S. & Follows, M. J. Microbial feedbacks optimize ocean iron availability. Proc. Natl Acad. Sci. USA 117, 4842–4849 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Colombo, C., Palumbo, G., He, J.-Z., Pinton, R. & Cesco, S. Review on iron availability in soil: interaction of Fe minerals, plants, and microbes. J. Soils Sediments 14, 538–548 (2014).Article 
    CAS 

    Google Scholar 
    Zuo, Y. & Zhang, F. Soil and crop management strategies to prevent iron deficiency in crops. Plant Soil 339, 83–95 (2011).Article 
    CAS 

    Google Scholar 
    Vélez-Bermúdez, I. C. & Schmidt, W. Plant strategies to mine iron from alkaline substrates. Plant Soil 483, 1–25 (2023).Article 

    Google Scholar 
    Cronin, S. J. F., Woolf, C. J., Weiss, G. & Penninger, J. M. The role of iron regulation in immunometabolism and immune-related disease. Front. Mol. Biosci. 6, 116 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Weffort, V. R. S. & Lamounier, J. A. Hidden hunger—a narrative review. J. Pediatr. (Rio J.) 100, S10–S17 (2024).Article 
    PubMed 

    Google Scholar 
    Jurkevitch, E. et al. Exploiting micronutrient interaction to optimize biofortification programs: the case for inclusion of selenium and iodine in the HarvestPlus program. Nutr. Rev. 62, 247–252 (2004).Article 

    Google Scholar 
    Röhmeld, V. & Marschner, H. Evidence for a specific uptake system for iron phytosiderophores in roots of grasses. Plant Physiol. 80, 175–180 (1986).Article 

    Google Scholar 
    Santi, S. & Schmidt, W. Dissecting iron deficiency-induced proton extrusion in Arabidopsis roots. N. Phytol. 183, 1072–1084 (2009).Article 
    CAS 

    Google Scholar 
    Robinson, N. J., Procter, C. M., Connolly, E. L. & Guerinot, M. L. A ferric-chelate reductase for iron uptake from soils. Nature 397, 694–697 (1999).Article 
    CAS 
    PubMed 

    Google Scholar 
    Vert, G. et al. IRT1, an Arabidopsis transporter essential for iron uptake from the soil and for plant growth. Plant Cell 14, 1223–1233 (2002).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Curie, C. et al. Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake. Nature 409, 346–349 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bashir, K. et al. Cloning and characterization of deoxymugineic acid synthase genes from graminaceous plants. J. Biol. Chem. 281, 32395–32402 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nozoye, T. et al. Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants. J. Biol. Chem. 286, 5446–5454 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Durrett, T. P., Gassmann, W. & Rogers, E. E. The FRD3-mediated efflux of citrate into the root vasculature is necessary for efficient iron translocation. Plant Physiol. 144, 197–205 (2007).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yokosho, K., Yamaji, N., Ueno, D., Mitani, N. & Ma, J. F. OsFRDL1 is a citrate transporter required for efficient translocation of iron in rice. Plant Physiol. 149, 297–305 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kim, S. A. et al. Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science 314, 1295–1298 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bashir, K. et al. The rice mitochondrial iron transporter is essential for plant growth. Nat. Commun. 2, 322 (2011).Article 
    PubMed 

    Google Scholar 
    Ling, H. Q., Bauer, P., Bereczky, Z., Keller, B. & Ganal, M. The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc. Natl Acad. Sci. USA 99, 13938–13943 (2002).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Colangelo, E. P. & Guerinot, M. L. The essential basic helix–loop–helix protein FIT1 is required for the iron deficiency response. Plant Cell 16, 3400–3412 (2004).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yuan, Y. et al. FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Res. 18, 385–397 (2008).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ogo, Y. et al. The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Plant J. 51, 366–377 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wang, S. et al. A transcription factor OsbHLH156 regulates Strategy II iron acquisition through localising IRO2 to the nucleus in rice. N. Phytol. 225, 1247–1260 (2020).Article 
    CAS 

    Google Scholar 
    Li, X., Zhang, H., Ai, Q., Liang, G. & Yu, D. Two bHLH transcription factors, bHLH34 and bHLH104, regulate iron homeostasis in Arabidopsis thaliana. Plant Physiol. 170, 2478–2493 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jakoby, M., Wang, H.-Y., Reidt, W., Weisshaar, B. & Bauer, P. FRU (BHLH029) is required for induction of iron mobilization genes in Arabidopsis thaliana. FEBS Lett. 577, 528–534 (2004).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zhang, H., Li, Y., Yao, X., Liang, G. & Yu, D. POSITIVE REGULATOR OF IRON HOMEOSTASIS1, OsPRI1, facilitates iron homeostasis. Plant Physiol. 175, 543–554 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kobayashi, T. et al. The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants. Proc. Natl Acad. Sci. USA 104, 19150–19155 (2007).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grillet, L., Lan, P., Li, W., Mokkapati, G. & Schmidt, W. IRON MAN is a ubiquitous family of peptides that control iron transport in plants. Nat. Plants 4, 953–963 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Selote, D., Samira, R., Matthiadis, A., Gillikin, J. W. & Long, T. A. Iron-binding E3 ligase mediates iron response in plants by targeting Basic Helix–Loop–Helix transcription factors. Plant Physiol. 167, 273–286 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Salahudeen, A. A. et al. An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis. Science 326, 722–726 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vashisht, A. A. et al. Control of iron homeostasis by an iron-regulated ubiquitin ligase. Science 326, 718–721 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Long, T. et al. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell 22, 2219–2236 (2010).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Stacey, M. G. et al. The Arabidopsis AtOPT3 protein functions in metal homeostasis and movement of iron to developing seeds. Plant Physiol. 146, 323–324 (2008).Article 

    Google Scholar 
    Li, Y. et al. IRON MAN interacts with BRUTUS to maintain iron homeostasis in Arabidopsis. Proc. Natl Acad. Sci. USA 118, e2109063118 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kumar, R. K. et al. Iron-nicotianamine transporters are required for proper long distance iron signaling. Plant Physiol. 175, 1254–1268 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brown, J. C. & Jolley, V. D. Strategy I and strategy II mechanisms affecting iron availability to plants may be established too narrow or limited. J. Plant Nutr. 11, 1077–1098 (1988).Article 
    CAS 

    Google Scholar 
    Martín-Barranco, A., Thomine, S., Vert, G. & Zelazny, E. A quick journey into the diversity of iron uptake strategies in photosynthetic organisms. Plant Signal. Behav. 16, 1975088 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chao, Z. & Chao, D. Similarities and differences in iron homeostasis strategies between graminaceous and nongraminaceous plants. N. Phytol. 236, 1655–1660 (2022).Article 
    CAS 

    Google Scholar 
    Ishimaru, Y. et al. Rice plants take up iron as an Fe 3+ -phytosiderophore and as Fe 2+. Plant J. 45, 335–346 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zuo, Y. M., Zhang, F. S., Li, X. L. & Cao, Y. P. Studies on the improvement in iron nutrition of peanut by intercropping with maize on a calcareous soil. Plant Soil 220, 13–25 (2000).Article 
    CAS 

    Google Scholar 
    Zuo, Y., Li, X., Cao, Y., Zhang, F. & Christie, P. Iron nutrition of peanut enhanced by mixed cropping with maize: possible role of root morphology and rhizosphere microflora. J. Plant Nutr. 26, 2093–2110 (2003).Article 
    CAS 

    Google Scholar 
    Guo, X. et al. Dynamics in the rhizosphere and iron-uptake gene expression in peanut induced by intercropping with maize: role in improving iron nutrition in peanut. Plant Physiol. Biochem. 76, 36–43 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Dai, J. et al. From Leguminosae/Gramineae intercropping systems to see benefits of intercropping on iron nutrition. Front. Plant Sci. 10, 605 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xiong, H. et al. Molecular evidence for phytosiderophore-induced improvement of iron nutrition of peanut intercropped with maize in calcareous soil. Plant Cell Environ. 38, 1888–1902 (2013).Article 

    Google Scholar 
    He, R. et al. SIDERITE: unveiling hidden siderophore diversity in the chemical space through digital exploration. iMeta 3, e192 (2024).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hider, R. C. & Kong, X. Chemistry and biology of siderophores. Nat. Prod. Rep. 27, 637–657 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kramer, J., Özkaya, Ö & Kümmerli, R. Bacterial siderophores in community and host interactions. Nat. Rev. Microbiol. 18, 152–163 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Masalha, J., Kosegarten, H., Elmaci, O. & Mengel, K. The central role of microbial activity for iron acquisition in maize and sunflower. Biol. Fertil. Soils 30, 433–439 (2000).Article 
    CAS 

    Google Scholar 
    Rroço, E., Kosegarten, H., Harizaj, F., Imani, J. & Mengel, K. The importance of soil microbial activity for the supply of iron to sorghum and rape. Eur. J. Agron. 19, 487–493 (2003).Article 

    Google Scholar 
    Jin, C. W., He, Y. F., Tang, C. X., Wu, P. & Zheng, S. J. Mechanisms of microbially enhanced Fe acquisition in red clover (Trifolium pratense L.). Plant Cell Environ. 29, 888–897 (2006).Article 
    PubMed 

    Google Scholar 
    Wang, N. et al. Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize. Nat. Commun. 15, 839 (2024).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gu, S. et al. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat. Microbiol. 5, 1002–1010 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Singh, D. et al. Prospecting endophytes from different Fe or Zn accumulating wheat genotypes for their influence as inoculants on plant growth, yield, and micronutrient content. Ann. Microbiol. 68, 815–833 (2018).Article 
    CAS 

    Google Scholar 
    Vansuyt, G., Robin, A., Briat, J. F., Curie, C. & Lemanceau, P. Iron acquisition from Fe-pyoverdine by Arabidopsis thaliana. Mol. Plant Microbe Interact. 20, 441–447 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Trapet, P. et al. The Pseudomonas fluorescens siderophore pyoverdine weakens Arabidopsis thaliana defense in favor of growth in iron-deficient conditions. Plant Physiol. 171, 675–693 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Avoscan, L. et al. Iron status and root cell morphology of Arabidopsis thaliana as modified by a bacterial ferri-siderophore. Physiol. Plant. 176, e14223 (2024).Article 
    CAS 
    PubMed 

    Google Scholar 
    Shirley, M., Avoscan, L., Bernaud, E., Vansuyt, G. & Lemanceau, P. Comparison of iron acquisition from Fe–pyoverdine by strategy I and strategy II plants. Botany 89, 731–735 (2011).Article 
    CAS 

    Google Scholar 
    Omidvari, M., Sharifi, R. A., Ahmadzadeh, M. & Dahaji, P. A. Role of fluorescent pseudomonads siderophore to increase bean growth factors. J. Agric. Sci. 2, 242–247 (2010).
    Google Scholar 
    Braun, V. & Killmann, H. Bacterial solutions to the iron-supply problem. Trends Biochem. Sci. 24, 104–109 (1999).Article 
    CAS 
    PubMed 

    Google Scholar 
    Robin, A. et al. in Advances in Agronomy, Vol. 99 (ed. Sparks D. L.) 183–225 (Elsevier, 2008).Crowley, D. E., Wang, Y. C., Reid, C. P. P. & Szaniszlo, P. J. Mechanisms of iron acquisition from siderophores by microorganisms and plants. Front. Microbiol. 130, 179–198 (1991).CAS 

    Google Scholar 
    Rai, V., Fisher, N., Duckworth, O. W. & Baars, O. Extraction and detection of structurally diverse siderophores in soil. Front. Microbiol. 11, 581508 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Harbort, C. J. et al. Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis. Cell Host Microbe 28, 825–837 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Johnson, G. V., Lopez, A. & Foster, N. L. Reduction and transport of Fe from siderophores—reduction of siderophores and chelates and uptake and transport of iron by cucumber seedlings. Plant Soil 241, 27–33 (2002).Article 
    CAS 

    Google Scholar 
    Yehuda, Z., Shenker, M., Hadar, Y. & Chen, Y. Remedy of chlorosis induced by iron deficiency in plants with the fungal siderophore rhizoferrin. J. Plant Nutr. 23, 1991–2006 (2000).Article 
    CAS 

    Google Scholar 
    Bienfait, H. F. Prevention of stress in iron metabolism of plants. Acta Bot. Neerl. 38, 105–129 (1989).Article 
    CAS 

    Google Scholar 
    Boukhalfa, H. & Crumbliss, A. Chemical aspects of siderophore mediated iron transport. Biometals 15, 325–339 (2002).Article 
    CAS 
    PubMed 

    Google Scholar 
    Jin, C. W., Ye, Y. Q. & Zheng, S. J. An underground tale: contribution of microbial activity to plant iron acquisition via ecological processes. Ann. Bot. 113, 7–18 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Yehuda, Z. et al. The role of ligand exchange in the uptake of iron from microbial siderophores by gramineous plants. Plant Physiol. 112, 1273–1280 (1996).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jurkevitch, E., Hadar, Y., Chen, Y., Chino, M. & Mori, S. Indirect utilization of the phytosiderophore mugineic acid as an iron source to rhizosphere fluorescent Pseudomonas. Biometals 6, 119–123 (1993).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ahmed, E. & Holmström, S. J. M. Siderophores in environmental research: roles and applications. Microb. Biotechnol. 7, 196–208 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nishizawa, N. & Mori, S. Invagination of plasmalemma: its role in the absorption of macromolecules in rice roots. Plant Cell Physiol. 18, 767–782 (1977).
    Google Scholar 
    Mori, S. Iron acquisition by plants. Curr. Opin. Plant Biol. 2, 250–253 (1999).Article 
    CAS 
    PubMed 

    Google Scholar 
    Singh, P., Kumar, R., Khan, A., Singh, A. & Srivastava, A. Bacillibactin siderophore induces iron mobilisation responses inside aerobic rice variety through YSL15 transporter. Rhizosphere 27, 100724 (2023).Article 

    Google Scholar 
    Singh, P. et al. In silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa. J. Biomol. Struct. Dyn. 41, 2733–2746 (2023).Article 
    CAS 
    PubMed 

    Google Scholar 
    Murata, Y. et al. A specific transporter for iron(III)–phytosiderophore in barley roots. Plant J. 46, 563–572 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chen, L. M., Dick, W. A. & Streeter, J. G. Production of aerobactin by microorganisms from a compost enrichment culture and soybean utilization. J. Plant Nutr. 23, 2047–2060 (2000).Article 
    CAS 

    Google Scholar 
    Dahhan, D. A. & Bednarek, S. Y. Advances in structural, spatial, and temporal mechanics of plant endocytosis. FEBS Lett. 596, 2269–2287 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Hayat, R. et al. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms. Sci. Adv. 4, eaar4536 (2018).Article 

    Google Scholar 
    Diggle, S. P. et al. The Pseudomonas aeruginosa 4-quinolone signal molecules HHQ and PQS play multifunctional roles in quorum sensing and iron entrapment. Chem. Biol. 14, 87–96 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lin, J. et al. A Pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition. Nat. Commun. 8, 14888 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chaney, R. L., Brown, J. C. & Tiffin, L. O. Obligatory reduction of ferric chelates in iron uptake by soybeans. Plant Physiol. 50, 208–213 (1972).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Eide, D., Broderius, M., Fett, J. & Guerinot, M. L. A novel iron-regulated metal transporter from plants identified by functional expression in yeast. Proc. Natl Acad. Sci. USA 93, 5624–5628 (1996).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rodríguez-Celma, J. et al. Root responses of Medicago truncatula plants grown in two different iron deficiency conditions: changes in root protein profile and riboflavin biosynthesis. J. Proteome Res. 10, 2590–2601 (2011).Article 
    PubMed 

    Google Scholar 
    Rodriguez-Celma, J. et al. Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. Plant Physiol. 162, 1473–1485 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fourcroy, P. et al. Involvement of the ABCG37 transporter in secretion of scopoletin and derivatives by Arabidopsis roots in response to iron deficiency. N. Phytol. 201, 155–167 (2014).Article 
    CAS 

    Google Scholar 
    Schmid, N. B. et al. Feruloyl-CoA 6′-hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis. Plant Physiol. 164, 160–172 (2014).Article 
    CAS 
    PubMed 

    Google Scholar 
    Schmidt, H. et al. Metabolome analysis of Arabidopsis thaliana roots identifies a key metabolic pathway for iron acquisition. PLoS ONE 9, e102444 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rajniak, J. et al. Biosynthesis of redox-active metabolites in response to iron deficiency in plants. Nat. Chem. Biol. 14, 442–450 (2018).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Robe, K. et al. Coumarin-facilitated iron transport: an IRT1-independent strategy for iron acquisition in Arabidopsis thaliana. Plant Commun. 6, 101431 (2025).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Takagi, S. Naturally occurring iron-chelating compounds in oat- and rice-root washings. J. Soil Sci. Plant Nutr. 22, 423–433 (1976).Article 
    CAS 

    Google Scholar 
    Takagi, S., Nomoto, K. & Takemoto, T. Physiological aspect of mugineic acid, a possible phytosiderophore of graminaceous plants. J. Plant Nutr. 7, 469–477 (1984).Article 
    CAS 

    Google Scholar 
    Mori, S. & Nishizawa, N. K. Methionine as a dominant precursor of phytosiderophores in Graminaceae plants. Plant Cell Physiol. 28, 1081–1092 (1987).CAS 

    Google Scholar 
    Shojima, S. et al. Biosynthesis of phytosiderophores: in vitro biosynthesis of 2′-deoxymugineic acid from L-methionine and nicotianamine. Plant Physiol. 93, 1497–1503 (1990).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Higuchi, K. et al. Cloning of nicotianamine synthase genes, novel genes involved in the biosynthesis of phytosiderophores. Plant Physiol. 119, 471–479 (1999).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Inoue, H. et al. Three rice nicotianamine synthase genes, OsNAS1, OsNAS2, and OsNAS3 are expressed in cells involved in long-distance transport of iron and differentially regulated by iron. Plant J. 36, 366–381 (2003).Article 
    CAS 
    PubMed 

    Google Scholar 
    Takahashi, M. et al. Cloning two genes for nicotianamine aminotransferase, a critical enzyme in iron acquisition (Strategy II) in graminaceous plants. Plant Physiol. 121, 947–956 (1999).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Inoue, H. et al. Identification and localisation of the rice nicotianamine aminotransferase gene OsNAAT1 expression suggests the site of phytosiderophore synthesis in rice. Plant Mol. Biol. 66, 193–203 (2008).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ma, J. F., Shinada, T., Matsuda, C. & Nomoto, K. Biosynthesis of phytosiderophores, mugineic acids, associated with methionine cycling. J. Biol. Chem. 270, 16549–16554 (1995).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ma, J. F. & Nomoto, K. Two related biosynthetic pathways of mugineic acids in gramineous plants. Plant Physiol. 102, 373–378 (1993).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Francis, J., Madinaveitia, J., Macturk, H. M. & Snow, G. A. Isolation from acid-fast bacteria of a growth-factor for Mycobacterium johnei and of a precursor of phthiocol. Nature 163, 365–366 (1949).Article 
    CAS 
    PubMed 

    Google Scholar 
    Neilands, J. B. in Bioinorganic Chemistry—II, Vol. 261 (ed. Raymond, K. N.) 3–32 (American Chemical Society, 1977).Powell, P. E., Szaniszlo, P. J., Cline, G. R. & Reid, C. P. P. Hydroxamate siderophores in the iron nutrition of plants. J. Plant Nutr. 5, 653–673 (1982).Article 
    CAS 

    Google Scholar 
    Download referencesAcknowledgementsWe thank the National Natural Science Foundation of China (grant nos 42325704, 32372810, 42577142 and 32573128), the Disciplinary Breakthrough Project of Ministry of Education (MOE, #00975101), the National Key Research and Development Program of China (grant nos 2022YFD1901500/2022YFD1901501 and 2023YFD1700203), the Tianchi Talent Introduction Program of Xinjiang Autonomous Region, China (2023—‘2+5’), the Tingzhou Talent Introduction Program of Changji Autonomous Region, China (2023) and the Swiss National Science Foundation (grant no. 310030_212266) for funding. We thank S. J. Zheng from Zhejiang University and J. F. Ma from Okayama University for valuable discussions and suggestions.Author informationAuthor notesThese authors contributed equally: Shaohua Gu, Nanqi Wang.Authors and AffiliationsCollege of Resources and Environmental Sciences, State Key Laboratory of Nutrient Use and Management, National Academy of Agriculture Green Development, China Agricultural University, Beijing, ChinaShaohua Gu, Tianqi Wang, Fusuo Zhang & Yuanmei ZuoNational Citrus Engineering Research Center, Chongqing Key Laboratory of Citrus, Citrus Research Institute, Southwest University, Chongqing, ChinaNanqi WangJiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Nanjing Agricultural University, Nanjing, ChinaYiran Zheng, Qirong Shen & Zhong WeiDepartment of Quantitative Biomedicine, University of Zurich, Zurich, SwitzerlandRolf KümmerliAuthorsShaohua GuView author publicationsSearch author on:PubMed Google ScholarNanqi WangView author publicationsSearch author on:PubMed Google ScholarYiran ZhengView author publicationsSearch author on:PubMed Google ScholarTianqi WangView author publicationsSearch author on:PubMed Google ScholarQirong ShenView author publicationsSearch author on:PubMed Google ScholarFusuo ZhangView author publicationsSearch author on:PubMed Google ScholarRolf KümmerliView author publicationsSearch author on:PubMed Google ScholarZhong WeiView author publicationsSearch author on:PubMed Google ScholarYuanmei ZuoView author publicationsSearch author on:PubMed Google ScholarContributionsY.Z. and Z.W. developed the concept. S.G., N.W., T.W. and Y.Z. performed the literature search and prepared the figures. F.Z. and Q.S. provided some intellectual input for this manuscript. S.G., N.W., R.K., Y.Z. and Z.W. wrote the manuscript with contributions and input from all authors.Corresponding authorsCorrespondence to
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    Impact of mixing duration on growth and nutrient removal efficiency of Scenedesmus sp. in a novel raceway pond system

    AbstractRaceway ponds are regarded as a popular and cost-effective method for microalgae cultivation; however, their performance is strongly influenced by hydrodynamic conditions. Conventional paddlewheel driven systems are restricted to low operating velocities to avoid culture spilling out which often leads to reduced mixing and stagnant zone formation. In this study, a raceway pond was designed with the inclusion of curved slits at the bent zones and submersible pump as an alternative mixing device to prevent culture overflow, improve flow stability and minimize dead zones. This novel integration of structural modifications and pump-based mixing represents a significant advancement over traditional paddlewheel systems by providing higher velocities, enhanced circulation and more uniform algal growth conditions. Experiments were conducted to evaluate the effect of mixing durations in 6 L raceway ponds under identical environmental conditions. The raceway systems permitted a broader velocity range (0.10–0.45 m s−1) without spillage. The system with continuous 24 h mixing compared to 20 and 16 h mixing resulted in the highest biomass productivity of 1.01 g L−1 d−1 and maximum nutrient removal rates of 5.18 mg L−1 d-1 and 3.41 mg L−1 d−1 for NO3− and PO43−, respectively. Submersible-pump configured open raceway pond achieved comparable or higher biomass yield, lower energy consumption with a net energy efficiency of 62%, demonstrating its practicality and cost-effectiveness as a viable alternative to conventional paddlewheel driven systems for large-scale Scenedesmus sp. cultivation.

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    Data will be made available on request. Requests for data should be directed to Dr. Rashid Iftikhar ([email protected]; [email protected]).
    ReferencesVadiveloo, A. & Moheimani, N. Effect of continuous and daytime mixing on Nannochloropsis growth in raceway ponds. Algal Res. 33, 190–196. https://doi.org/10.1016/j.algal.2018.05.018 (2018).
    Google Scholar 
    Wijffels, R. H., Kruse, O. & Hellingwerf, K. J. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae. Curr. Opin. Biotechnol. 24, 405–413. https://doi.org/10.1016/j.copbio.2013.04.004 (2013).
    Google Scholar 
    Vanthoor-Koopmans, M., Wijffels, R. H., Barbosa, M. J. & Eppink, M. H. M. Biorefinery of microalgae for food and fuel. Bioresour. Technol. 135, 142–149. https://doi.org/10.1016/j.biortech.2012.10.135 (2013).
    Google Scholar 
    Valverde, F., Romero-Campero, F. J., León, R., Guerrero, M. G. & Serrano, A. New challenges in microalgae biotechnology. Eur. J. Protistol. 55, 95–101. https://doi.org/10.1016/j.ejop.2016.03.002 (2016).
    Google Scholar 
    Borowitzka, M. Large-scale algal culture systems: the next generation. Australasian Biotechnology (1994).Jorquera, O., Kiperstok, A., Sales, E. A., Embiruçu, M. & Ghirardi, M. L. Comparative energy life-cycle analyses of microalgal biomass production in open ponds and photobioreactors. Bioresour. Technol. 101, 1406–1413. https://doi.org/10.1016/j.biortech.2009.09.038 (2010).
    Google Scholar 
    Kumar, K., Mishra, S. K., Shrivastav, A., Park, M. S. & Yang, J. W. Recent trends in the mass cultivation of algae in raceway ponds. Renew. Sustain. Energy Rev. 51, 875–885. https://doi.org/10.1016/j.rser.2015.06.033 (2015).
    Google Scholar 
    Borowitzka, M. A. & Moheimani, N. R. Open Pond Culture Systems. in Algae for Biofuels and Energy (eds Borowitzka, M. A. & Moheimani, N. R.) 133–152 (2013). https://doi.org/10.1007/978-94-007-5479-9_8Lundquist, T. J., Woertz, I. C., Quinn, N. W. T. & Benemann, J. R. A Realistic Technology and Engineering Assessment of Algae Biofuel Production. (2010).Rogers, J. N. et al. A critical analysis of paddlewheel-driven raceway ponds for algal biofuel production at commercial scales. Algal Res. 4, 76–88. https://doi.org/10.1016/j.algal.2013.11.007 (2014).
    Google Scholar 
    Stephens, E. et al. An economic and technical evaluation of microalgal biofuels. Nat. Biotechnol. 28, 126–128. https://doi.org/10.1038/nbt0210-126 (2010).
    Google Scholar 
    Kusmayadi, A., Philippidis, G. P. & Yen, H. W. Application of computational fluid dynamics to raceways combining paddlewheel and CO2 spargers to enhance microalgae growth. J. Biosci. Bioeng. 129, 93–98. https://doi.org/10.1016/j.jbiosc.2019.06.013 (2020).
    Google Scholar 
    Cheng, J., Yang, Z., Ye, Q., Zhou, J. & Cen, K. Enhanced flashing light effect with up-down chute baffles to improve microalgal growth in a raceway pond. Bioresour. Technol. 190, 29–35. https://doi.org/10.1016/j.biortech.2015.04.050 (2015).
    Google Scholar 
    Huang, J. et al. Design and optimization of a novel airlift-driven sloping raceway pond with numerical and practical experiments. Algal Res. 20, 164–171. https://doi.org/10.1016/j.algal.2016.09.023 (2016).
    Google Scholar 
    Jebali, A., Acién, F. G., Sayadi, S. & Molina-Grima, E. Utilization of centrate from urban wastewater plants for the production of scenedesmus sp. in a raceway-simulating reactor. J. Environ. Manage. 211, 112–124. https://doi.org/10.1016/j.jenvman.2018.01.043 (2018).
    Google Scholar 
    Chakraborty, B., Gayen, K. & Bhowmick, T. K. Transition from synthetic to alternative media for microalgae cultivation: A critical review. Sci. Total Environ. 897, 165412. https://doi.org/10.1016/j.scitotenv.2023.165412 (2023).
    Google Scholar 
    Saleem, S. et al. Operation of microalgal horizontal twin layer system for treatment of real wastewater and production of lipids. J. Water Process. Eng. 48, 102932. https://doi.org/10.1016/j.jwpe.2022.102932 (2022).
    Google Scholar 
    Bulynina, S. S., Ziganshina, E. E. & Ziganshin, A. M. Growth Efficiency of Chlorella sorokiniana in Synthetic Media and Unsterilized Domestic Wastewater. BioTech 12, 53 (2023). https://doi.org/10.3390/biotech12030053Malek, A., Zullo, L. C. & Daoutidis, P. Modeling and dynamic optimization of microalgae cultivation in outdoor open ponds. Ind. Eng. Chem. Res. 55, 3327–3337. https://doi.org/10.1021/acs.iecr.5b03209 (2016).
    Google Scholar 
    Matanguihan, A. E. D. et al. Design, fabrication, and performance evaluation of open raceway ponds for the cultivation of chlorella vulgaris Beijerinck in the Philippines. Philippine J. Sci. 149, 353–362. https://doi.org/10.56899/149.02.13 (2020).
    Google Scholar 
    Ahmad, S., Pathak, V. V., Kothari, R., Kumar, A. & Naidu Krishna, S. B. Optimization of nutrient stress using C. pyrenoidosa for lipid and biodiesel production in integration with remediation in dairy industry wastewater using response surface methodology. 3 Biotech. 8, 326. https://doi.org/10.1007/s13205-018-1342-8 (2018).
    Google Scholar 
    Xu, C., Wang, L., Liu, Z., Cai, G. & Zhan, J. Nitrogen and phosphorus removal efficiency and algae viability in an immobilized algae and bacteria symbiosis system with Pink luminescent filler. Water Sci. Technol. 85, 104–115. https://doi.org/10.2166/wst.2021.606 (2022).
    Google Scholar 
    Liu, Y. et al. Treatment of real aquaculture wastewater from a fishery utilizing phytoremediation with microalgae. J. Chem. Technol. Biotechnol. 94, 900–910. https://doi.org/10.1002/jctb.5837 (2019).
    Google Scholar 
    Saleem, S., Sheikh, Z., Iftikhar, R. & Zafar, M. I. Eco-friendly cultivation of microalgae using a horizontal twin layer system for treatment of real solid waste leachate. J. Environ. Manage. 351, 119847. https://doi.org/10.1016/j.jenvman.2023.119847 (2024).
    Google Scholar 
    APHA. Standard Methods for the Examination of Water and Wastewater. (2017).Hemalatha, M., Sravan, J. S., Min, B. & Venkata Mohan, S. Microalgae-biorefinery with cascading resource recovery design associated to dairy wastewater treatment. Bioresour. Technol. 284, 424–429. https://doi.org/10.1016/j.biortech.2019.03.106 (2019).
    Google Scholar 
    Richmond, A. Biological Principles of Mass Cultivation of Photoautotrophic Microalgae. in Handbook of Microalgal Culture 169–204 (2013). https://doi.org/10.1002/9781118567166.ch11Hadiyanto, H., Elmore, S., Van Gerven, T. & Stankiewicz, A. Hydrodynamic evaluations in high rate algae pond (HRAP) design. Chem. Eng. J. 217, 231–239. https://doi.org/10.1016/j.cej.2012.12.015 (2013).
    Google Scholar 
    Kazbar, A. et al. Effect of dissolved oxygen concentration on microalgal culture in photobioreactors. Algal Res. 39, 101432. https://doi.org/10.1016/j.algal.2019.101432 (2019).
    Google Scholar 
    Chisti, Y. Large-Scale Production of Algal Biomass: Raceway Ponds. in Algae Biotechnology: Products and Processes (eds Bux, F. & Chisti, Y.) 21–40 (2016). https://doi.org/10.1007/978-3-319-12334-9_2Sutherland, D. L., Howard-Williams, C., Turnbull, M. H., Broady, P. A. & Craggs, R. J. The effects of CO2 addition along a pH gradient on wastewater microalgal photo-physiology, biomass production and nutrient removal. Water Res. 70, 9–26. https://doi.org/10.1016/j.watres.2014.10.064 (2015).
    Google Scholar 
    Ketheesan, B. & Nirmalakhandan, N. Feasibility of microalgal cultivation in a pilot-scale airlift-driven raceway reactor. Bioresour. Technol. 108, 196–202. https://doi.org/10.1016/j.biortech.2011.12.146 (2012).
    Google Scholar 
    Sun, Y. et al. Boosting Nannochloropsis oculata growth and lipid accumulation in a lab-scale open raceway pond characterized by improved light distributions employing built-in planar waveguide modules. Bioresour. Technol. 249, 880–889. https://doi.org/10.1016/j.biortech.2017.11.013 (2018).
    Google Scholar 
    Posadas, E., Morales, M. M., Gomez, C., Acién, F. G. & Muñoz, R. Influence of pH and CO2 source on the performance of microalgae-based secondary domestic wastewater treatment in outdoors pilot raceways. Chem. Eng. J. 265, 239–248. https://doi.org/10.1016/j.cej.2014.12.059 (2015).
    Google Scholar 
    Ledda, C., Romero Villegas, G. I., Adani, F. & Acién Fernández, F. G. Molina Grima, E. Utilization of centrate from wastewater treatment for the outdoor production of Nannochloropsis Gaditana biomass at pilot-scale. Algal Res. 12, 17–25. https://doi.org/10.1016/j.algal.2015.08.002 (2015).
    Google Scholar 
    Huang, J. et al. Investigation on the performance of raceway ponds with internal structures by the means of CFD simulations and experiments. Algal Res. 10, 64–71. https://doi.org/10.1016/j.algal.2015.04.012 (2015).
    Google Scholar 
    Friedrich, K. et al. Reservoir Evaporation in the Western United States: Current Science, Challenges, and Future Needs 99, (2018). https://doi.org/10.1175/BAMS-D-15-00224.1Carrier, O. et al. Evaporation of water: evaporation rate and collective effects. J. Fluid Mech. 798, 774–786. https://doi.org/10.1017/jfm.2016.356 (2016).
    Google Scholar 
    Cuello, M. C., Cosgrove, J. J., Randhir, A., Vadiveloo, A. & Moheimani, N. R. Comparison of continuous and day time only mixing on tetraselmis Suecica (Chlorophyta) in outdoor raceway ponds. J. Appl. Phycol. 27, 1783–1791. https://doi.org/10.1007/s10811-014-0420-5 (2015).
    Google Scholar 
    Trainor, F. R. Reproduction in scenedesmus. Algae (The Korean J. Phycology). 11 (2), 183–201 (1996).
    Google Scholar 
    Barsanti, L. & Gualtieri, P. Algae: Anatomy, Biochemistry, and Biotechnology, Second Edition. (2014). https://doi.org/10.1201/b16544Rayen, F., Behnam, T. & Dominique, P. Optimization of a raceway pond system for wastewater treatment: a review. Crit. Rev. Biotechnol. 39, 422–435. https://doi.org/10.1080/07388551.2019.1571007 (2019).
    Google Scholar 
    Chuka-ogwude, D. et al. Effect of medium recycling, culture depth, and mixing duration on D. salina growth. Algal Res. 60, 102495. https://doi.org/10.1016/j.algal.2021.102495 (2021).
    Google Scholar 
    Zhu, L. et al. Nutrient removal and biodiesel production by integration of freshwater algae cultivation with piggery wastewater treatment. Water Res. 47, 4294–4302. https://doi.org/10.1016/j.watres.2013.05.004 (2013).
    Google Scholar 
    Marra, J., Bidigare, R. R. & Dickey, T. D. Nutrients and mixing, chlorophyll and phytoplankton growth. Deep Sea Res. Part. Oceanogr. Res. Papers. 37, 127–143. https://doi.org/10.1016/0198-0149(90)90032-Q (1990).
    Google Scholar 
    Lachmann, S. C., Mettler-Altmann, T., Wacker, A. & Spijkerman, E. Nitrate or ammonium: influences of nitrogen source on the physiology of a green Alga. Ecol. Evol. 9, 1070–1082. https://doi.org/10.1002/ece3.4790 (2019).
    Google Scholar 
    Jiang, R. et al. The joint effect of ammonium and pH on the growth of Chlorella vulgaris and ammonium removal in artificial liquid digestate. Bioresour. Technol. 325, 124690. https://doi.org/10.1016/j.biortech.2021.124690 (2021).
    Google Scholar 
    Tan, F. et al. Nitrogen and phosphorus removal coupled with carbohydrate production by five microalgae cultures cultivated in biogas slurry. Bioresour. Technol. 221, 385–393. https://doi.org/10.1016/j.biortech.2016.09.030 (2016).
    Google Scholar 
    Beuckels, A., Smolders, E. & Muylaert, K. Nitrogen availability influences phosphorus removal in microalgae-based wastewater treatment. Water Res. 77, 98–106. https://doi.org/10.1016/j.watres.2015.03.018 (2015).
    Google Scholar 
    Pena, A. C. C., Agustini, C. B., Trierweiler, L. F. & Gutterres, M. Influence of period light on cultivation of microalgae consortium for the treatment of tannery wastewaters from leather finishing stage. J. Clean. Prod. 263, 121618. https://doi.org/10.1016/j.jclepro.2020.121618 (2020).
    Google Scholar 
    Barboza-Rodríguez, R., Rodríguez-Jasso, R. M., Rosero-Chasoy, G., Rosales Aguado, M. L. & Ruiz, H. A. Photobioreactor configurations in cultivating microalgae biomass for biorefinery. Bioresour. Technol. 394, 130208. https://doi.org/10.1016/j.biortech.2023.130208 (2024).
    Google Scholar 
    Li, Y., Zhang, Q., Wang, Z., Wu, X. & Cong, W. Evaluation of power consumption of paddle wheel in an open raceway pond. Bioprocess. Biosyst Eng. 37, 1325–1336. https://doi.org/10.1007/s00449-013-1103-3 (2014).
    Google Scholar 
    Yadala, S. & Cremaschi, S. A. Dynamic Optimization Model for Designing Open-Channel Raceway Ponds for Batch Production of Algal Biomass. Processes 4, 10 (2016). https://doi.org/10.3390/pr4020010El-Chaghaby, A., Rashad, G., Abdel-Kader, S. F. & Rawash, S. A. Abdul Moneem, M. Assessment of phytochemical components, proximate composition and antioxidant properties of scenedesmus obliquus, chlorella vulgaris and spirulina platensis algae extracts. Egypt. J. Aquat. Biology Fisheries. 23, 521–526. https://doi.org/10.21608/ejabf.2019.57884 (2019).
    Google Scholar 
    Chen, M., Chen, Y. & Zhang, Q. A. Review of energy consumption in the acquisition of Bio-Feedstock for microalgae biofuel production. Sustainability 13, 8873. https://doi.org/10.3390/su13168873 (2021).
    Google Scholar 
    Bhatt, P. et al. Algae in wastewater treatment, mechanism, and application of biomass for production of value-added product. Environ. Pollut. 309, 119688. https://doi.org/10.1016/j.envpol.2022.119688 (2022).
    Google Scholar 
    Amorim, M. L., Soares, J., Vieira, B. B., Batista-Silva, W. & Martins, M. A. Extraction of proteins from the microalga scenedesmus obliquus BR003 followed by lipid extraction of the wet deproteinized biomass using hexane and Ethyl acetate. Bioresour Technol. 307, 123190. https://doi.org/10.1016/j.biortech.2020.123190 (2020).
    Google Scholar 
    Patnaik, R., Singh, N. K., Bagchi, S. K., Rao, P. S. & Mallick, N. Utilization of scenedesmus obliquus protein as a replacement of the commercially available fish meal under an algal refinery approach. Front. Microbiol. 10 https://doi.org/10.3389/fmicb.2019.02114 (2019).Olsen, M. F. L. et al. Outdoor cultivation of a novel isolate of the microalgae scenedesmus sp. and the evaluation of its potential as a novel protein crop. Physiol. Plant. 173 (2), 483–494. https://doi.org/10.1111/ppl.13532 (2021).
    Google Scholar 
    Skifa, I., Chauchat, N., Cocquet, P. H. & Guer, Y. L. Microalgae cultivation in raceway ponds: Advances, challenges, and hydrodynamic considerations. EFB Bioeconomy J. 5, 100073. https://doi.org/10.1016/j.bioeco.2024.100073 (2025).
    Google Scholar 
    Fakher, S., Khlaifat, A., Hossain, M. E. & Nameer, H. Rigorous review of electrical submersible pump failure mechanisms and their mitigation measures. J. Petroleum Explor. Prod. Technol. 11, 1507–1525. https://doi.org/10.1007/s13202-021-01271-6 (2021).
    Google Scholar 
    Zhang, Q. et al. Installation of flow deflectors and wing baffles to reduce dead zone and enhance flashing light effect in an open raceway pond. Bioresour Technol. 198, 150–156. https://doi.org/10.1016/j.biortech.2015.08.144 (2015).
    Google Scholar 
    Hoeniges, J., Zhu, K., Pruvost, J. & Legrand, J. Impact of Dropwise condensation on the biomass production rate in covered raceway ponds. Energies 14, 268 (2021).
    Google Scholar 
    Download referencesFundingThis research was funded by Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2025R589), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.Author informationAuthors and AffiliationsInstitute of Environmental Sciences and Engineering (IESE), School of Civil and Environmental Engineering (SCEE), National University of Sciences and Technology (NUST), Islamabad, 44000, PakistanMuhammad Umer Abbas, Rashid Iftikhar, Nadeem Ullah & Faras Ahmad ShahbazDepartment of Sciences, School of Interdisciplinary Engineering & Science (SINES), National University of Science and Technology (NUST), Islamabad, PakistanSahar SaleemDepartment of Teaching and Learning, College of Education and Human Development, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi ArabiaSarah Bader Alotaibi & Mashael M. AlfgehInstitute of Water Resources and Water Supply, Hamburg University of Technology (TUHH), Am Schwarzenberg-Campus 3, 21073, Hamburg, GermanyMuhammad Ali InamDepartment of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, Bologna, 40126, ItalyAhmad AakashAuthorsMuhammad Umer AbbasView author publicationsSearch author on:PubMed Google ScholarRashid IftikharView author publicationsSearch author on:PubMed Google ScholarSahar SaleemView author publicationsSearch author on:PubMed Google ScholarSarah Bader AlotaibiView author publicationsSearch author on:PubMed Google ScholarNadeem UllahView author publicationsSearch author on:PubMed Google ScholarMashael M. AlfgehView author publicationsSearch author on:PubMed Google ScholarMuhammad Ali InamView author publicationsSearch author on:PubMed Google ScholarFaras Ahmad ShahbazView author publicationsSearch author on:PubMed Google ScholarAhmad AakashView author publicationsSearch author on:PubMed Google ScholarContributionsMuhammad Umer Abbas: Writing—original draft, Writing—review & editing, Methodology, Validation, Conceptualization. Rashid Iftikhar: Writing—review & editing, Conceptualization, Validation, Project administration, Funding acquisition, Supervision. Sahar Saleem: Writing—review & editing and Methodology. Sarah Bader Alotaibi: Funding, resources & review. Nadeem Ullah: Resources and Review. Mashael M. Alfge: Funding & review. Muhammad Ali Inam: Methodology, Supervision, Validation, Investigation, final approval. Faras Ahmad Shahbaz: Writing—review & editing. Ahmad Aakash: Writing—review & editing.Corresponding authorCorrespondence to
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    Reprints and permissionsAbout this articleCite this articleAbbas, M.U., Iftikhar, R., Saleem, S. et al. Impact of mixing duration on growth and nutrient removal efficiency of Scenedesmus sp. in a novel raceway pond system.
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    Functional trait variations of the invasive plant Alternanthera Philoxeroides and the native plant Ludwigia peploides under nitrogen addition

    AbstractQuantifying the variation and coordination patterns of plant functional traits across different organs under environmental changes is crucial for understanding plant invasion and adaptation mechanisms. This study employed a space-for-time substitution experiment to compare the differential responses of root and leaf functional traits and their coordination in the invasive plant Alternanthera philoxeroides and the native plant Ludwigia peploides to nitrogen addition during different invasion degree. The results showed that: (1) nitrogen addition promoted the growth of both species, with A. philoxeroides exhibited greater biomass sensitivity. Compared to the positive effects of nitrogen fertilization, nitrogen addition facilitated A. philoxeroides in displacing L. peploides in communities with 50% (2 A. philoxeroides seedlings) and 75% (3 A. philoxeroides seedlings) invasion degree. (2) invasion degree, nitrogen addition, and their interaction significantly influenced most root and leaf traits of both species. But the two species differed markedly in their response of root and leaf traits to environmental factors. (3) The correlations between root traits, leaf traits, and total biomass were stronger in A. philoxeroides than in L. peploides, as were the linkages between root and leaf traits. Under environmental changes, the two species exhibited distinct adaptive strategies in root and leaf traits, with A. philoxeroides’s trait advantages likely contributing to its invasion success. In conclusion, our study demonstrates that nitrogen deposition facilitates alien plant invasion, particularly in mixed communities experiencing moderate to severe invasion.

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    IntroductionIn natural environments, native plant communities often face varying degrees of invasion pressure from exotic plants1,2,3,4. During the establishment phase, invasive plants must overcome resistance from native vegetation, yet they often succeed in occupying niches due to their superior competitive abilities4. In the expansion phase, competitive advantages directly determine the degree of dominance by invasive species and the severity of their ecological impacts, where intense interspecific competition may even lead to the exclusion of native species4. These competitive dynamics are fundamentally driven by differences in functional traits among species and are maintained through niche differentiation and mechanisms of competitive coexistence5,6,7.Plants optimize key physiological processes such as photosynthetic carbon acquisition, structural support, and nutrient uptake by adjusting biomass allocation patterns to organs like roots and leaves8. Variations in root and leaf morphology, along with tissue nutrient content (e.g., nitrogen concentration), directly reflect plant strategies and efficiency in resource utilization8,9,10. Furthermore, secondary metabolites serve as critical biochemical traits, not only providing defensive compounds but also significantly influencing plant adaptation to biotic and abiotic environments5,8. Non-structural carbohydrates (NSCs), as labile carbon reserves, play a central role in plant growth and environmental adaptation by supplying carbon skeletons for development, fueling respiratory metabolism, and participating in osmotic regulation, among other processes10. Previous research has shown that invasive plants often exhibit greater leaf mass fraction, specific root length (SRL), and root nitrogen concentration, as well as release higher amounts of allelochemicals, compared to co-occurring native species5,8,9,10.However, most existing studies in invasion ecology focus on either “pre-invasion” or “post-invasion” community states1,9,11,12,13,14, often overlooking the continuum of invasion degree and failing to systematically analyze how different invasion degrees differentially affect the functional traits of invasive and native plants. This knowledge gap hinders the identification of key invasive traits that determine competitive outcomes8,9,10.Moreover, as a critical component of global change, biological invasions often interact synergistically with anthropogenic drivers such as nitrogen deposition, climate warming, and rising atmospheric CO₂ levels15,16. Research indicates that the success of invasive plants in establishment and expansion closely depends on resource availability and plasticity in their functional traits12. In recent decades, global fossil fuel combustion and synthetic fertilizer use have led to a significant increase in atmospheric nitrogen deposition17,18. China has become the world’s third-largest nitrogen deposition hotspot after Europe and North America, with southern regions experiencing an annual deposition rate of up to 63.53 kg N ha⁻¹ yr⁻¹5,19. As a key nutrient for plant growth, nitrogen availability profoundly influences plant performance and adaptive strategies during invasion16,20,21,22,23,24,25. For instance, in high-nutrient microenvironments, invasive plants often enhance their competitiveness through rapid adjustments in root and leaf trait plasticity5. Nevertheless, there remains a scarcity of systematic research on the responses of above- and below-ground traits in invasive and native plants under varying nitrogen levels and invasion degree.Previous studies have found that aboveground and belowground components of plants are closely interconnected: plants compete for light through above-ground organs (e.g., leaves) while simultaneously vying for nutrients and water via below-ground structures (e.g., roots)4. Recent studies have highlighted the critical importance of coordinated root and leaf functional traits in responding to heterogeneous above- and below-ground resource availability26,27. Such coordination enhances a plant’s capacity to either optimize acquisition of limited resources or minimize demand for specific resources28. For instance, research has demonstrated systematic correlations between root morphological traits and leaf traits associated with nutrient utilization26,29. This reflects an integrated whole-plant strategy where above- and below-ground components function synergistically to adapt to environmental variables including temperature, light intensity, and nutrient/water availability30. Despite their well-established role in plant resource-use strategies31, current understanding of how inter-organ trait coordination responds to environmental changes remains fragmented.Our earlier study observed that, in a 60-day short-term experiment, although invasive and native plant communities exhibited differential responses in total and root biomass, root morphology, and exudate composition to nitrogen addition, neither showed a significant preference for ammonium vs. nitrate nitrogen8. Since leaves are central organs in above-ground resource competition4, the physiological and morphological responses of leaves to nitrogen addition were not sufficiently addressed in previous work. Therefore, this study systematically investigates the effects of nitrogen addition on whole-plant biomass, root and leaf morphology, and root exudates in the invasive species Alternanthera philoxeroides and the native species Ludwigia peploides.Based on the above background, this study establishes three nitrogen addition levels (i.e., control, low, and high nitrogen treatments) and five invasion scenarios (i.e., no invasion, early invasion, mid-invasion, dominant invasion, and native species migration period). We hypothesize that: (1) nitrogen addition will promote the growth of both A. philoxeroides and L. peploides, but increasing invasion degree will suppress the growth of L. peploides; (2) nitrogen addition and invasion degree will significantly alter key root and leaf functional traits in both species; (3) nitrogen addition and invasion degree can regulate the invasion success of A. philoxeroides by modulating root traits, leaf traits, and their interactions, whereas this pattern will not be observed in L. peploides.ResultVariation in total biomassBoth invasion degree and nitrogen level significantly affected the individual plant biomass of A. philoxeroides and L. peploides, although their interaction was not significant (Fig. 1). Under the same invasion degree, both nitrogen addition treatments significantly increased total individual biomass of A. philoxeroides compared to the control (Fig. 1a). But only high nitrogen significantly increased the total individual biomass of L. peploides (Fig. 1b). Under the same nitrogen treatment, the total biomass of A. philoxeroides showed an increasing trend with the degree of invasion, while the opposite was true for L. peploides (Fig. 1a, b).Fig. 1Effect of invasion degree and nitrogen addition on the total dry biomass of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. Three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as CK, low nitrogen (Low N), and high nitrogen (High N) treatments, respectively. Five invasion scenarios: no invasion (0%), early invasion (25%), mid-invasion (50%), dominant invasion (75%), and native species migration period (100%). Sample sizes: n = 60.Full size imageVariation in root traitsAs shown in Fig. 2, the invasion degree and nitrogen level, as well as their interaction, significantly affected all root trait indices of A. philoxeroides (except for RMF and SRL) and L. peploides (except for RD).For A. philoxeroides, under different invasion degree, both nitrogen application treatments tended to decrease RMF, RD, and SRL (at early invasion (25%) and mid-invasion (50%)) compared to the CK. In contrast, both nitrogen levels increased root starch, NSC, nitrogen content, and SRL (at dominant invasion (75%) and native species migration period (100%)) (Fig. 2a-f). For L. peploides, across invasion degree, RMF gradually decreased with increasing nitrogen application, while RD showed the opposite trend (Fig. 2g, h). High nitrogen significantly reduced SRL, whereas the effect of low nitrogen varied depending on invasion degree (Fig. 2i). Both nitrogen treatments significantly decreased root starch and NSC content but markedly increased root nitrogen content (Fig. 2j-l).Compared to the native species migration period (100%), the presence of L. peploides significantly increased root starch and NSC content in A. philoxeroides (Fig. 2d, e). Under the CK treatment, the presence of L. peploides significantly reduced RMF and RD but increased SRL in A. philoxeroides, while its effect on root nitrogen content was minimal (Fig. 2a-c, f). Under both nitrogen application levels, the presence of L. peploides significantly decreased RMF (at mid-invasion (50%) and dominant invasion (75%)) and increased SRL, root starch, and NSC content in A. philoxeroides (Fig. 2a, c-e). Under low nitrogen, the presence of L. peploides significantly reduced root nitrogen content but increased RD (Fig. 2b, f). Under high nitrogen, it significantly increased RD (at early invasion (25%) and mid-invasion (50%)) and root nitrogen content (at mid-invasion (50%) and dominant invasion (75%)) in A. philoxeroides (Fig. 2b, f).Compared to the absence of A. philoxeroides invasion, the presence of A. philoxeroides showed no significant effect on the RD of L. peploides (Fig. 2h). Under the CK conditions, A. philoxeroides presence exhibited a decreasing trend in RMF, root starch, NSC and nitrogen content of L. peploides, while no significant effect was observed on SRL (Fig. 2g, i-l). Under both nitrogen application treatments, A. philoxeroides presence had minimal effects on root starch and NSC content of L. peploides (Fig. 2j, k). With low nitrogen treatment, A. philoxeroides presence showed limited influence on RMF but significantly increased SRL and root nitrogen content of L. peploides (Fig. 2g, i, l). Under high nitrogen treatment, A. philoxeroides presence significantly reduced RMF of L. peploides while demonstrating minor effects on SRL and root nitrogen content (Fig. 2g, i, l).Changes in root-secreted secondary metabolitesThe results of the Adonis analysis revealed that invasion degree significantly affected the composition of root exudates in both plant species, whereas nitrogen application showed no significant effect on their root exudate profiles (Fig. 3a and c).For A. philoxeroides, compared to the native species migration period (100%), the presence of L. peploides significantly reduced phenolic compound content in root exudates and showed a decreasing trend for terpenoids (except under both nitrogen treatments) and alkanes content. In contrast, organic acids and amides exhibited opposite trends, while alkaloids content remained unaffected (Fig. 3b). For L. peploides, compared to the absence of A. philoxeroides invasion, the presence of A. philoxeroides showed minimal effects on the content of phenolic compounds, alkanes, alkaloids, organic acids (under both nitrogen treatments), and amides (under CK and low nitrogen treatments) in its root exudates. However, a decreasing trend was observed for terpenoids content, while an increasing trend was noted for organic acids (under CK treatment) and amides (under high nitrogen treatment) (Fig. 3d).The Pearson correlation analysis revealed significant relationships between root traits and total biomass for both species (Fig. 4). For A. philoxeroides, RD, SRL, and root-secreted amides content showed significant negative correlations with total biomass, whereas root nitrogen concentration, phenolics, and alkanes content in root exudates exhibited significant positive correlations (Fig. 4). For L. peploides, RMF, and root-secreted terpenoids content showed significant positive correlations with total biomass, whereas SRL, root starch and root-secreted organic acids content exhibited significant negative correlations (Fig. 4).Fig. 2Effect of invasion degree and nitrogen addition on the root traits of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. (a, g) root mass fraction; (b, h) root diameter; (c, i) specific root length (SRL); (d, j) root starch content; (e, k) root total non-structural carbohydrates content (Root NSC); (f, l) root nitrogen content. Three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as CK, low nitrogen (Low N), and high nitrogen (High N) treatments, respectively. Five invasion scenarios: no invasion (0%), early invasion (25%), mid-invasion (50%), dominant invasion (75%), and native species migration period (100%). Sample sizes: n = 60.Full size imageFig. 3Effect of invasion degree and nitrogen addition on the content of secondary metabolites produced by the roots of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. (a, c) show the principal component analysis (PCA) of secondary metabolites produced by the roots of A. philoxeroides and L. peploides over invasion degree and nitrogen addition gradient analyzed using gas chromatography-mass spectrometry (GC–MS); (b, d) displays the percentage distribution of secondary metabolites produced by the roots (alkaloids, alkanes, amides, organic acids, phenols and terpenes) of A. philoxeroides and L. peploides under different invasion degree and nitrogen level treatments. RPA(%) represents the percentage of secretory products relative to the total secondary metabolite content. Three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as CK (N0), low nitrogen (N6, Low N), and high nitrogen (N12, High N) treatments, respectively. Five invasion scenarios: no invasion (0%), early invasion (25%), mid-invasion (50%), dominant invasion (75%), and native species migration period (100%).Full size imageFig. 4Pearson correlation analysis between total biomass and root traits of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. RMF represents root mass fraction; RD represents root diameter; SRL represents specific root length; Root NSC represents total root non-structural carbohydrates content; and Root N represents root nitrogen concentration.Full size imageChanges in leaf traitsAs shown in Fig. 5, invasion degree, nitrogen level, and their interaction significantly affected all leaf trait indices of A. philoxeroides (except LMF and SLA) and L. peploides (except SLA).Compared to the CK, nitrogen addition exhibited an increasing trend in LMF for both A. philoxeroides and L. peploides, with a more pronounced effect in A. philoxeroides (Fig. 5a, f). Both nitrogen levels significantly enhanced leaf nitrogen concentration in both species (Fig. 5e, j) but markedly reduced leaf starch (Fig. 5c, h) and NSC content (Fig. 5d, i). Differently, nitrogen application showed a trend of reducing the SLA of A. philoxeroides, but significantly increased the SLA of L. peploides (Fig. 5b, g).Compared with the native species migration period (100%), the presence of L. peploides non-significant effects the SLA of A. philoxeroides, and had a moderate effect on the LMF under nitrogen treatment. However, it significantly increased the leaf starch and NSC content under CK treatment, and significantly reduced the LMF under CK treatment (at early invasion (25%) and mid-invasion (50%)) and NSC content and leaf nitrogen content under high nitrogen treatment (Fig. 5a-e). Compared to the absence of A. philoxeroides invasion, the presence of A. philoxeroides had minimal effects on LMF and leaf nitrogen content of L. peploides, but significantly reduces its SLA (except at early invasion (25%)), the starch and NSC content in its leaves vary depending on the invasion degree of A. philoxeroides (Fig. 5f-j).Changes in leaf-secreted secondary metabolitesResults from the Adonis analysis revealed that invasion degree, nitrogen level, and their interaction significantly influenced the leaf exudate composition of A. philoxeroides (Fig. 6a). In contrast, only nitrogen level exhibited a significant effect on the leaf exudate profile of L. peploides (Fig. 6c).For A. philoxeroides, nitrogen application showed an increasing trend in leaf terpenoids content compared to the CK, while demonstrating decreasing trends for organic acids and alkaloids (under high nitrogen treatment). No significant effects were observed on phenols, amides, alkanes, or alkaloids (under low nitrogen treatment) (Fig. 6b). In contrast, for L. peploides, nitrogen application had no significant effect on leaf terpenoids, amides, and alkanes relative to CK. Minor effects were observed on phenols and alkaloids, while an increasing trend was noted for organic acids content (Fig. 6d).For A. philoxeroides, compared to the native species migration period (100%), the presence of L. peploides exhibited minimal effects on leaf terpenoids and amides content, no significant effects on leaf phenols and alkaloids content (under both CK and low nitrogen treatments), a decreasing trend in organic acids content, but significant increases in alkanes content, significant reductions in alkaloids content (under high nitrogen treatment) (Fig. 6b).The Pearson correlation analysis revealed that the biomass of A. philoxeroides was significantly positively correlated with its LMF, leaf nitrogen concentration, and terpenoids content secreted by leaves, whereas its SLA, leaf starch, NSC, and alkanes, amides secreted by leaves showed a significant negative correlation with total biomass (Fig. 7). For L. peploides, its individual biomass was significantly positively correlated with its SLA, leaf nitrogen concentration, and terpenoids content secreted by its leaves, whereas its leaf starch, NSC, and phenols, amides secreted by leaves showed a significant negative correlation with total biomass (Fig. 7).Fig. 5Effect of invasion degree and nitrogen addition on the leaf traits of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. (a, f) leaf mass fraction; (b, g) specific leaf area (SLA); (c, h) leaf starch content; (d, i) leaf total non-structural carbohydrates content (Leaf NSC); (e, j) leaf nitrogen content. Three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as CK, low nitrogen (Low N), and high nitrogen (High N) treatments, respectively. Five invasion scenarios: no invasion (0%), early invasion (25%), mid-invasion (50%), dominant invasion (75%), and native species migration period (100%). Sample sizes: n = 60.Full size imageFig. 6Effect of invasion degree and nitrogen addition on the content of secondary metabolites produced by the leaves of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. (a, c) show the principal component analysis (PCA) of secondary metabolites produced by the leaves of A. philoxeroides and L. peploides over invasion degree and nitrogen addition gradient analyzed using gas chromatography–mass spectrometry (GC–MS); (b, d) displays the percentage distribution of secondary metabolites produced by the leaves (alkaloids, alkanes, amides, organic acids, phenols and terpenes) of A. philoxeroides and L. peploides under different invasion degree and nitrogen level treatments. RPA(%) represents the percentage of secretory products relative to the total secondary metabolite content. Three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as CK (N0), low nitrogen (N6, Low N), and high nitrogen (N12, High N) treatments, respectively. Five invasion scenarios: no invasion (0%), early invasion (25%), mid-invasion (50%), dominant invasion (75%), and native species migration period (100%).Full size imageFig. 7Pearson correlation analysis between total biomass and leaf traits of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. LMF represents leaf mass fraction; SLA represents specific leaf area; Leaf NSC represents total leaf non-structural carbohydrates content; and leaf N represents leaf nitrogen concentration.Full size imageCorrelations among total biomass, root traits, and leaf traitsA. philoxeroides exhibited 56 significant root-leaf trait correlations, whereas L. peploides showed 50 significant root-leaf trait correlations (Fig. 8a, b). The PLS-PM model showed that nitrogen application level (path coefficient = 0.340, P < 0.001) and invasion degree (path coefficient = 0.249, P < 0.05) had a significant positive effect on the total biomass of A. philoxeroides, while nitrogen application level (P < 0.001) and invasion degree (P < 0.001) had a significant negative effect on the root traits of A. philoxeroides; At the same time, nitrogen application level (P < 0.001) and invasion degree (P < 0.05) also had a significant negative effect on the leaf traits of A. philoxeroides, but subsequently, changes in leaf traits promoted the growth of A. philoxeroides (Fig. 9a). There was a significant negative correlation between the invasion degree (P < 0.001) and the total biomass of L. peploides; There was also a significant negative correlation between nitrogen application level and its root traits (P < 0.001) and leaf traits (P < 0.001), but there was a significant positive correlation between invasion degree and its root traits (P < 0.001) and leaf traits (P < 0.01) (Fig. 9b).Fig. 8Pearson correlation analysis between root traits and leaf traits of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides under different invasion degree and nitrogen addition. RMF and LMF: represent root/leaf mass fraction; RD represent root diameter; SRL represent specific root length; SLA represent specific leaf area; RS and LS: represent root/leaf starch content; RNSC and LNSC: represent root/leaf total non-structural carbohydrate content; RNC and LNC: represent root/leaf nitrogen content.Full size imageFig. 9The partial least squares path model of invasive plant Alternanthera philoxeroides and native plant Ludwigia peploides. The Partial Least Squares Path Model illustrates the influence of nitrogen level and invasion degree on total biomass of A. philoxeroides (a) and L. peploides (b) by modulating their root traits and leaf traits. Arrow widths represent the strength of the path coefficient, and solid lines indicate significant correlations. Red and blue lines denote positive and negative pathways, respectively. Significance levels are denoted by asterisks: *p < 0.05, **p < 0.01, ***p < 0.001. Reflective latent variables (orange blocks) are indicated by the measured variables (blue blocks), with their respective weights shown. RMF and LMF: represent root/leaf mass fraction; RD represent root diameter; SRL represent specific root length; SLA represent specific leaf area; Root NSC and Leaf NSC: represent root/leaf total non-structural carbohydrate content; Root N and Leaf N: represent root/leaf nitrogen content.Full size imageDiscussionWhile the 90-day experimental period cannot fully capture the long-term dynamics of invasion processes, the short-term response patterns observed in this study remain highly significant. These early adaptive changes may represent critical first steps toward successful invasion.Nitrogen addition was likely to facilitate the displacement of L. peploides by A. philoxeroides in plant communities experiencing mid-invasion (50%) and dominant invasion (75%)Biomass serves as a direct measure of plant growth performance and resource-use efficiency28,30. Nitrogen enrichment generally promotes biomass production of invasive species and native species, invasive plants typically exhibit greater sensitivity to nitrogen enrichment compared to their native counterparts24,28,32,33,34, a pattern consistently observed in our study (Fig. 1a, b). As a critical nutrient regulating plant growth and productivity, nitrogen availability often determines the degree of biomass accumulation by fulfilling metabolic demands16,21,25,35. Compared to the native L. peploides, A. philoxeroides was a fast-growing, opportunistic perennial herb that typically exhibits faster phenotypic adjustments to nutrient addition or shifts in nutrient availability13.Notably, under nitrogen addition, A. philoxeroides outproduced L. peploides in biomass accumulation within mid-invasion (50%) and dominant invasion (75%) communities (Fig. 1a, b). In coexisting communities, A. philoxeroides and L. peploides occupy analogous ecological niches, and the high overlap of ecological niches may lead to fierce competition between invasive species and closely related native species occupying the same domain range5. Previous studies have shown that invasive plants can suppress native species by forming high-density canopies that intercept light, fiercely compete for nutrients, and even secrete allelopathic substances2. Therefore, as the relative abundance of A. philoxeroides increases, its ability to compete for space and nutrients in the community becomes stronger, and the growth of most native plants is inhibited, resulting in a decrease in individual biomass12. Atmospheric nitrogen deposition levels have increased significantly in recent years (cite source), with demonstrated impacts on plant communities in highly invaded ecosystems36. Our findings reveal that the early-stage invasive L. peploides exhibited superior growth performance compared to A. philoxeroides under these conditions (Fig. 1a, b). This temporal advantage suggests that early detection and intervention may represent the most effective strategy for mitigating A. philoxeroides invasion, particularly in the context of rising nitrogen availability.Variation in root traitsPlant roots, as critical organs for soil nutrient absorption, play a vital role in mediating plant-plant interactions and acquiring soil resources27. Their morphological and architectural traits can also predict a plant’s ability to tolerate competitors5. In this experiment, A. philoxeroides exhibited a higher SRL (Fig. 2c, i). Compared to the CK, nitrogen application tended to reduce its RD, whereas low nitrogen had no effect on L. peploides RD, and high nitrogen even increased it (Fig. 2b, h). Generally, thinner roots (but with higher SRL) may possess narrower water-conducting vessels and faster turnover rates, enhancing soil exploration and exploitation efficiency37,38. This trait reduces the cost of root proliferation in fluctuating environments, thereby improving nutrient absorption efficiency37,38.Differences in root trait changes were also observed between the two plant species at different invasion stages. In this experiment, compared to the native species migration period (100%), the presence of L. peploides had a minor effect on the root nitrogen content of A. philoxeroides under the CK treatment. However, under low nitrogen treatment, L. peploides significantly reduced the root nitrogen content of A. philoxeroides, while a slight increasing trend was observed under high nitrogen treatment (Fig. 2f). Conversely, compared to plots without A. philoxeroides invasion, the presence of A. philoxeroides tended to decrease the root nitrogen content of L. peploides under CK treatment, significantly increased it under low nitrogen treatment, and had a negligible effect under high nitrogen treatment (Fig. 2l). These patterns may be linked to changes in root exudate composition between the two species. Generally, higher root nutrient concentrations may correlate with greater abundance of soil-borne pathogens and root-feeding insects39,40. Consequently, plants may allocate additional resources to defense structures, including the secretion of secondary metabolites into roots for chemical protection41. Among the secondary metabolites detected in root exudates, we observed that the presence of L. peploides tended to elevate the secretion of organic acids and amides by A. philoxeroides roots compared to the native species migration period (100%) (Fig. 3b). In contrast, the presence of A. philoxeroides had minimal effects on the composition of L. peploides root exudates (Fig. 3d). Given that organic acids and amides are known allelochemicals which can affect the growth of neighboring plants8. Our finding suggests a potential feedback mechanism: the presence of L. peploides induces A. philoxeroides to release such compounds, likely to negatively impacting the growth of the native species itself.Further, physiological traits serve as sensitive indicators of plant environmental responses, typically detectable earlier than morphological traits42. Among these, non-structural carbohydrates (NSC, including soluble sugars and starch) availability profoundly influences plant growth and long-term survival43,44,45,46. In this experiment, nitrogen application and the presence of L. peploides significantly increased starch and NSC content in A. philoxeroides roots compared to both the CK and native species migration period (100%) (Fig. 2d, e). In contrast, nitrogen fertilization significantly reduced starch and NSC content in L. peploides roots relative to CK. Furthermore, compared to plots without A. philoxeroides invasion, the invasive species’ presence showed a tendency to decrease starch and NSC content in L. peploides roots under CK treatment, with minimal effects under nitrogen addition (Fig. 2j, k). These findings suggest divergent resource allocation strategies: A. philoxeroides allocates substantial resources to root storage, while L. peploides prioritizes rapid growth.Variation in leaf traitsLeaves, as the primary photosynthetic organs of plants, exhibit higher metabolic activity than roots and stems44. Typically, increased leaf biomass exerts strong control over aboveground resource acquisition47. Traits such as high SLA and elevated leaf nitrogen content were generally associated with enhanced photosynthetic capacity25,37,48. Additionally, the mobilization of starch and NSC stored in leaves can increase leaf respiration rates, thereby meeting the elevated carbohydrate demands of maintenance respiration44. Collectively, these adaptive traits improve a plant’s ability to absorb and utilize resources under changing environmental conditions, ultimately supporting greater aboveground growth. In this study, we found that nitrogen application enhanced the photosynthetic capacity of both study species compared to the CK, as evidenced by increased LMF, higher leaf nitrogen content, and reduced starch and NSC concentrations in leaves (Fig. 5). These results align with prior research demonstrating that nitrogen fertilization generally promotes leaf photosynthesis and plant growth44.We observed distinct patterns in leaf trait modifications of A. philoxeroides compared to L. peploides under varying invasion scenarios. Generally, elevated leaf nitrogen content alters plant interactions with nutrient-rich organisms and increases palatability to herbivores39,40. In our experiments, the presence of L. peploides significantly reduced leaf nitrogen content in A. philoxeroides relative to the native species migration period (100%) (Fig. 5e). Conversely, A. philoxeroides invasion showed minimal effects on L. peploides leaf nitrogen content (Fig. 5j). These differential responses may reflect variations in leaf exudate composition between the species. Compared to the native species migration period (100%), L. peploides presence exerted limited effects on terpenoids, amides, phenols, and alkaloids (under CK and low nitrogen treatments) in A. philoxeroides leaves, while showing a tendency to reduce organic acids and significantly decreasing alkaloids content under high nitrogen treatment (Fig. 6b). Notably, A. philoxeroides invasion did not alter the exudate profile of L. peploides leaves (Fig. 6d). The observed reduction in leaf nitrogen content, coupled with limited allelochemical secretion, we hypothesize that an adaptive strategy in A. philoxeroides to minimize herbivory pressure.The correlation between root and leaf functional traits and their adaptive strategiesTrait correlations were considered to reflect either trade-offs or synergistic optimization in resource allocation to meet fundamental survival requirements38,49. Plants exhibiting stronger root-leaf trait coordination may demonstrate greater growth success and survival when exposed to environmental variability30,50. This study revealed that under different nitrogen addition and invasion degree treatments, most root-leaf traits of both plant species exhibited significant correlations, though the strength and patterns of these correlations differed markedly. Compared to the native species L. peploides (involving 50 root-leaf trait correlations), A. philoxeroides demonstrated stronger root-leaf trait integration (involving 56 root-leaf trait correlations) (Fig. 8). This divergent trait correlation pattern may confer important adaptive value: it not only helps plants minimize negative impacts in unfavorable environments but also effectively enhances their capacity for survival, growth, and reproduction30. The differences in trait correlation strategies between A. philoxeroides and L. peploides reflect the diverse manifestations of ecological trait plasticity during environmental adaptation among different species.Results of the Partial Least Squares Path Modeling (PLS-PM) revealed that nitrogen addition and invasion degree can modulate the growth of A. philoxeroides through regulating root traits, leaf traits, and their interactions – a pattern not observed in L. peploides (Fig. 9a, b). Specifically, nitrogen addition and invasion degree not only directly increased the per-plant biomass of A. philoxeroides, but also indirectly promoted its biomass accumulation by altering leaf traits—such as increasing the leaf mass fraction and leaf nitrogen content, while reducing leaf starch content (Fig. 9a). In contrast, nitrogen addition had no significant effect on the per-plant biomass of L. peploides, whereas its biomass significantly decreased with increasing invasion degree. Furthermore, under conditions of nitrogen addition and invasion degree, the root traits, leaf traits, and their interrelationships in L. peploides did not exhibit significant regulatory effects on its total biomass (Fig. 9b). Previous research has indicated that trait plasticity and trait coordination play crucial roles in plant adaptation to environmental changes and may facilitate niche expansion30. Our findings further corroborate that, compared to the native species L. peploides, A. philoxeroides exhibits greater phenotypic plasticity in response to environmental variation. This advantage was likely attributable to its more tightly coordinated root-leaf trait relationships. This enhanced trait integration may be a key mechanism underlying the ecological success of this invasive species in heterogeneous habitats.In summary, a critical invasion mechanism of successful alien species lies in their superior trait values compared to co-occurring native species, enabling them to outcompete native flora and facilitate establishment in recipient habitats8,28. Notably, variations in root and leaf traits result from complex interactions between multiple biotic and abiotic factors26,51. Consequently, comprehensive quantification of interspecific differences in these traits is essential for elucidating the mechanisms underlying plant invasions.ConclusionIn conclusion, we observed that A. philoxeroides and L. peploides displayed differing belowground and aboveground trait responses under varying invasion scenarios and nitrogen treatments. Nitrogen addition promoted growth in both species, whereas invasion pressure had a more pronounced negative effect on L. peploides. These species-specific patterns appear linked to differential adjustments in root and leaf trait expression. Overall, compared to the native plant L. peploides, the invasive plant A. philoxeroides had more advantages in root and leaf traits under environmental treatment, and the correlation between root and leaf traits was stronger. These findings suggest that under progressive atmospheric nitrogen deposition, A. philoxeroides may progressively displace L. peploides, particularly in communities experiencing mid-invasion (50%) to dominant invasion (75%) invasion degrees. However, the limited soil types and plant species used in this study constrain the generalizability of our findings. Future experimental designs should incorporate more naturalistic scenarios to enhance ecological relevance.Materials and methodsStudy speciesThis study selected the invasive plant Alternanthera philoxeroides and the native plant Ludwigia peploides as research subjects. A. philoxeroides and L. peploides both exhibit rapid expansion capability through clonal growth and can quickly adapt to environmental changes by adjusting their above- and below-ground traits46,52. In natural ecosystems, these two species often co-occur over broad geographical ranges, sharing similar habitat types such as rice paddies, wetlands, canals, ponds, and ditches52. A. philoxeroides, native to South America, was now widely distributed across many regions worldwide and has become one of the most aggressive invasive alien species in China, causing significant ecological and economic impacts in China and numerous other countries46. In contrast, L. peploides is native to Zhejiang, Fujian, and eastern Guangdong in China and serves as a dominant native species in subtropical to tropical regions of the country52.Experimental designIn April 2022, 300 seedlings of A. philoxeroides and 300 seedlings of L. peploides were collected at the Liangzihu national field ecological research station of Wuhan University (N30°05–30°18, E114°21–114°39). They were then cultured in a aquarium tanks (100 × 30 × 50 cm, L × W × H) filled with 30 cm deep lake sediment (TC, 31.22 mg·g⁻¹; TN, 4.09 mg·g⁻¹; TP, 2.27 mg·g⁻¹). These two types of clonal plants were grown under greenhouse conditions (The mean annual temperature is 25 °C with an average annual sunshine duration of 1,810 h) for one year.On May 1, 2023, we selected 150 ramets each of A. philoxeroides and L. peploides from the pre-cultured seedlings, choosing individuals with biomass (approximately 1.9 g) and height (approximately 15 cm). These selected plants were then transplanted into stainless steel pots (70 cm inner diameter × 20 cm height) according to experimental treatments. Each pot was filled with approximately 15 cm of lake sediment (TC: 31.22 mg·g⁻¹; TN: 4.09 mg·g⁻¹; TP: 2.27 mg·g⁻¹). The experimental pots were randomly arranged on the outdoor cement platform at Liangzi Lake Ecological Station, which featured an open, flat terrain without obstructions and received ample sunlight.Following established methodologies14, we employed a space-for-time substitution approach to simulate the progressive invasion process of A. philoxeroides. Five invasion scenarios were established: the total biomass of 4 plants per pot was strictly controlled within the range of 7.40–7.60 g. (1) no invasion period (0%): composed exclusively of 4 L. peploides seedlings; (2) early invasion period (25%): consisting of 1 A. philoxeroides and 3 L. peploides seedlings; (3) mid-invasion period (50%): containing 2 A. philoxeroides and 2 L. peploides seedlings; (4) dominant invasion period (75%): comprising 3 A. philoxeroides and 1 L. peploides seedling; (5) native species migration period (100%): represented by 4 A. philoxeroides seedlings. Throughout the experiment, any spontaneously occurring rare weeds in the pots were manually removed. Furthermore, according to previous research1,8,16,23, each invasion treatment was coupled with three nitrogen addition levels: 0, 6, and 12 g N·m⁻²·yr⁻¹, designated as N0 (control, CK), N6 (low nitrogen), and N12 (high nitrogen) treatments, respectively. The N6 level represents the current average nitrogen deposition rate recorded in certain regions of China, while N12 corresponds to potential future high nitrogen deposition scenarios1,16,23. Starting in May 7, 2023, artificial nitrogen addition (NH4NO3) to the pots on a weekly basis according to the designated nitrogen deposition levels. The experiment was conducted for 90 days, concluding on August 5, 2023. The complete experimental design was illustrated in Fig. 10. Although the space-for-time substitution approach has inherent limitations, this study implemented strict controls to ensure consistent total biomass and plant numbers per pot, which helps partially compensate for the constraints of short-term observations.Fig. 10Illustrates the experimental design and provides a visual representation of the experiment. Five invasion scenarios were established: native species migration period (100%), 4 A. philoxeroides seedlings; dominant invasion period (75%), 3 A. philoxeroides and 1 L. peploides seedling; mid-invasion period (50%), 2 A. philoxeroides and 2 L. peploides seedlings; early invasion period (25%), 1 A. philoxeroides and 3 L. peploides seedlings; no invasion period (0%), 4 L. peploides seedlings.Full size imageSampling collect and trait measurementIn accordance with established methodologies, we collected a comprehensive dataset of above- and below-ground functional traits for both plant species. These trait parameters are widely recognized in ecological research as key indicators of plants’ acquisition, utilization, and conservation strategies for critical resources41,53,54,55,56,57,58. Specifically, each stainless steel pot was fully submerged in water, and soil particles were removed under running tap water (water pressure: 0.2 MPa; duration: 5 min per sample). This process yielded intact plant specimens completely free of adhering soil particles.Randomly selected 4 intact leaves from the uppermost canopy, and collected 3 intact root segments representing the complete root system architecture8,31. Arranged samples on A4-sized acrylic trays with minimal overlap, scanned using a calibrated scanner (600 dpi, Epson 1680, Seiko Epson Corporation) following standardized calibration procedures, and analyzed using WinRHIZO software (Regent Instruments, Quebec, Canada) to determine leaf area (LA), average root diameter (RD), and total root length (RL)56. The scanned leaves and roots were dried to a constant mass in a 70 ℃ oven, then weighed, and these data were used to determine the specific leaf area (SLA) and specific root length (SRL)18,29,59.After these measurements, the residual parts of the plant material were divided into three parts: roots, stems, and leaves. Then place it in a 70 ℃ oven to dry until a constant weight was reached, and weigh it. We separately measured the total biomass of individual plants of A. philoxeroides and L. peploides. The leaf mass fraction (LMF) was calculated as the ratio of the leaf mass to the total mass32; The root mass fraction (RMF) was calculated as the ratio of the root mass to the total mass28.Collection and quantification of secondary metabolites in roots and leavesFollowing previous research methods60,61, randomly select 3–6 mature and intact leaves from harvested plants of weigh 1 g, and immediately grind them in a 10 ml sterile centrifuge tube. Add 5 ml of ethyl acetate for extraction and immerse for 72 h. Similarly, for collected belowground plant tissues and randomly select 2–5 intact root systems of weigh 1 g, and repeat the aforementioned steps. Preserve the obtained extracts in the dark at a low temperature (-20℃). Subsequently, filter the excess cellular debris using a 0.45 μm syringe filter, concentrate using a rotary evaporator (RE-52AA), dissolve in 1 ml of ethyl acetate, transfer to a GC-MS sample vial, and store in the dark at a low temperature (-40℃) until analysis62. The ethyl acetate extract of each sample was analysed by GC-MS (GCMS-QP 2020NX, SHIMADZU, Japan)63. The GC injector temperature was 250 °C. The oven temperature was maintained at 45 °C, then increased from 45 °C to 150 °C at 10 °C/min, and then increased to 250 °C at 15 °C/min for 10 min. The transfer line temperature was set to 250 °C. Helium was used as the carrier gas at a flow rate of 1 mL/min. The MS source was operated in electron impact (EI) mode at 70 eV. The MS was scanned from 45 to 450 m/z. For the GC–MS data of root exudates, we normalized the peak area of each compound with the sum of all peak area for allidentified metabolites for each sample. Relative peak area was then used to calculate compound-specific concentrations8,60,61,62,63.Determination of non-structural carbohydrates and C, N, P elementsThe total carbon and nitrogen concentrations in leaf and root plant tissues were analyzed using an organic elemental analyzer (Elementar, UNICUBE, Germany) via the dry combustion method. Total phosphorus content was measured using the molybdenum antimony anti-colorimetric method64. For the extraction and determination of soluble sugars and starch, 80% anhydrous ethanol and ethyl anthraquinone acetate reagents were utilized, respectively45. The sum of soluble sugar and starch content was considered the concentration of non-structural carbohydrates (NSC)65.Data analysisSince the data from each pot were not completely independent, prior to statistical analysis, we calculated the mean values of measurements for each plant species within individual pots. This approach ensures the validity of our statistical analysis.We employed two-way ANOVA to examine the effects of nitrogen addition, invasion degree, and their interaction on the total biomass, root traits, and leaf traits of A. philoxeroides and L. peploides. Means were compared using Duncan’s multiple range test. P-values ≤ 0.05 were considered statistically significant. Prior to analyses, we tested whether the assumptions of an ANOVA, homogeneity of variances and normally distributed residuals were achieved. The homogeneity of variances for all the studied parameters was evaluated by Levene’s test and the distribution of the residuals was assessed by Kolmogorov-Smirnov test. When necessary, logarithmic, reciprocal, or square root transformations were applied to meet assumptions.Based on their chemical properties, plant tissue metabolites were classified into six categories: phenols, alkaloids, amides, alkanes, organic acids, and terpenoids. Each value represents the total concentration of all compounds within a given category. Principal Component Analysis (PCA) was performed to visualize differences in exudate composition between the two plant species under varying nitrogen levels and invasion degree. Adonis analysis was used to test for significant differences between the nitrogen level and invasion degree. At the same time, two-way ANOVA was performed for each compound using the “dplyr” and “agricolae” packages in R 4.2.3 (R, 2022) to analyze the significant differences in the relative concentrations of the compounds, with nitrogen addition and invasion degree as independent variables.To examine the relationships between root/leaf functional traits and total biomass, we conducted Pearson correlation analyses separately for A. philoxeroides and L. peploides, assessing the associations between their respective root/leaf traits and total biomass. Furthermore, we quantified pairwise correlations between root and leaf traits under different nitrogen levels and invasion degree using Pearson’s correlation coefficients. This approach allowed us to investigate how these two species coordinate their root-leaf trait relationships in response to environmental changes.To further investigate the potential relationships among plant biomass, root traits, and leaf traits under different environmental factors, we employed partial least squares path modeling (PLS-PM) to evaluate the direct and indirect effects of invasion degree and nitrogen level on root traits, leaf traits, and total biomass in A. philoxeroides and L. peploides. The model was constructed using the “innerplot” function from the “plspm” package in R software (4.2.3). Hypothesized pathways were defined a priori based on ecological theory, with invasion degree and nitrogen levels as exogenous variables, and root traits, leaf traits, and total biomass as endogenous variables. All variables were standardized (mean = 0, SD = 1) to ensure comparability of path coefficients. Non-normality was addressed using the package’s robust weighting algorithm.All statistical analyses were performed using SPSS (SPSS Inc.) and R software (4.2.3), while figures were generated using Origin (Version 9.0, OriginLab Co.) and R software (4.2.3)63.

    Data availability

    The datasets generated and analyzed during the present study are accessible from the corresponding author upon reasonable request.
    ReferencesRen, G. Q. et al. Warming and elevated nitrogen deposition accelerate the invasion process of Solidago Canadensis L. Ecol. Process. 11, 3879 (2022).Article 

    Google Scholar 
    Sun, K. et al. Relative abundance of invasive plants more effectively explains the response of wetland communities to different invasion degrees than phylogenetic evenness. J. Plant. Ecol. 15, 625–638 (2022).Article 

    Google Scholar 
    Siebenkas, A., Schumacher, J. & Roscher, C. Phenotypic plasticity to light and nutrient availability alters functional trait ranking across eight perennial grassland species. AoB Plants. 7, plv029 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ni, M., Liu, Y., Chu, C. J., Xu, H. & Fang, S. Q. Fast seedling root growth leads to competitive superiority of invasive plants. Biol. Invasions. 20, 1821–1832 (2018).Article 

    Google Scholar 
    Chen, L. H. et al. Effects of simulated nitrogen deposition on the ecophysiological responses of Populus beijingensis and P. cathayana under intra- and interspecific competition. Plant. Soil. 481, 127–146 (2022).Article 
    CAS 

    Google Scholar 
    Li, L., Ding, M. M. & Jeppesen, E. Variation in growth, reproduction, and resource allocation in an aquatic plant, Vallisneria spinulosa: the influence of amplitude and frequency of water level fluctuations. Aquat. Sci. 82, 983 (2020).Article 

    Google Scholar 
    Read, Q. D., Henning, J. A., Classen, A. T. & Sanders, N. J. Aboveground resilience to species loss but belowground resistance to nitrogen addition in a montane plant community. J. Plant. Ecol. 11, 351–363 (2018).Article 

    Google Scholar 
    Li, D. X. et al. The impacts of different nitrogen supply on root traits, root exudates, and soil enzyme activities of exotic and native plant communities. Plant. Soil. 508, 209–226 (2024).Article 

    Google Scholar 
    Wang, T., Hu, J. T., Miao, L. L., Yu, D. & Liu, C. H. The invasive stoloniferous clonal plant Alternanthera Philoxeroides outperforms its co-occurring non-invasive functional counterparts in heterogeneous soil environments – invasion implications. Sci. Rep. 6, 38036 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, P. et al. Contrasting coordination of non-structural carbohydrates with leaf and root economic strategies of alpine coniferous forests. New. Phytol. 243, 580–590 (2024).Article 
    CAS 
    PubMed 

    Google Scholar 
    Sun, J. K. et al. Advantages of growth and competitive ability of the invasive plant Solanum rostratum over two co-occurring natives and the effects of nitrogen levels and forms. Front. Plant. Sci. 14, 1169317 (2023).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, J. L., Huang, W. & Ding, J. Q. Phenotypic plasticity in resource allocation to sexual trait of alligatorweed in wetland and terrestrial habitats. Sci. Total Environ. 757, 143819 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Si, C. C. et al. Different degrees of plant invasion significantly affect the richness of the soil fungal community. PLoS One. 8, e85490 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, H. Y. et al. Invasion by the weed Conyza Canadensis alters soil nutrient supply and shifts microbiota structure. Soil. Biol. Biochem. 143, 107739 (2020).Article 
    CAS 

    Google Scholar 
    Xing, L. J. et al. Comparison between the exotic Coreopsis grandiflora and native Dendranthema indicum across variable nitrogen deposition conditions. Acta Physiol. Plant. 44, 349 (2022).Article 

    Google Scholar 
    Guo, X. et al. Nitrogen deposition effects on invasive and native plant competition: implications for future invasions. Ecotoxicol. Environ. Saf. 259, 115029 (2023).Article 
    CAS 
    PubMed 

    Google Scholar 
    Xu, F. W. et al. Linking leaf traits to the Temporal stability of above- and belowground productivity under global change and land use scenarios in a semi-arid grassland of inner Mongolia. Sci. Total Environ. 818, 151858 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Gong, J. R. et al. N addition rebalances the carbon and nitrogen metabolisms of Leymus chinensis through leaf N investment. Plant. Physiol. Biochem. 185, 221–232 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wu, H. et al. Nitrogen enrichment alters the resistance of a noninvasive alien plant species to Alternanthera Philoxeroides invasion. Front. Ecol. Evol. 11, 1215191 (2023).Article 

    Google Scholar 
    Wang, B. et al. Nitrogen addition alters photosynthetic carbon fixation, allocation of photoassimilates, and carbon partitioning of Leymus chinensis in a temperate grassland of inner Mongolia. Agric. Meteorol. 279, 107743 (2019).Article 

    Google Scholar 
    Zhang, Q. Z. et al. Nitrogen addition and drought affect nitrogen uptake patterns and biomass production of four urban greening tree species in North China. Sci. Total Environ. 893, 164893 (2023).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zhao, Z. W. et al. Effects of nitrogen addition on plant-soil-microbe stoichiometry characteristics of different functional group species in Bothriochloa ischemum community. Soil. Ecol. Lett. 4, 362–375 (2021).Article 

    Google Scholar 
    Jamieson, M. A., Seastedt, T. R. & Bowers, M. D. Nitrogen enrichment differentially affects above- and belowground plant defense. Am. J. Bot. 99, 1630–1637 (2012).Article 
    PubMed 

    Google Scholar 
    Wang, A. O. et al. Nitrogen addition increases intraspecific competition in the invasive wetland plant Alternanthera philoxeroides, but not in its native congener Alternanthera sessilis. Plant. Species Biol. 30, 176–183 (2014).Article 

    Google Scholar 
    Wei, X. W. et al. Improved utilization of nitrate nitrogen through within-leaf nitrogen allocation trade-offs in Leymus chinensis. Front. Plant. Sci. 13, 870681 (2022).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hu, Y. K. et al. Is there coordination of leaf and fine root traits at local scales? A test in temperate forest swamps. Ecol. Evol. 9, 8714–8723 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hu, Y. K., Pan, X., Liu, X. Y., Fu, Z. X. & Zhang, M. Y. Above- and belowground plant functional composition show similar changes during temperate forest swamp succession. Front. Plant. Sci. 12, 658883 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, Q. et al. Trait value and phenotypic integration contribute to the response of exotic Rhus typhina to heterogeneous nitrogen deposition: a comparison with native Rhus chinensis. Sci. Total Environ. 844, 157199 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    de la Riva, E. G. et al. Root traits across environmental gradients in mediterranean Woody communities: are they aligned along the root economics spectrum? Plant. Soil. 424, 35–48 (2017).Article 

    Google Scholar 
    Du, L. S., Liu, H. Y., Guan, W. B., Li, J. M. & Li, J. S. Drought affects the coordination of belowground and aboveground resource-related traits in Solidago Canadensis in China. Ecol. Evol. 9, 9948–9960 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jo, I., Fridley, J. D. & Frank, D. A. Linking above- and belowground resource use strategies for native and invasive species of temperate deciduous forests. Biol. Invasions. 17, 1545–1554 (2014).Article 

    Google Scholar 
    Ren, G. Q. et al. The enhancement of root biomass increases the competitiveness of an invasive plant against a co-occurring native plant under elevated nitrogen deposition. Flora 261, 151486 (2019).Article 

    Google Scholar 
    Xu, K. et al. Nitrogen deposition further increases Ambrosia trifida root exudate invasiveness under global warming. Environ. Monit. Assess. 195, 759 (2023).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, C. Y., Zhou, J. W., Liu, J. & Jiang, K. Differences in functional traits between invasive and native Amaranthus species under different forms of N deposition. Sci. Nat. 104, 927 (2017).Article 

    Google Scholar 
    Witzell, J. & Shevtsova, A. Nitrogen-induced changes in phenolics of Vaccinium myrtillus–implications for interaction with a parasitic fungus. J. Chem. Ecol. 30, 1937–1956 (2004).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zhou, J. L. et al. Nitrogen influence to the independent invasion and the co-invasion of Solidago Canadensis and Conyza Canadensis via intensified allelopathy. Sustainability 14, 11970 (2022).Article 
    CAS 

    Google Scholar 
    Liese, R., Alings, K. & Meier, I. C. Root branching is a leading root trait of the plant economics spectrum in temperate trees. Front. Plant. Sci. 8, 315 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, A. R. et al. Integrating nitrogen fixing structures into above- and belowground functional trait spectra in soy (Glycine max). Plant. Soil. 440, 53–69 (2019).Article 
    CAS 

    Google Scholar 
    van Geem, M. et al. The importance of aboveground-belowground interactions on the evolution and maintenance of variation in plant defense traits. Front. Plant. Sci. 4, 431 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shi, M. Z. et al. Plant volatile compounds of the invasive alligatorweed, Alternanthera Philoxeroides (Mart.) Griseb, infested by Agasicles hygrophila Selman and Vogt (Coleoptera: Chrysomelidae). Life (Basel). 12, 1257 (2022).CAS 
    PubMed 

    Google Scholar 
    Weemstra, M. et al. Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species. Front. Glob Change. 6, 7127 (2023).Article 

    Google Scholar 
    Roiloa, S. R., Rodríguez-Echeverría, S., Freitas, H. & Retuerto, R. Developmentally-programmed division of labour in the clonal invader Carpobrotus Edulis. Biol. Invasions. 15, 1895–1905 (2013).Article 

    Google Scholar 
    Huang, J., Wang, X. M., Zheng, M. H. & Mo, J. M. 13-year nitrogen addition increases nonstructural carbon pools in subtropical forest trees in Southern China. Ecol. Manag. 481, 118748 (2021).Article 

    Google Scholar 
    Du, Y., Lu, R. L. & Xia, J. Y. Impacts of global environmental change drivers on non-structural carbohydrates in terrestrial plants. Funct. Ecol. 34, 1525–1536 (2020).Article 

    Google Scholar 
    Yin, J. L. et al. Carbohydrate, phytohormone, and associated transcriptome changes during storage root formation in alligatorweed (Alternanthera philoxeroides). Weed Sci. 68, 382–395 (2020).Article 

    Google Scholar 
    Geng, Y. P. et al. Plasticity and ontogenetic drift of biomass allocation in response to above- and below-ground resource availabilities in perennial herbs: a case study of Alternanthera Philoxeroides. Ecol. Res. 22, 255–260 (2006).Article 

    Google Scholar 
    Smith, M. S., Fridley, J. D., Goebel, M. & Bauerle, T. L. Links between belowground and aboveground resource-related traits reveal species growth strategies that promote invasive advantages. PLoS One. 9, e104189 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, Y. J. et al. Vertical distribution patterns of community biomass, carbon and nitrogen content in grasslands on the Eastern Qinghai–Tibet plateau. Ecol. Indic. 154, 110726 (2023).Article 
    CAS 

    Google Scholar 
    Xian, L. et al. Which has a greater impact on plant functional traits: plant source or environment? Plants (Basel). 13, 903 (2024).CAS 
    PubMed 

    Google Scholar 
    Fan, R., Hua, J. G., Huang, Y. L., Lin, J. Y. & Ji, W. L. What role do dauciform roots play? Responses of Carex filispica to trampling in alpine meadows based on functional traits. Ecol. Evol. 13, e9875 (2023).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marques, E. et al. The impact of domestication on aboveground and belowground trait responses to nitrogen fertilization in wild and cultivated genotypes of Chickpea (Cicer sp). Front. Genet. 11, 576338 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huang, X. L. et al. Root morphological and structural comparisons of introduced and native aquatic plant species in multiple substrates. Aquat. Ecol. 52, 65–76 (2017).Article 

    Google Scholar 
    Fry, E. L. et al. Soil multifunctionality and drought resistance are determined by plant structural traits in restoring grassland. Ecology 99, 2260–2271 (2018).Article 
    PubMed 

    Google Scholar 
    Weemstra, M. et al. Towards a multidimensional root trait framework: a tree root review. New. Phytol. 211, 1159–1169 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wu, D. et al. Plant phenols contents and their changes with nitrogen availability in peatlands of Northeastern China. J. Plant. Ecol. 13, 713–721 (2020).Article 
    CAS 

    Google Scholar 
    Lin, G. G., Gao, M. X., Zeng, D. H. & Fang, Y. T. Aboveground conservation acts in synergy with belowground uptake to alleviate phosphorus deficiency caused by nitrogen addition in a larch plantation. Ecol. Manag. 473, 118309 (2020).Article 

    Google Scholar 
    Lv, T. et al. Invasive submerged plant has a stronger inhibitory effect on epiphytic algae than native plant. Biol. Invasions. 26, 1001–1014 (2023).Article 

    Google Scholar 
    Gervais-Bergeron, B., Chagnon, P. L. & Labrecque, M. Willow aboveground and belowground traits can predict phytoremediation services. Plants (Basel). 10, 1824 (2021).CAS 
    PubMed 

    Google Scholar 
    Bakker, L. M., Mommer, L. & van Ruijven, J. Using root traits to understand Temporal changes in biodiversity effects in grassland mixtures. Oikos 128, 208–220 (2018).Article 

    Google Scholar 
    Bi, J. W. et al. Divergent geographic variation in above- versus below‐ground secondary metabolites of Reynoutria Japonica. J. Ecol. 112, 514–527 (2024).Article 

    Google Scholar 
    Yu, H. W. et al. Greater chemical signaling in root exudates enhances soil mutualistic associations in invasive plants compared to natives. New. Phytol. 236, 1140–1153 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Vivanco, J. M., Bais, H. P., Stermitz, F. R., Thelen, G. C. & Callaway, R. M. Biogeographical variation in community response to root allelochemistry: novel weapons and exotic invasion. Ecol. Lett. 7, 285–292 (2004).Article 

    Google Scholar 
    Lv, T. et al. Invasion of water hyacinth and water lettuce inhibits the abundance of epiphytic algae. Divers. Distrib. 28, 1650–1662 (2022).Article 

    Google Scholar 
    Chen, C., Xing, F., Li, Z. & Zhang, R. H. Nitrogen addition changes the allelopathic effects of the root leachate from the invasive weed Stellera Chamaejasme L. on a dominant grass in the Songnen grassland. J. Plant. Biol. 66, 243–255 (2023).Article 
    CAS 

    Google Scholar 
    Zhou, L. F. et al. Latitudinal and longitudinal trends of seed traits indicate adaptive strategies of an invasive plant. Front. Plant. Sci. 12, 657813 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Download referencesAcknowledgementsThe authors gratefully acknowledge funding support from the Fundamental Research Funds for the Central Universities (2042020kf1025).Author informationAuthors and AffiliationsDepartment of Ecology, College of Life Science, The National Field Station of Freshwater Ecosystem of Liangzi Lake, Wuhan University, 299 Bayi Rd., Wuhan, ChinaDexiang Li, Tian Lv, Yang Li, Haihao Yu, Dan Yu & Chunhua LiuAuthorsDexiang LiView author publicationsSearch author on:PubMed Google ScholarTian LvView author publicationsSearch author on:PubMed Google ScholarYang LiView author publicationsSearch author on:PubMed Google ScholarHaihao YuView author publicationsSearch author on:PubMed Google ScholarDan YuView author publicationsSearch author on:PubMed Google ScholarChunhua LiuView author publicationsSearch author on:PubMed Google ScholarContributionsDexiang Li led the research design. Dexiang Li, Tian Lv and Yang Li collected raw data set and integrated. Dexiang Li conducted data management, led a statistical analysis and led the writing of the first manuscript. Haihao Yu, Dan Yu, and Chunhua Liu commented on previous versions of the manuscript. All authors interpreted the results and significantly contributed to improve the manuscript. All authors read and approved the final manuscript.Corresponding authorCorrespondence to
    Chunhua Liu.Ethics declarations

    Competing interests
    The authors declare no competing interests.

    Statement
    The collection of plant materials (Alternanthera philoxeroides and Ludwigia peploides) and experimental research conducted in this study comply with relevant institutional, national, and international guidelines and regulations. We confirm that this study adheres to all applicable institutional, national, and international standards and legislation.

    Plant guidelines
    The plant materials used in this study (Alternanthera philoxeroides and Ludwigia peploides) were formally identified by Professor Dan Yu from the Department of Aquatic Ecology, College of Life Sciences, Wuhan University, to ensure species accuracy. Professor Dan Yu (email: [email protected]), a professor in the Department of Aquatic Ecology, College of Life Sciences, Wuhan University, specializes in plant taxonomy and identification. Prior to experimentation, both plant species used in this study were authenticated by Prof. Yu to ensure taxonomic accuracy. Additionally, voucher specimens of both A. philoxeroides and L. peploides have been deposited at the Liangzi Lake National Field Station for Freshwater Ecosystem Research, Wuhan University. The voucher specimens have been deposited with the following accession numbers, A. philoxeroides: Collection No. WHU-AP-20220401-001; L. peploides: Collection No. WHU-LP-20220401-001. This research obtained the necessary collection permits for Alternanthera philoxeroides and Ludwigia peploides from the Liangzi Lake National Field Station for Freshwater Ecosystem Research, Wuhan University.

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    Reprints and permissionsAbout this articleCite this articleLi, D., Lv, T., Li, Y. et al. Functional trait variations of the invasive plant Alternanthera Philoxeroides and the native plant Ludwigia peploides under nitrogen addition.
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    New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales

    AbstractThe bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.

    Data availability

    We have deposited the assembled sequence data for newly sequenced genomes, including raw sequencing reads, under NCBI BioProject ID PRJNA1170004. Ribosomal RNA gene sequence data were published previously under NCBI BioProject ID PRJNA673898. The Supplementary Data includes all remaining data, including accession numbers for all previously sequenced genomes and metagenomes. The URL https://seqco.de/r:r4auejub serves as the SeqCode registry for all taxon names defined in this study.
    Code availability

    All custom R, BASH, and Python scripts used for data analyses in this study are publicly available on GitHub at https://github.com/kcfreel/SAR11-genomes-from-the-tropical-Pacific and archived with Zenodo (https://doi.org/10.5281/zenodo.17614008). Additionally, a fully reproducible bioinformatics workflow for the analysis of SAR11 genomes is available at https://merenlab.org/data/sar11-phylogenomics/, enabling the reproduction of our phylogenomic tree and its extension with new genomes.
    ReferencesGrote, J. et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3, e00252–12 (2012).Morris, R. M. et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420, 806–810 (2002).
    Google Scholar 
    Carlson, C. A. et al. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J. 3, 283–295 (2009).
    Google Scholar 
    Schattenhofer, M. et al. Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environ. Microbiol. 11, 2078–2093 (2009).
    Google Scholar 
    Eiler, A., Hayakawa, D. H., Church, M. J., Karl, D. M. & Rappé, M. S. Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre. Environ. Microbiol. 11, 2291–2300 (2009).
    Google Scholar 
    Becker, J. W., Hogle, S. L., Rosendo, K. & Chisholm, S. W. Co-culture and biogeography of Prochlorococcus and SAR11. ISME J. 13, 1506–1519 (2019).
    Google Scholar 
    Eren, A. M. et al. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4, 1111–1119 (2013).
    Google Scholar 
    Delmont, T. O. et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. Elife 8, e46497 (2019).Tucker, S. J. et al. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 9, e12274 (2021).
    Google Scholar 
    Haro-Moreno, J. M. et al. Ecogenomics of the SAR11 clade. Environ. Microbiol. 22, 1748–1763 (2020).
    Google Scholar 
    Tucker, S. J., Freel, K. C., Eren, A. M. & Rappé, M. S. Habitat-specificity in SAR11 is associated with a few genes under high selection. ISME J. 19, wraf216 https://doi.org/10.1093/ismejo/wraf216 (2025).Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60–63 (1990).
    Google Scholar 
    Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).
    Google Scholar 
    Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022).
    Google Scholar 
    Tsementzi, D. et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536, 179–183 (2016).
    Google Scholar 
    Kiefl, E. et al. Structure-informed microbial population genetics elucidates selective pressures that shape protein evolution. Sci. Adv. 9, eabq4632 (2023).
    Google Scholar 
    López-Pérez, M., Haro-Moreno, J. M., Coutinho, F. H., Martinez-Garcia, M. & Rodriguez-Valera, F. The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5, e00605–20 (2020).Delmont, T. O. et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat. Microbiol. 3, 804–813 (2018).
    Google Scholar 
    Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5, 170203 (2018).
    Google Scholar 
    Chang, T., Gavelis, G. S., Brown, J. M. & Stepanauskas, R. Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton. Microbiome 12, 126 (2024).
    Google Scholar 
    Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623–1635.e11 (2019).
    Google Scholar 
    Thrash, J. C. et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci. Rep. 1, 13 (2011).
    Google Scholar 
    Muñoz-Gómez, S. A. et al. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. Elife 8, e42535 (2019).Vergin, K. L. et al. High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ. Microbiol. 9, 2430–2440 (2007).
    Google Scholar 
    Wilhelm, L. J., Tripp, H. J., Givan, S. A., Smith, D. P. & Giovannoni, S. J. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol. Direct 2, 27 (2007).
    Google Scholar 
    Carini, P., Steindler, L., Beszteri, S. & Giovannoni, S. J. Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. ISME J. 7, 592–602 (2013).
    Google Scholar 
    Sun, J. et al. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nat. Microbiol. 1, 16065 (2016).
    Google Scholar 
    Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008).
    Google Scholar 
    Rappé, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002).
    Google Scholar 
    Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).
    Google Scholar 
    Schwalbach, M. S., Tripp, H. J., Steindler, L., Smith, D. P. & Giovannoni, S. J. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. Environ. Microbiol. 12, 490–500 (2010).
    Google Scholar 
    Sun, J. et al. One-carbon metabolism in SAR11 pelagic marine bacteria. PLoS ONE 6, e23973 (2011).
    Google Scholar 
    Giovannoni, S. J. SAR11 Bacteria: The Most Abundant Plankton in the Oceans. Ann. Rev. Mar. Sci. 9, 231–255 (2017).
    Google Scholar 
    Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).
    Google Scholar 
    Viklund, J., Ettema, T. J. G. & Andersson, S. G. E. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599–615 (2012).
    Google Scholar 
    Carini, P. et al. Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea. ISME J. 8, 1727–1738 (2014).
    Google Scholar 
    Brandon, M. L. High-Throughput Isolation of Pelagic Marine Bacteria from the Coastal Subtropical Pacific Ocean Master’s thesis (University of Hawaiʻi at Mānoa, Department of Oceanography, 2006).Vergin, K. L. et al. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series study site by phylogenetic placement of pyrosequences. ISME J. 7, 1322–1332 (2013).
    Google Scholar 
    Thrash, J. C. et al. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J. 8, 1440–1451 (2014).
    Google Scholar 
    Wang, Z. & Wu, M. A phylum-level bacterial phylogenetic marker database. Mol. Biol. Evol. 30, 1258–1262 (2013).
    Google Scholar 
    Suzuki, M. T., Béjà, O., Taylor, L. T. & Delong, E. F. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ. Microbiol. 3, 323–331 (2001).
    Google Scholar 
    Getz, E. W. et al. The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct. mSystems 8, e0017923 (2023).
    Google Scholar 
    Viklund, J., Martijn, J., Ettema, T. J. G. & Andersson, S. G. E. Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS ONE 8, e78858 (2013).
    Google Scholar 
    Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).
    Google Scholar 
    Muñoz-Gómez, S. A. et al. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. 6, 253–262 (2022).
    Google Scholar 
    Evans, J. T. & Denef, V. J. To dereplicate or not to dereplicate? mSphere 5, e00971–19 (2020).Zhao, J. et al. Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean. ISME J. 19, wraf072 (2025).Hellweger, F. L., van Sebille, E. & Fredrick, N. D. Biogeographic patterns in ocean microbes emerge in a neutral agent-based model. Science 345, 1346–1349 (2014).
    Google Scholar 
    Villarreal-Chiu, J. F., Quinn, J. P. & McGrath, J. W. The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. Front. Microbiol. 3, 19 (2012).
    Google Scholar 
    Carini, P., White, A. E., Campbell, E. O. & Giovannoni, S. J. Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nat. Commun. 5, 4346 (2014).
    Google Scholar 
    Sosa, O. A., Repeta, D. J., DeLong, E. F., Ashkezari, M. D. & Karl, D. M. Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation. Environ. Microbiol. 21, 2402–2414 (2019).
    Google Scholar 
    Acker, M. et al. Phosphonate production by marine microbes: exploring new sources and potential function. Proc. Natl Acad. Sci. USA. 119, e2113386119 (2022).
    Google Scholar 
    Zhao, X. et al. Three-dimensional structure of the ultraoligotrophic marine bacterium ‘Candidatus Pelagibacter ubique’. Appl. Environ. Microbiol. 83, e02807–16 (2017).Craig, L. & Li, J. Type IV pili: paradoxes in form and function. Curr. Opin. Struct. Biol. 18, 267–277 (2008).
    Google Scholar 
    Braakman, R. et al. Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes. Sci. Adv. 11, eadp1949 (2025).Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011).
    Google Scholar 
    Brown, M. V. et al. Global biogeography of SAR11 marine bacteria. Mol. Syst. Biol. 8, 595 (2012).
    Google Scholar 
    Davies, T. J. Evolutionary ecology: when relatives cannot live together. Curr. Biol. 16, R645–R647 (2006).
    Google Scholar 
    Ramfelt, O., Freel, K. C., Tucker, S. J., Nigro, O. D. & Rappé, M. S. Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria. ISME J. 18, wrae227 (2024).Tucker, S. J. et al. Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific. Limnol. Oceanogr. 70, 1693–1708 (2025).
    Google Scholar 
    Ramfelt, O., Tucker, S. J., Freel, K. C., Eren, A. M. & Rappe, M. S. Magnimaribacterales marine bacteria genetically partition across the nearshore to open-ocean in the tropical Pacific Ocean. Preprint at https://doi.org/10.1101/2025.06.17.660167 (2025).Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
    Google Scholar 
    Olm, M. R. et al. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 5, e00731–19 (2020).Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785–D794 (2022).
    Google Scholar 
    Waite, D. W. et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int. J. Syst. Evol. Microbiol. 70, 5972–6016 (2020).
    Google Scholar 
    Sanford, R. A., Lloyd, K. G., Konstantinidis, K. T. & Löffler, F. E. Microbial taxonomy run amok. Trends Microbiol. 29, 394–404 (2021).
    Google Scholar 
    Monaghan, E. A., Freel, K. C. & Rappé, M. S. Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater. mSystems 5, e00954–20 (2020).Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).
    Google Scholar 
    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
    Google Scholar 
    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
    Google Scholar 
    Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
    Google Scholar 
    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
    Google Scholar 
    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
    Google Scholar 
    Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).
    Google Scholar 
    Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).
    Google Scholar 
    Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
    Google Scholar 
    Milne, I. et al. Using tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193–202 (2013).
    Google Scholar 
    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
    Google Scholar 
    Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
    Google Scholar 
    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
    Google Scholar 
    Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
    Google Scholar 
    Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the Genomic Era. Mol. Biol. Evol. 37, 1530–1534 (2020).
    Google Scholar 
    Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
    Google Scholar 
    Revell, L. J. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12, e16505 (2024).
    Google Scholar 
    R Development Core Team, R. R: A Language and Environment for Statistical Computing https://doi.org/10.1007/978-3-540-74686-7 (2011).Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
    Google Scholar 
    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
    Google Scholar 
    Winter, K. B. et al. Collaborative Research To Inform Adaptive Comanagement: A Framework For The Heʻeia National Estuarine Research Reserve. Ecol. Soc. 25, 15 (2020).Kūlana Noiʻi Working Group. Kūlana Noiʻi version 2. [online] URL: https://seagrant.soest.hawaii.edu/wp-content/uploads/2021/09/Kulana-Noii-2.0_LowRes.pdf (Hawaiʻi Sea Grant, 2021).Sunagawa, S. et al. Ocean plankton. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
    Google Scholar 
    Mende, D. R. et al. Environmental drivers of a microbial genomic transition zone in the ocean’s interior. Nat. Microbiol. 2, 1367–1373 (2017).
    Google Scholar 
    Biller, S. J. et al. Marine microbial metagenomes sampled across space and time. Sci. Data 5, 180176 (2018).
    Google Scholar 
    Kudo, T. et al. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene 665, 174–184 (2018).
    Google Scholar 
    Yoshitake, K. et al. Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Sci. Rep. 11, 12222 (2021).
    Google Scholar 
    Mueller, R. S. et al. Metagenome sequencing of a coastal marine microbial community from Monterey Bay, California. Genome Announc. 3, e00341–15 (2015).Kopf, A. et al. The Ocean Sampling Day Consortium. Gigascience 4, 27 (2015).
    Google Scholar 
    Shaiber, A. et al. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol. 21, 292 (2020).
    Google Scholar 
    Köster, J. & Rahmann, S. Building and documenting workflows with Python-based snakemake. GCB 49, 56 (2012).
    Google Scholar 
    Eren, A. M., Vineis, J. H., Morrison, H. G. & Sogin, M. L. A filtering method to generate high-quality short reads using Illumina paired-end technology. PLoS ONE 8, e66643 (2013).
    Google Scholar 
    Utter, D. R. et al. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biol. 21, 293 (2020).
    Google Scholar 
    Community Ecology Package [R package vegan version 2.7-1]. Comprehensive R Archive Network (CRAN) https://cran.r-project.org/web/packages/vegan/index.html (2025).Delmont, T. O. & Eren, A. M. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ https://doi.org/10.7717/peerj.4320 (2018).Download referencesAcknowledgementsWe thank Kumu Hula, Kawaikapuokalani Hewett and Aimee Sato for their generous guidance in using appropriate ʻŌlelo Hawaiʻi (Hawaiian Language) words to create species names for isolates cultivated on Moku o Loʻe. We also thank K. Luttrell for help with Latin grammar, R. Malmstrom and N. Nath for sequencing the genomes of isolates HIMB109 and HIMB123, R. Ouye for assistance with HTC experiments, O. Ramfelt for bioinformatic support, and C. Foley for her generous help with creating the map used in Supplementary Fig. 1b. We also thank F. Trigodet for their help with the high-performance computing at the University of Oldenburg. Finally, we sincerely thank Luis Miguel Rodriquez-R, Marike Palmer, and the entire SeqCode team for their expert grammatical and taxonomic guidance. This research was supported by funding from the National Science Foundation grants OCE-1538628 (MSR), DEB-2224832 (MSR), and OCE-2149128 (MSR) as well as the Simons Postdoctoral Fellowship in Marine Microbial Ecology (LS-FMME-00989028) (SJT). This is HIMB publication 2025 and SOEST publication 12043.Author informationAuthors and AffiliationsHawai‘i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USAKelle C. Freel, Sarah J. Tucker, Evan B. Freel & Michael S. RappéMarine Biology Graduate Program, University of Hawaiʻi at Mānoa, Honolulu, HI, USASarah J. TuckerJosephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USASarah J. Tucker & A. Murat ErenHelmholtz Institute for Functional Marine Biodiversity, Oldenburg, GermanySarah J. Tucker & A. Murat ErenAlfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, GermanySarah J. Tucker & A. Murat ErenFort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USAUlrich StinglDepartment of Microbiology, Oregon State University, Corvallis, OR, USAStephen J. GiovannoniInstitute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, GermanyA. Murat ErenMax Planck Institute for Marine Microbiology, Bremen, GermanyA. Murat ErenAuthorsKelle C. FreelView author publicationsSearch author on:PubMed Google ScholarSarah J. TuckerView author publicationsSearch author on:PubMed Google ScholarEvan B. FreelView author publicationsSearch author on:PubMed Google ScholarUlrich StinglView author publicationsSearch author on:PubMed Google ScholarStephen J. GiovannoniView author publicationsSearch author on:PubMed Google ScholarA. Murat ErenView author publicationsSearch author on:PubMed Google ScholarMichael S. RappéView author publicationsSearch author on:PubMed Google ScholarContributionsK.C.F., S.J.T., A.M.E. and M.S.R. conceived the study, developed methodology and led the investigation and visualization for the study. A.M.E. and M.S.R. supervised the study. KCF wrote the original draft. K.C.F., S.J.T., E.B.F., U.S., S.J.G., A.M.E. and M.S.R. reviewed and edited the manuscript.Corresponding authorCorrespondence to
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    Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding

    AbstractAcid stress is a central environmental factor shaping the structure and function of microbial communities worldwide. However, there is a lack of predictive understanding of how microbial communities respond physiologically and metabolically to acid stress. Here, we find that higher acid stress favors slower-growing species, promoting population growth and coexistence. Our experiments show that acid stress influences the spatial structure of communities, wherein coexistence is ordered over centimeter-length scales and determined by growth-tolerance trade-offs. We find that interspecific interactions are highly dynamic during acid stress changes, with shifts from competition to cooperation, enhancing resilience under high-stress intensities. Slower-growing species may bolster interspecific coexistence through stress-dependent excretion and cross-feeding of public goods. We construct a resource-consumer-based mathematical model to unravel the processes experienced by species in stress-induced coexistence and their distinct physiological states. Finally, our pairwise bacterial-fungal interaction experiments elucidate universalities in stress-induced coexistence between closely related and phylogenetically distant species with complementary phenotypic profiles. Overall, our work provides insights into how acid stress affects physiological and metabolic responses, as well as overall fitness, resilience, and coexistence.

    Data availability

    All data that support the findings of this study are provided in the Supplementary Information, Source Data file, and databases. Raw mass spectral data is deposited to MassIVE and accessible with the accession code MSV000099939. Source data are provided with this paper, and can also be found at https://doi.org/10.5281/zenodo.1732030972. Source data are provided as a Source Data file. Source data are provided with this paper.
    Code availability

    Based on the mathematical model provided in the Supplementary Notes, the code can be found at https://zenodo.org/records/17330958.
    ReferencesThe Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).Montoya, J. M., Pimm, S. L. & Solé, R. V. Ecological networks and their fragility. Nature 442, 259–264 (2006).
    Google Scholar 
    Liu, W., Cremer, J., Li, D., Hwa, T. & Liu, C. An evolutionarily stable strategy to colonize spatially extended habitats. Nature 575, 664–668 (2019).
    Google Scholar 
    Camenzind, T., Philipp Grenz, K., Lehmann, J. & Rillig, M. C. Soil fungal mycelia have unexpectedly flexible stoichiometric C:N and C:P ratios. Ecol. Lett. 24, 208–218 (2021).
    Google Scholar 
    Jiang, Y., Dong, W., Xin, F. & Jiang, M. Designing synthetic microbial consortia for biofuel production. Trends Biotechnol. 38, 828–831 (2020).
    Google Scholar 
    Cheng, M., Chen, D., Parales, R. E. & Jiang, J. Oxygenases as powerful weapons in the microbial degradation of pesticides. Annu. Rev. Microbiol. 76, 325–348 (2022).
    Google Scholar 
    Blasche, S. et al. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nat. Microbiol. 6, 196–208 (2021).
    Google Scholar 
    Gopaulchan, D. et al. A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Nat. Microbiol. 10, 2130–2152 (2025).
    Google Scholar 
    Ruan, Z. et al. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat. Commun. 15, 4694 (2024).
    Google Scholar 
    Hu, S. et al. A synergistic consortium involved in rac-dichlorprop degradation as revealed by DNA stable isotope probing and metagenomic analysis. Appl. Environ. Microbiol. 87, e0156221 (2021).
    Google Scholar 
    Widdig, M. et al. Effects of nitrogen and phosphorus addition on microbial community composition and element cycling in a grassland soil. Soil. Biol. Biochem. 151, 108041 (2020).Xun, W. et al. Diversity-triggered deterministic bacterial assembly constrains community functions. Nat. Commun. 10, 3833 (2019).
    Google Scholar 
    Hutchins, D. A. & Fu, F. Microorganisms and ocean global change. Nat. Microbiol. 2, 17058 (2017).
    Google Scholar 
    Hu, N., Bourdeau, P. E. & Hollander, J. Responses of marine trophic levels to the combined effects of ocean acidification and warming. Nat. Commun. 15, 3400 (2024).
    Google Scholar 
    Lampe, R. H. et al. Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton. Nat. Commun. 14, 7215 (2023).
    Google Scholar 
    Bitter, M. C., Kapsenberg, L., Gattuso, J. P. & Pfister, C. A. Standing genetic variation fuels rapid adaptation to ocean acidification. Nat. Commun. 10, 5821 (2019).
    Google Scholar 
    Bokulich, N. A., Thorngate, J. H., Richardson, P. M. & Mills, D. A. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc. Natl. Acad. Sci. USA 111, E139–E148 (2014).
    Google Scholar 
    Rath, K. M., Fierer, N., Murphy, D. V. & Rousk, J. Linking bacterial community composition to soil salinity along environmental gradients. Isme J. 13, 836–846 (2019).
    Google Scholar 
    De Vos, W. M. et al. Phytate metabolism is mediated by microbial cross-feeding in the gut microbiota. Nat. Microbiol. 9, 1812–1827 (2024).
    Google Scholar 
    Ross, F. C. et al. The interplay between diet and the gut microbiome: implications for health and disease. Nat. Rev. Microbiol. 22, 671–686 (2024).Ghoul, M. & Mitri, S. The ecology and evolution of microbial competition. Trends Microbiol. 24, 833–845 (2016).
    Google Scholar 
    Tecon, R. et al. Bridging the holistic-reductionist divide in microbial ecology. mSystems 4, 10–1128 (2019).Zhao, Y. et al. Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation. Nat. Commun. 14, 5394 (2023).
    Google Scholar 
    Michielsen, S., Vercelli, G. T., Cordero, O. X. & Bachmann, H. Spatially structured microbial consortia and their role in food fermentations. Curr. Opin. Biotechnol. 87, 103102 (2024).
    Google Scholar 
    Luo, N. et al. The collapse of cooperation during range expansion of Pseudomonas aeruginosa. Nat. Microbiol. 9, 1220–1230 (2024).
    Google Scholar 
    Grandel, N. E., Reyes Gamas, K. & Bennett, M. R. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol. 29, 1095–1105 (2021).
    Google Scholar 
    Palmer, J. D. & Foster, K. R. Bacterial species rarely work together. Science 376, 581–582 (2022).
    Google Scholar 
    Piccardi, P., Vessman, B. & Mitri, S. Toxicity drives facilitation between 4 bacterial species. Proc. Natl. Acad. Sci. USA 116, 15979–15984 (2019).
    Google Scholar 
    García, F. C. et al. The temperature dependence of microbial community respiration is amplified by changes in species interactions. Nat. Microbiol. 8, 272–283 (2023).
    Google Scholar 
    Li, S. et al. Regulation of species metabolism in synthetic community systems by environmental pH oscillations. Nat. Commun. 14, 7507 (2023).
    Google Scholar 
    Gänzle, M. G. Lactic metabolism revisited: metabolism of lactic acid bacteria in food fermentations and food spoilage. Curr. Opin. Food Sci. 2, 106–117 (2015).
    Google Scholar 
    Wang, Y., Zhang, C., Liu, F., Jin, Z. & Xia, X. Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods. Crit. Rev. Food Sci. Nutr. 63, 5841–5855 (2022).Yanni, D., Márquez-Zacarías, P., Yunker, P. J. & Ratcliff, W. C. Drivers of spatial structure in social microbial communities. Curr. Biol. 29, R545–r550 (2019).
    Google Scholar 
    Chacón, J. M., Möbius, W. & Harcombe, W. R. The spatial and metabolic basis of colony size variation. Isme J. 12, 669–680 (2018).
    Google Scholar 
    Gude, S. et al. Bacterial coexistence driven by motility and spatial competition. Nature 578, 588–592 (2020).
    Google Scholar 
    Liao, H., Luo, Y., Huang, X. & Xia, X. Dynamics of quality attributes, flavor compounds, and microbial communities during multi-driven-levels chili fermentation: interactions between the metabolome and microbiome. Food Chem. 405, 134936 (2023).
    Google Scholar 
    Goldford, J. E. et al. Emergent simplicity in microbial community assembly. Science 361, 469–474 (2018).
    Google Scholar 
    Dal Bello, M., Lee, H., Goyal, A. & Gore, J. Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. Nat. Ecol. Evol. 5, 1424–1434 (2021).
    Google Scholar 
    Burkart, T., Willeke, J. & Frey, E. Periodic temporal environmental variations induce coexistence in resource competition models. Phys. Rev. E 108, 034404 (2023).
    Google Scholar 
    Ratzke, C. & Gore, J. Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol. 16, e2004248 (2018).
    Google Scholar 
    Herschend, J. et al. In vitro community synergy between bacterial soil isolates can be facilitated by pH Stabilization of the Environment. Appl. Environ. Microbiol. 84, e01450–18 (2018).Souza, A. L. & Patti, G. J. A protocol for untargeted metabolomic analysis: from sample preparation to data processing. Methods Mol. Biol. 2276, 357–382 (2021).
    Google Scholar 
    Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K. & Dorrestein, P. C. Mass spectrometry-based metabolomics in microbiome investigations. Nat. Rev. Microbiol. 20, 143–160 (2022).
    Google Scholar 
    Liu, Y., Tang, H., Lin, Z. & Xu, P. Mechanisms of acid tolerance in bacteria and prospects in biotechnology and bioremediation. Biotechnol. Adv. 33, 1484–1492 (2015).
    Google Scholar 
    Bennett, B. D. et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593–599 (2009).
    Google Scholar 
    Widder, S. et al. Challenges in microbial ecology: building predictive understanding of community function and dynamics. Isme J. 10, 2557–2568 (2016).
    Google Scholar 
    Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).
    Google Scholar 
    Martin-Gallausiaux, C., Marinelli, L., Blottière, H. M., Larraufie, P. & Lapaque, N. SCFA: mechanisms and functional importance in the gut. Proc. Nutr. Soc. 80, 37–49 (2021).
    Google Scholar 
    Ponomarova, O. et al. Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow. Cell Syst. 5, e346 (2017).
    Google Scholar 
    Daudé, D., Remaud-Siméon, M. & André, I. Sucrose analogs: an attractive (bio)source for glycodiversification. Nat. Prod. Rep. 29, 945–960 (2012).
    Google Scholar 
    Hernandez, D. J., David, A. S., Menges, E. S., Searcy, C. A. & Afkhami, M. E. Environmental stress destabilizes microbial networks. Isme J. 15, 1722–1734 (2021).
    Google Scholar 
    Gao, C. et al. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. Nat. Commun. 13, 3867 (2022).
    Google Scholar 
    Hofmann, G. E. et al. High-frequency dynamics of ocean pH: a multi-ecosystem comparison. PLoS One 6, e28983 (2011).
    Google Scholar 
    Hallatschek, O., Hersen, P., Ramanathan, S. & Nelson, D. R. Genetic drift at expanding frontiers promotes gene segregation. Proc. Natl. Acad. Sci. USA 104, 19926–19930 (2007).
    Google Scholar 
    Datta, M. S., Korolev, K. S., Cvijovic, I., Dudley, C. & Gore, J. Range expansion promotes cooperation in an experimental microbial metapopulation. Proc. Natl. Acad. Sci. USA 110, 7354–7359 (2013).
    Google Scholar 
    Dal Co, A., van Vliet, S., Kiviet, D. J., Schlegel, S. & Ackermann, M. Short-range interactions govern the dynamics and functions of microbial communities. Nat. Ecol. Evol. 4, 366–375 (2020).
    Google Scholar 
    Abreu, C. I., Dal Bello, M., Bunse, C., Pinhassi, J. & Gore, J. Warmer temperatures favor slower-growing bacteria in natural marine communities. Sci. Adv. 9, eade8352 (2023).
    Google Scholar 
    Frey, E. Evolutionary game theory: theoretical concepts and applications to microbial communities. Phys. A 389, 4265–4298 (2010).
    Google Scholar 
    West, S. A., Griffin, A. S. & Gardner, A. Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J. Evol. Biol. 20, 415–432 (2007).
    Google Scholar 
    Tripathi, B. M. et al. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. Isme J. 12, 1072–1083 (2018).
    Google Scholar 
    Di Martino, R., Picot, A. & Mitri, S. Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative. PLoS Biol. 22, e3002482 (2024).
    Google Scholar 
    Maestre, F. T., Callaway, R. M., Valladares, F. & Lortie, C. J. Refining the stress-gradient hypothesis for competition and facilitation in plant communities. J. Ecol. 97, 199–205 (2009).
    Google Scholar 
    Basan, M. et al. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature 528, 99–104 (2015).
    Google Scholar 
    Schink, S. J. et al. Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol. Syst. Biol. 18, e10704 (2022).
    Google Scholar 
    Kaleta, C., Schäuble, S., Rinas, U. & Schuster, S. Metabolic costs of amino acid and protein production in Escherichia coli. Biotechnol. J. 8, 1105–1114 (2013).
    Google Scholar 
    Guan, N. et al. Microbial response to environmental stresses: from fundamental mechanisms to practical applications. Appl. Microbiol. Biotechnol. 101, 3991–4008 (2017).
    Google Scholar 
    Russell, J. B. & Diez-Gonzalez, F. The effects of fermentation acids on bacterial growth. Adv. Micro. Physiol. 39, 205–234 (1998).
    Google Scholar 
    Iffland-Stettner, A. et al. A genome-scale metabolic model of marine heterotroph Vibrio splendidus strain 1A01. mSystems 8, e0037722 (2023).
    Google Scholar 
    Young, J. W. et al. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat. Protoc. 7, 80–88 (2011).
    Google Scholar 
    Skinner, S. O., Sepúlveda, L. A., Xu, H. & Golding, I. Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat. Protoc. 8, 1100–1113 (2013).
    Google Scholar 
    Ikeda, T. P., Shauger, A. E. & Kustu, S. Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J. Mol. Biol. 259, 589–607 (1996).
    Google Scholar 
    Liao, H. et al. Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding. Zenodo https://doi.org/10.5281/zenodo.17320309 (2025).Download referencesAcknowledgementsThis work was funded by a grant from the National Natural Science Foundation of China (31972064 (X.X.)), the Basic Research Program of Jiangsu (BK20252085 (X.X.), BK20251603 (H.L.)), and Jiangsu Funding Program for Excellent Postdoctoral Talent (2025ZB880 (H.L.)).Author informationAuthor notesThese authors contributed equally: Hui Liao, Liming Wu.Authors and AffiliationsThe Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangnan, ChinaHui Liao, Yi Luo, Hussain Asif, Xinlei Huang & Xiaole XiaCollege of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, ChinaLiming Wu & Xiaole XiaAuthorsHui LiaoView author publicationsSearch author on:PubMed Google ScholarLiming WuView author publicationsSearch author on:PubMed Google ScholarYi LuoView author publicationsSearch author on:PubMed Google ScholarHussain AsifView author publicationsSearch author on:PubMed Google ScholarXinlei HuangView author publicationsSearch author on:PubMed Google ScholarXiaole XiaView author publicationsSearch author on:PubMed Google ScholarContributionsH.L., L.W., Y.L., and X.H. performed the experiments. H.L. analyzed the experimental data. A.H. and X.X. carried out manuscript revisions. X.X. directed the study. H.L. and L.W. wrote the manuscript, and all authors read and approved the final manuscript.Corresponding authorCorrespondence to
    Xiaole Xia.Ethics declarations

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    The authors declare no competing interests.

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    Nature Communications thanks Wenping Cui, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

    Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary informationSupplementary InformationReporting SummaryTransparent Peer Review fileSource dataSource DataRights and permissions
    Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
    Reprints and permissionsAbout this articleCite this articleLiao, H., Wu, L., Luo, Y. et al. Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding.
    Nat Commun (2025). https://doi.org/10.1038/s41467-025-67395-zDownload citationReceived: 02 August 2024Accepted: 28 November 2025Published: 14 December 2025DOI: https://doi.org/10.1038/s41467-025-67395-zShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    Defensive responses of titan triggerfish to tiger sharks at a provisioned reef

    AbstractTitan triggerfish (Balistoides viridescens) are among the most territorial reef fishes, known for aggressively defending nests from intruders. In the Maldives’ Fuvahmulah atoll, where tiger sharks (Galeocerdo cuvier) aggregate in high numbers year-round, we opportunistically documented 10 interactions between these species from February to August 2024 during daily diving operations. Video footage from experienced divers was analyzed to identify and categorize aggressive behaviors, defined as bites (rapid, forceful closure of the jaws on the shark’s body) and chases (short pursuits following an aggressive display). All observed aggression was initiated by titan triggerfish, most often targeting the caudal fin of individual tiger sharks. Biting accounted for 70% of interactions, with chases comprising the remainder; over half of bites were immediately followed by a chase. Several interactions occurred near the new moon, coinciding with the species’ nesting period, suggesting that many of these interactions may have been linked to breeding-season territoriality; however, the opportunistic nature of the observations precluded any formal analysis of lunar phase patterns. These behaviors likely function as risk-based defense, exploiting anatomical vulnerabilities to deter much larger predators. The high frequency of these interactions in a location with artificially dense tiger shark populations suggests that provisioning and predator aggregation may increase the likelihood of such cross-trophic encounters. By linking detailed behavioral observations with the ecological context of predator aggregation, this study highlights the defensive capabilities of titan triggerfish and raises questions about how ecotourism-driven changes in predator distribution influence the behavior of non-target reef species.

    Data availability

    Data and data sets are available from the corresponding author upon reasonable request.
    ReferencesHiatt, R. W. & Strasburg, D. W. Ecological relationships of the fish fauna on coral reefs of the Marshall Islands. Ecol. Monogr. 30, 65–127 (1960).
    Google Scholar 
    Meyer, C. G., Papastamatiou, Y. P. & Holland, K. N. A multiple instrument approach to quantifying the movement patterns and habitat use of tiger (Galeocerdo cuvier) and Galápagos sharks (Carcharhinus galapagensis) at French frigate Shoals, Hawaii. Mar. Biol. 157, 1857–1868 (2010).
    Google Scholar 
    Tietbohl, M. D., Tricas, T. C. & Bernal, D. Intentional partial beaching in a coral reef fish: A newly recorded hunting behavior of Titan triggerfish, balistoides viridescens. J. Fish. Biol. 97, 566–570 (2020).
    Google Scholar 
    Lobel, P. S. & Johannes, R. E. Nesting behavior of triggerfishes (Balistidae): Description of nest, spawning, and parental care. Environ. Biol. Fishes. 5, 273–277 (1980).
    Google Scholar 
    Gladstone, W. Lek-like spawning, parental care and mating periodicity of the triggerfish Pseudobalistes flavimarginatus (Balistidae). Environ. Biol. Fish. 41, 385–398 (1994).
    Google Scholar 
    Vossgaetter, L. et al. Non-invasive methods characterise the world’s largest tiger shark aggregation in Fuvahmulah. Maldives Sci. Rep. 14, 21998 (2024).
    Google Scholar 
    Sulikowski, J. A. et al. Reproductive ecology of tiger sharks (Galeocerdo cuvier) in the central Indian ocean: Evidence for gestation at a provisioning site. Front. Mar. Sci. 11, 1500176 (2024).
    Google Scholar 
    Clua, E., Buray, N., Legendre, P., Mourier, J. & Planes, S. Behavioural response of sicklefin lemon sharks negaprion acutidens to underwater feeding for ecotourism purposes. Mar. Ecol. Prog Ser. 414, 257–266 (2010).
    Google Scholar 
    Lester, E. K., Langlois, T. J., Simpson, S. D., McCormick, M. I. & Meekan, M. G. Reef-wide evidence that the presence of sharks modifies behaviours of teleost mesopredators. Ecosphere 12, e03301 (2021).
    Google Scholar 
    Froese, R. & Pauly, D. (eds). FishBase. Balistoides viridescens (Lacepède, 1801). (2025). Available at: https://www.fishbase.se/summary/5046 Accessed 13.Jan, R. Q. & Ho, C. H. Feeding habits of the Titan triggerfish, balistoides viridescens, in Southern Taiwan. J. Mar. Sci. Technol. 16, 38–42 (2008).
    Google Scholar 
    Hemingson, C. R. & Bellwood, D. R. Patterns of predator vulnerability: A predator functional group framework for coral reef fishes. Oikos 130, 1425–1435 (2021).
    Google Scholar 
    Courter, J. R. & Ritchison, G. Mobbing calls increase stress-related behavior in raptors: Implications for anti-predator community dynamics. Behav. Ecol. 23, 302–308 (2012).
    Google Scholar 
    Consla, R. et al. Mobbing call efficacy across avian predators and habitat contexts. Ethology 118, 863–872 (2012).
    Google Scholar 
    Jelley, S. L. & Moreau, C. S. Nonlethal aggression as a community defense mechanism in ant societies. Proc. R. Soc. B 290, 20230236 (2023).Madin, E. M. P., Gaines, S. D., Madin, J. S. & Warner, R. R. Fishing indirectly structures macroalgal assemblages by altering herbivore behavior. Am. Nat. 176, 785–801 (2010).
    Google Scholar 
    Feary, D. A., Pratchett, M. S., Emslie, M. J. & Fowler, A. M. Predator invasion alters community structure in coral reef fish assemblages. Ecology 88, 2291–2300 (2007).
    Google Scholar 
    Ruppert, J. L. W., Stat, M., Forsman, Z. H. & Toonen, R. J. The conservation implications of predator aggregation at coral reefs. Conserv. Lett. 6, 294–302 (2013).
    Google Scholar 
    Download referencesAcknowledgementsWe want to extend our sincere gratitude to the individuals who contributed to this study by providing valuable video footage of interactions between titan triggerfish and tiger sharks. This study could not have been completed without the support of Fuvahmulah Dive School and Pelagic Divers Fuvahmulah, and the authors are grateful for their assistance. The authors extend special thanks to Mathieu Noé, Anoos, Sadhar Suresh, Nikita Kornilov, and Ahmed Ashhal Abdulla for capturing and sharing the essential videos that formed the foundation of this research. Their efforts were crucial in documenting the behavioral dynamics observed in this study. We also thank Luca Asshauer and Max Kimble for their assistance with the artistic figures included in this manuscript. Additionally, we thank Gonzalo Araujo for their insightful feedback during the analysis process. This research would not have been possible without the support and contributions of all those involved. The study was conducted following the guidelines and under the research permits issued by the Ministry of Fisheries, Marine Resources and Agriculture, Maldives (annually renewable permit: 30-D/PRIV/2021/190). The methods were non-invasive, ensuring no harm was caused to the animals involved.FundingThis research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.Author informationAuthor notesThese authors jointly supervised this work: Filippo Bocchi and Nathan Perisic.Authors and AffiliationsNature Friends of Maldives NGO, Fuvahmulah, MaldivesFilippo Bocchi & Ahmed InahFuvahmulah Dream NGO, Fuvahmulah, MaldivesNathan Perisic & Tatiana IvanovaAuthorsFilippo BocchiView author publicationsSearch author on:PubMed Google ScholarNathan PerisicView author publicationsSearch author on:PubMed Google ScholarAhmed InahView author publicationsSearch author on:PubMed Google ScholarTatiana IvanovaView author publicationsSearch author on:PubMed Google ScholarContributionsNathan Perisic and Filippo Bocchi were responsible for the analysis, manuscript writing, and review. Ahmed Inah and Tatiana Ivanova contributed to the study’s inception, preparation of the manuscript, and review.Corresponding authorCorrespondence to
    Nathan Perisic.Ethics declarations

    Competing interests
    The authors declare no competing interests.

    Additional informationPublisher’s noteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary InformationBelow is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2Supplementary Material 3Supplementary Material 4Supplementary Material 5Supplementary Material 6Supplementary Material 7Rights and permissions
    Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
    Reprints and permissionsAbout this articleCite this articleBocchi, F., Perisic, N., Inah, A. et al. Defensive responses of titan triggerfish to tiger sharks at a provisioned reef.
    Sci Rep (2025). https://doi.org/10.1038/s41598-025-31560-7Download citationReceived: 19 August 2025Accepted: 03 December 2025Published: 14 December 2025DOI: https://doi.org/10.1038/s41598-025-31560-7Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    KeywordsSpecies interactionIndian oceanSharksTropical ecologyTriggerfishSupplementary Material 1Supplementary Material 2Supplementary Material 3Supplementary Material 4Supplementary Material 5Supplementary Material 6Supplementary Material 7 More

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    Barrier impermeability is associated with migratory ungulate survival rates

    AbstractBarriers can affect the movement, migratory patterns, and demographic rates of ungulates. Even in highly remote areas with relatively little development, like northwest Alaska, isolated roads can alter the movements of ungulates such as caribou (Rangifer tarandus). Here, a solitary, 80-km long industrial road connecting a large zinc and lead mine to a port affects caribou migrations. Using location and survival data from 366 GPS collared, adult female caribou representing > 850 caribou-years from 2010 to 2023, we assessed whether caribou whose fall movements were altered by the road experienced higher mortality risk compared to those whose movements were unaltered. Of the 101 caribou-years that came within 20 km of the road, 58% displayed altered movements. The survival rate of caribou whose movements were unaltered by the road was 20% higher than those caribou whose movements were altered by it, though difference was not significant (p > 0.05). Increased movements, delayed migration, and/or changes in habitat selection related to altered movements could still have energetic and demographic consequences. Caribou that crossed or circumvented the road had significantly higher survival rates (78.5% survived until calving) than caribou that did not cross or circumvent the road (i.e., it acted as an impermeable barrier and the caribou wintered north of it; 57.9%). Given our results, we posit that enhancing the permeability of roads could improve the survival of caribou in the region.

    Data availability

    Survival data used for this analysis will be made available in the NPS’ publicly-accessible database (IRMA; https://irma.nps.gov) upon manuscript acceptance.
    ReferencesFryxell, J. M. & Sinclair, A. R. E. Causes and consequences of migration by large herbivores. Trends Ecol. Evol. 3, 237–241 (1988).
    Google Scholar 
    Avgar, T., Street, G. & Fryxell, J. M. On the adaptive benefits of mammal migration. Can. J. Zool. 92, 481–490. https://doi.org/10.1139/cjz-2013-0076 (2014).
    Google Scholar 
    Mariani, P., Krivan, V., MacKenzie, B. R. & Mullon, C. The migration game in habitat network: the case of tuna. Theoretical Ecol. 9, 219–232 (2016).
    Google Scholar 
    Van Moorter, B. et al. Consequences of barriers and changing seasonality on population dynamics and harvest of migratory ungulates. Theoretical Ecol. 13, 595–605. https://doi.org/10.1007/s12080-020-00471-w (2020).
    Google Scholar 
    Berger, J. The last mile: how to sustain long-distance migration in mammals. Conserv. Biol. 18, 320–331 (2004).
    Google Scholar 
    Wilcove, D. S., Wikelski, M. & Going, going, gone: is animal migration disappearing? PLoS Biol. 6, 1361–1364 (2008).
    Google Scholar 
    Harris, G., Thirgood, S., Hopcraft, J. G. C., Cromsigt, J. P. G. M. & Berger, J. Global decline in aggregated migrations of large terrestrial mammals. Endanger. Species Res. 7, 55–76 (2009).
    Google Scholar 
    Ito, T. Y. et al. Fragmentation of the habitat of wild ungulates by anthropogenic barriers in Mongolia. PLoS ONE. 8, e56995. https://doi.org/10.1371/journal.pone.0056995 (2013).
    Google Scholar 
    Kauffman, M. J. et al. Mapping out a future for ungulate migrations. Science 372, 566–569. https://doi.org/10.1126/science.abf0998 (2021).
    Google Scholar 
    Klein, D. R. Reaction of reindeer to obstructions and disturbances: experience in Scandinavia May aid in anticipating problems with caribou in Canada and Alaska. Science 173, 393–398 (1971).
    Google Scholar 
    Sawyer, H. et al. A framework for Understanding semi-permeable barrier effects on migratory ungulates. J. Appl. Ecol. 50, 68–78 (2013).
    Google Scholar 
    Beyer, H. L. et al. You shall not pass!’: quantifying barrier permeability and proximity avoidance by animals. J. Anim. Ecol. 85, 43–53 (2016).
    Google Scholar 
    Xu, W., Gigliotti, L. C., Royauté, R., Sawyer, H. & Middleton, A. D. Fencing amplifies individual differences in movement with implications on survival for two migratory ungulates. J. Anim. Ecol. 92, 677–689. https://doi.org/10.1111/1365-2656.13879 (2023).
    Google Scholar 
    Harrington, J. L. & Conover, M. R. Characteristics of ungulate behavior and mortality associated with wire fences. Wildl. Soc. Bull. 34, 1295–1305 (2006).
    Google Scholar 
    Rey, A., Novaro, A. J. & Guichón, M. L. Guanaco (Lama guanicoe) mortality by entanglement in wire fences. J. Nat. Conserv. 20, 280–283 (2012).
    Google Scholar 
    Wilson, R. R., Parrett, L. S., Joly, K. & Dau. J. R Effects of roads on individual caribou movements during migration. Biol. Conserv. 195, 2–8. https://doi.org/10.1016/j.biocon.2015.12.035 (2016).
    Google Scholar 
    Boulanger, J. et al. Estimating the effects of roads on migration: a barren-ground caribou case study. Can. J. Zool. 102, 476–493. https://doi.org/10.1139/cjz-2023-0121 (2024).
    Google Scholar 
    Eacker, D. R., Jakes, A. F. & Jones, P. F. Spatiotemporal risk factors predict landscape-scale survivorship for a Northern ungulate. Ecosphere 14, e4341. https://doi.org/10.1002/ecs2.4341 (2023).
    Google Scholar 
    Severson, J. P., Vosburgh, T. C. & Johnson, H. E. Effects of vehicle traffic on space use and road crossings of caribou in the Arctic. Ecol. Appl. 33, e2923. https://doi.org/10.1002/eap.2923 (2023).
    Google Scholar 
    Bråthen, K. A. et al. Induced shift in ecosystem productivity? Extensive scale effects of abundant large herbivores. Ecosystems 10, 773–789 (2007).
    Google Scholar 
    Bernes, C., Bråthen, K. A., Forbes, B. C., Speed, J. D. M. & Moen, J. What are the impacts of reindeer/caribou (Rangifer Tarandus L.) on Arctic and alpine vegetation? A systematic review. Environ. Evid. 4, 4. https://doi.org/10.1186/s13750-014-0030-3 (2015).
    Google Scholar 
    Joly, K. et al. Longest terrestrial migrations and movements around the world. Sci. Rep. 9, 1–10. https://doi.org/10.1038/s41598-019-51884-5 (2019). Article 15333.
    Google Scholar 
    Cameron, M. D., Eisaguirre, J. M., Breed, G. A., Joly, K. & Kielland, K. Mechanistic movement models identify continuously updated autumn migration cues in Arctic caribou. Mov. Ecol. 9, 54. https://doi.org/10.1186/s40462-021-00288-0 (2021).
    Google Scholar 
    Joly, K. & Cameron, M. D. Early fall and late winter diets of migratory caribou in Northwest Alaska. Rangifer 38, 27–38. https://doi.org/10.7557/2.38.1.4107 (2018).
    Google Scholar 
    Webber, Q. M. R., Ferraro, K. M., Hendrix, J. G. & Vander Wal, E. What do caribou eat? A review of the literature on caribou diet. Can. J. Zool. 100, 197–207. https://doi.org/10.1139/cjz-2021-0162 (2022).
    Google Scholar 
    Joly, K., Cameron, M. D. & White, R. G. Behavioral adaptation to seasonal resource scarcity by caribou (Rangifer tarandus) and its role in partial migration. J. Mammal. 106, 96–104. https://doi.org/10.1093/jmammal/gyae100 (2025).
    Google Scholar 
    Gordon, B. C. 8000 years of caribou and human seasonal migration in the Canadian barrenlands. Rangifer Special Issue. 16, 155–162 (2005).
    Google Scholar 
    Borish, D. et al. Relationships between Rangifer and Indigenous well-being in the North American Arctic and subarctic: a review based on the academic published literature. Arctic 75, 86–104 (2022).
    Google Scholar 
    Watson, J. E. M. et al. Catastrophic declines in wilderness areas undermine global environment targets. Curr. Biol. 26, 2929–2934 (2016).
    Google Scholar 
    Bartsch, A. et al. Expanding infrastructure and growing anthropogenic impacts along Arctic Coasts. Environ. Res. Lett. 16, 115013. https://doi.org/10.1088/1748-9326/ac3176 (2021).
    Google Scholar 
    Panzacchi, M. et al. Predicting the continuum between corridors and barriers to animal movements using step selection functions and randomized shortest paths. J. Anim. Ecol. 85, 32–42. https://doi.org/10.1111/1365-2656.12386 (2016).
    Google Scholar 
    Smith, A. & Johnson, C. J. Why didn’t the caribou (Rangifer Tarandus groenlandicus) cross the winter road? The effect of industrial traffic on the road-crossing decisions of caribou. Biodivers. Conserv. 32, 2943–2959. https://doi.org/10.1007/s10531-023-02637-4 (2023).
    Google Scholar 
    Joly, K. & Cameron, M. D. Caribou vital sign annual report for the Arctic Network Inventory and Monitoring Program. Sci. Rep. https://doi.org/10.36967/2306687 (2024).
    Google Scholar 
    Joly, K. et al. Caribou and reindeer migrations in the changing Arctic. Anim. Migrations. 8, 156–167. https://doi.org/10.1515/ami-2020-0110 (2021).
    Google Scholar 
    Graham, M. Feds approve key step towards expansion at major Northwest Alaska zinc mine. Northern J. https://www.adn.com/business-economy/2024/12/14/feds-approve-key-step-toward-expansion-at-major-northwest-alaska-zinc-mine/ (2024).Dau, J. Western Arctic herd. In Caribou Management Report of Survey and Inventory activities, 1 July 2000–30 June 2002. Study 3.0 (ed. Healy, C.) 204–251 (Alaska Department of Fish and Game, 2003).
    Google Scholar 
    Gunn, A. Voles, lemmings and caribou-population cycles revisited? Rangifer Special Issue. 14, 105–111 (2003).
    Google Scholar 
    Joly, K., Klein, D. R., Verbyla, D. L., Rupp, T. S. & Chapin, F. S. III Linkages between large-scale climate patterns and the dynamics of Alaska caribou populations. Ecography 34, 345–352. https://doi.org/10.1111/j.1600-0587.2010.06377.x (2011).
    Google Scholar 
    Teck Resources Limited. Red Dog. https://www.teck.com/operations/united-states/operations/red-dog/ (2024).Macander, M. J., Swingley, C. S., Joly, K. & Raynolds, M. Landsat-based snow persistence map for Northwest Alaska. Remote Sens. Environ. 163, 23–31. https://doi.org/10.1016/j.rse.2015.02.028 (2015).
    Google Scholar 
    Swanson, D. K. Trends in greenness and snow cover in alaska’s Arctic National Parks, 2000–2016. Remote Sens. 9, 514. https://doi.org/10.3390/rs9060514 (2017).
    Google Scholar 
    Joly, K., Gurarie, E., Hansen, D. A., Cameron, M. D. & M D Seasonal patterns of Spatial fidelity and Temporal consistency in the distribution and movements of a migratory ungulate. Ecol. Evol. 11, 8183–8200. https://doi.org/10.1002/ece3.7650 (2021).
    Google Scholar 
    Prichard, A. K. et al. Achieving a representative sample of marked animals: a Spatial approach to evaluating post-capture randomization. Wildl. Soc. Bull. 47 (1), e1398. https://doi.org/10.1002/wsb.1398 (2023).
    Google Scholar 
    Fullman, T. J., Gustine, J. K., Cameron, M. D. & D. D. & Behavioral responses of migratory caribou to semi-permeable roads in Arctic Alaska. Sci. Rep. 15, 24712. https://doi.org/10.1038/s41598-025-10216-6 (2025).
    Google Scholar 
    Xu, W., Dejid, N., Herrmann, V., Sawyer, H. & Middleton, A. D. Barrier behaviour analysis (BaBA) reveals extensive effects of fencing on wide-ranging ungulates. J. Appl. Ecol. 58, 690–698 (2021).
    Google Scholar 
    Therneau, T. M. & Grambsch, P. M. Modeling Survival Data: Extending the Cox Model. (Springer, 2000).Therneau, T. M. A package for survival analysis in R. Manual. https://CRAN. R-project.org/package = survival (2022).R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2024).Cameron, M. D., Joly, K., Breed, G. A., Parrett, L. S. & Kielland, K. Movement-based methods to infer parturition events in migratory ungulates. Can. J. Zool. 96, 1187–1195. https://doi.org/10.1139/cjz-2017-0314 (2018).
    Google Scholar 
    Kelsall, J. P. The Migratory Barren-Ground Caribou Of Canada. 339 (Queen’s Printer, 1968).Bergerud, A. T. Rutting behaviour of Newfoundland caribou. In The Behaviour Of Ungulates And Its Relation To Management. V. Geist and F. Walther, editors. International Union for Conservation of Nature and Natural Resources. 395–435 (1974).Whitten, K. R., Garner, G. W., Mauer, F. J. & Harris, R. B. Productivity and early calf survival in the Porcupine caribou herd. J. Wildl. Manage. 56, 201–212 (1992).
    Google Scholar 
    Gurarie, E. et al. Evidence for an adaptive, large-scale range shift in a long-distance terrestrial migrant. Glob. Change Biol. 30, e17589. https://doi.org/10.1111/gcb.17589 (2024).
    Google Scholar 
    Miller, F. L., Jonkel, C. J. & Tessier, G. D. Group cohesion and leadership response by barren-ground caribou to man-made barriers. Arctic 25, 193–202 (1972). https://www.jstor.org/stable/40508046
    Google Scholar 
    Bart, J., Fligner, M. A. & Notz, W. I. Sampling and Statistical Methods for Behavioral Ecologists. 330 (Cambridge University Press, 1998).Fancy, S. G. & White, R. G. Energy expenditures for locomotion by barren-ground caribou. Can. J. Zool. 65, 122–128. https://doi.org/10.1139/z87-018 (1987).
    Google Scholar 
    Parker, K. L., Barboza, P. S. & Gillingham, M. P. Nutrition integrates environmental responses of ungulates. Funct. Ecol. 23, 57–69. https://doi.org/10.1111/j.1365-2435.2009.01528.x (2009).
    Google Scholar 
    Wasser, S. K., Keim, J. L., Taper, M. L. & Lele, S. R. The influences of Wolf predation, habitat loss, and human activity on caribou and moose in the Alberta oil sands. Front. Ecol. Environ. 9, 546–551. https://doi.org/10.1890/100071 (2011).
    Google Scholar 
    Cameron, R. D. & Ver Hoef, J. M. Predicting parturition rate of caribou from autumn body mass. J. Wildl. Manage. 58, 674–679 (1994).
    Google Scholar 
    Gerhart, K. L., Russell, D. E., Van DeWetering, D., White, R. G. & Cameron, R. D. Pregnancy of adult caribou (Rangifer tarandus): evidence for lactational infertility. J. Zool. 242, 17–30 (1997).
    Google Scholar 
    Johnson, C. J., Venter, O., Ray, J. C. & Watson, J. E. M. Growth-inducing infrastructure represents transformative yet ignored keystone environmental decisions. Conserv. Lett. 13, e12696. https://doi.org/10.1111/conl.12696 (2020).
    Google Scholar 
    Download referencesAcknowledgementsWe thank A. Hansen (Alaska Department of Fish and Game) for his ongoing collaboration that makes our long-term monitoring program possible. We also thank the many people that have helped deploy GPS collars over the years. Funding for this project was provided by the National Park Service, the Alaska Department of Fish and Game, and NSF Navigating the New Arctic grant 212727 (Fate of the Caribou). We thank H. Johnson, A. Hansen, S. Karpovich, and N. Edmison for reviews of a previous draft of this manuscript.Author informationAuthors and AffiliationsArctic Inventory and Monitoring Program, National Park Service, Gates of the Arctic National Park and Preserve, Fairbanks, AK, USAKyle Joly & Matthew D. CameronCollege of Environmental Science and Forestry, State University of New York, Syracuse, NY, USAChloe Beaupré, Nicole Barbour & Eliezer GurarieThe Wilderness Society, Anchorage, AK, USATimothy J. FullmanAuthorsKyle JolyView author publicationsSearch author on:PubMed Google ScholarChloe BeaupréView author publicationsSearch author on:PubMed Google ScholarTimothy J. FullmanView author publicationsSearch author on:PubMed Google ScholarMatthew D. CameronView author publicationsSearch author on:PubMed Google ScholarNicole BarbourView author publicationsSearch author on:PubMed Google ScholarEliezer GurarieView author publicationsSearch author on:PubMed Google ScholarContributionsData acquisition: KJ and MDC. Data management: KJ, MDC, and CB. Conceptualization and data interpretation: all authors. Data Analysis: CB, EG, TJF, KJ, and MDC. Original draft: KJ. Manuscript review, revision, and submission approval: all authors.Corresponding authorCorrespondence to
    Eliezer Gurarie.Ethics declarations

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    Reprints and permissionsAbout this articleCite this articleJoly, K., Beaupré, C., Fullman, T.J. et al. Barrier impermeability is associated with migratory ungulate survival rates.
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    KeywordsAlaskaCaribouMortality riskPermeabilityRangifer tarandusRoads More