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    Insight into impact of sewage discharge on microbial dynamics and pathogenicity in river ecosystem

    Zhang, Y., Wu, J. & Xu, B. Human health risk assessment of groundwater nitrogen pollution in Jinghui canal irrigation area of the loess region, northwest China. Environ. Earth Sci. 77, 273 (2018).Article 
    CAS 

    Google Scholar 
    Zhang, D. et al. Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital. Sci. Total Environ. 741, 140445 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ahmed, W. et al. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community. Sci. Total Environ. 728, 138764 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Haramoto, E., Malla, B., Thakali, O. & Kitajima, M. First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan. Sci. Total Environ. 737, 140405 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Naddeo, V. & Liu, H. Editorial Perspectives: 2019 novel coronavirus (SARS-CoV-2): What is its fate in urban water cycle and how can the water research community respond?. Environ. Sci. Water Res. Technol. 6, 1213–1216 (2020).CAS 
    Article 

    Google Scholar 
    Cornelisen, C. D., Gillespie, P. A., Kirs, M., Young, R. G. & Harwood, V. J. Motueka River plume facilitates transport of ruminant faecal contaminants into shellfish growing waters, Tasman Bay, New Zealand. N. Z. J. Mar. Freshw. Res. 45, 477–495 (2011).Article 

    Google Scholar 
    Devane, M. L., Moriarty, E. M., Wood, D., Webster-Brown, J. & Gilpin, B. J. The impact of major earthquakes and subsequent sewage discharges on the microbial quality of water and sediments in an urban river. Sci. Total Environ. 485–486, 666–680 (2014).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Duttagupta, S. et al. Achieving sustainable development goal for clean water in India: Influence of natural and anthropogenic factors on groundwater microbial pollution. Environ. Manag. 66, 42–755 (2020).Article 

    Google Scholar 
    Huelsen, T. et al. Domestic wastewater treatment with purple phototrophic bacteria using a novel continuous photo anaerobic membrane bioreactor. Water Res. 100, 486–495 (2016).Article 
    CAS 

    Google Scholar 
    Johnson, D. R. et al. The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability. Environ. Microbiol. 17(12), 4851–4860 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lei, Z. J. M. Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China. Soil Biol. Biochem. 44(1), 31–38 (2012).Article 
    CAS 

    Google Scholar 
    Jian, L. Effects of nitrogen and phosphorus addition on soil microbial community in a secondary tropical forest of China. Biol. Fertil. Soils 51, 207–215 (2015).Article 
    CAS 

    Google Scholar 
    Yu, S. X., Pang, Y. L., Wang, Y. C., Li, J. L. & Qin, S. Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay. Mar. Pollut. Bull. 76, 1048–1056 (2017).
    Google Scholar 
    Reidl, J. & Klose, K. E. Vibrio cholerae and cholera: Out of the water and into the host. FEMS Microbiol. Rev. 26(2), 125–139 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chin, C.-S. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364, 33–42 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Minoru, K., Miho, F., Mao, T., Yoko, S. & Kanae, M. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucl. Acids Res. 45, D353–D361 (2017).Article 
    CAS 

    Google Scholar 
    Zieliński, W. et al. The prevalence of drug-resistant and virulent Staphylococcus spp. in a municipal wastewater treatment plant and their spread in the environment. Environ. Int. 143, 105914 (2020).PubMed 
    Article 
    CAS 

    Google Scholar 
    Dietrich, J. E. S. & Doherty, T. M. Interaction of Mycobacterium tuberculosis with the host: Consequences for vaccine development. APMIS 117, 440–457 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Velayati, A. A. et al. Identification and genotyping of Mycobacterium tuberculosis isolated from water and soil samples of a metropolitan city. Chest 147, 1094–1102 (2015).PubMed 
    Article 

    Google Scholar 
    Pereira, M. I. & Medeiros, J. A. Role of Helicobacter pylori in gastric mucosa-associated lymphoid tissue lymphomas. World J. Gastroenterol. 20, 684–698 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    West, A. P., Millar, M. R. & Tompkins, D. S. Effect of physical environment on survival of Helicobacter pylori. J. Clin. Pathol. 45, 228–231 (1992).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Miller, W. A. et al. Salmonella spp., Vibrio spp., Clostridium perfringens, and Plesiomonas shigelloides in marine and freshwater invertebrates from coastal California ecosystems. Microb. Ecol. 52, 198–206 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    McCarthy, S. A. Effects of temperature and salinity on survival of toxigenic Vibrio cholerae O1 in seawater. Microb Ecol 31, 167–175 (1996).CAS 
    PubMed 
    Article 

    Google Scholar 
    Heaney, N. et al. Effects of softwood biochar on the status of nitrogen species and elements of potential toxicity in soils. Ecotoxicol. Environ. Saf. 166, 383–389 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wang, Z. B., Miao, M. S., Kong, Q. & Ni, S. Q. Evaluation of microbial diversity of activated sludge in a municipal wastewater treatment plant of northern China by high-throughput sequencing technology. Desalin. Water Treat. 57, 1–6 (2016).Article 
    CAS 

    Google Scholar 
    Wang, Z. et al. Weak magnetic field: A powerful strategy to enhance partial nitrification. Water Res. 120, 190–198 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, X. et al. Reduction of nitrous oxide emissions from partial nitrification process by using innovative carbon source (mannitol). Bioresour. Technol. 218, 789–795 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Liu, X. et al. N2O emission and bacterial community dynamics during realization of the partial nitrification process. RSC Adv. 8, 24305–24311 (2018).ADS 
    CAS 
    Article 

    Google Scholar 
    Lv, L., Ren, L. F., Ni, S. Q., Gao, B. Y. & Wang, Y. N. The effect of magnetite on the start-up and N2O emission reduction of the anammox process. RSC Adv. 6, 99989–99996 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Yang, S., Liebner, S., Alawi, M., Ebenhöh, O. & Wagner, D. Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR. J. Microbiol. Methods 103, 3–5 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Xu, F. et al. Electricity production and evolution of microbial community in the constructed wetland-microbial fuel cell. Chem. Eng. J. 339, 479–486 (2018).CAS 
    Article 

    Google Scholar 
    Bu, C. et al. Dissimilatory nitrate reduction to ammonium in the yellow river estuary: Rates, abundance, and community diversity. Sci. Rep. 7, 6830 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Zhou, J., Fries, M. R., Cheesanford, J. C. & Tiedje, J. M. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov.. Int. J. Syst. Bacteriol. 194, 500–506 (1995).Article 

    Google Scholar 
    Casanova, L., Rutala, W. A., Weber, D. J. & Sobsey, M. D. Survival of surrogate coronaviruses in water. Water Res. 43, 1893–1898 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Elreedy, A. et al. Unraveling the capability of graphene nanosheets and γ-Fe2O3 nanoparticles to stimulate anammox granular sludge. J. Environ. Manag. 277, 111495 (2021).CAS 
    Article 

    Google Scholar 
    Ismail, S. et al. Response of anammox bacteria to short-term exposure of 1,4-dioxane: Bacterial activity and community dynamics. Sep. Purif. Technol. 266, 118539 (2021).CAS 
    Article 

    Google Scholar 
    Shen, X., Xu, M., Li, M., Zhao, Y. & Shao, X. Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons. Sci. Total Environ. 717, 137180 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Ismail, S. et al. Fatigue of anammox consortia under long-term 1,4-dioxane exposure and recovery potential: N-kinetics and microbial dynamics. J. Hazard. Mater. 414, 125533 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Li, H. F., Li, B. Z., Wang, E. T., Yang, J. S. & Yuan, H. L. Removal of low concentration of phosphorus from solution by free and immobilized cells of Pseudomonas stutzeri YG-24. Desalination 286, 242–247 (2012).CAS 
    Article 

    Google Scholar 
    Xia, J., Ye, L., Ren, H. & Zhang, X. X. Microbial community structure and function in aerobic granular sludge. Appl. Microbiol. Biotechnol. 102(9), 3967–3979 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Akizuki, S. et al. Effects of substrate COD/NO2-N ratio on simultaneous methanogenesis and short-cut denitrification in the treatment of blue mussel using acclimated sludge. Biochem. Eng. J. 99, 16–23 (2015).CAS 
    Article 

    Google Scholar 
    Liao, K. et al. Use of convertible flow cells to simulate the impacts of anthropogenic activities on river biofilm bacterial communities. Sci. Total Environ. 653, 148–156 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Marassi, R. J. et al. Performance and toxicity assessment of an up-flow tubular microbial fuel cell during long-term operation with high-strength dairy wastewater. J. Clean. Prod. 259, 120882 (2020).CAS 
    Article 

    Google Scholar 
    Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Medema, G. J., Schets, F. M., Teunis, P. F. M. & Havelaar, A. H. Sedimentation of free and attached Cryptosporidium oocysts and Giardia cysts in water. Appl. Environ. Microbiol. 64, 4460–4466 (1998).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Igbinosa, E. O., Obi, L. C. & Okoh, A. I. Occurrence of potentially pathogenic vibrios in final effluents of a wastewater treatment facility in a rural community of the Eastern Cape Province of South Africa. Res. Microbiol. 160, 531–537 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Goh, S. G., Bayen, S., Burger, D., Kelly, B. C. & Gin, Y. H. Occurrence and distribution of bacteria indicators, chemical tracers and pathogenic vibrios in Singapore coastal waters. Mar. Pollut. Bull. 114, 627–634 (2016).PubMed 
    Article 
    CAS 

    Google Scholar 
    Cui, Q., Huang, Y., Wang, H. & Fang, T. Diversity and abundance of bacterial pathogens in urban rivers impacted by domestic sewage. Environ. Pollut. 249, 24–35 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Suzuki, Y. et al. Growth and antibiotic resistance acquisition of Escherichia coli in a river that receives treated sewage effluent. Sci. Total Environ. 690, 696–704 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Silva, D. C. V. R. et al. Predicting zebrafish spatial avoidance triggered by discharges of dairy wastewater: An experimental approach based on self-purification in a model river. Environ. Pollut. 266, 115325 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wagner, I. & Zalewski, M. Temporal changes in the abiotic/biotic drivers of selfpurification in a temperate river. Ecol. Eng. 94, 275–285 (2016).Article 

    Google Scholar 
    Clements, W. H. & Rohr, J. R. Community responses to contaminants: Using basic ecological principles to predict ecotoxicological effects. Environ. Toxicol. Chem. 28, 1789–1800 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ismail, S. & Tawfik, A. Comprehensive study for Anammox process via multistage anaerobic baffled reactors. E3S Web Conf. 22, 4–11 (2017).Article 
    CAS 

    Google Scholar  More

  • in

    Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic

    Szulkin, M. et al. How to quantify urbanization when testing for urban evolution?. Urban Evol. Biol. https://doi.org/10.1093/oso/9780198836841.003.0002 (2020).Article 

    Google Scholar 
    Slabbekoorn, H. Songs of the city: Noise-dependent spectral plasticity in the acoustic phenotype of urban birds. Anim. Behav. https://doi.org/10.1016/j.anbehav.2013.01.021 (2013).Article 

    Google Scholar 
    Christiansen, N. A., Fryirs, K. A., Green, T. J. & Hose, G. C. The impact of urbanisation on community structure, gene abundance and transcription rates of microbes in upland swamps of Eastern Australia. PLoS ONE https://doi.org/10.1371/journal.pone.0213275 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Alberti, M. et al. Global urban signatures of phenotypic change in animal and plant populations. Proc. Natl. Acad. Sci. USA https://doi.org/10.1073/pnas.1606034114 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    McFall-Ngai, M. M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. https://doi.org/10.1073/pnas.1218525110 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. https://doi.org/10.1111/j.1574-6976.2008.00123.x (2008).Article 
    PubMed 

    Google Scholar 
    Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2018.2448 (2019).Article 

    Google Scholar 
    Jarrett, C., Powell, L. L., McDevitt, H., Helm, B. & Welch, A. J. Bitter fruits of hard labour: diet metabarcoding and telemetry reveal that urban songbirds travel further for lower-quality food. Oecologia https://doi.org/10.1007/s00442-020-04678-w (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zollinger, S. A. et al. Traffic noise exposure depresses plasma corticosterone and delays offspring growth in breeding zebra finches. Conserv. Physiol. https://doi.org/10.1093/conphys/coz056 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sprau, P., Mouchet, A. & Dingemanse, N. J. Multidimensional environmental predictors of variation in avian forest and city life histories. Behav. Ecol. https://doi.org/10.1093/beheco/arw130 (2017).Article 

    Google Scholar 
    Teyssier, A. et al. Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2017.09.035 (2018).Article 
    PubMed 

    Google Scholar 
    Murray, M. H. et al. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS ONE https://doi.org/10.1371/journal.pone.0220926 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fuirst, M., Veit, R. R., Hahn, M., Dheilly, N. & Thorne, L. H. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS ONE https://doi.org/10.1371/journal.pone.0209200 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Phillips, J. N., Berlow, M. & Derryberry, E. P. The effects of landscape urbanization on the gut microbiome: An exploration into the gut of urban and rural white-crowned sparrows. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2018.00148 (2018).Article 

    Google Scholar 
    Berlow, M., Phillips, J. N. & Derryberry, E. P. Effects of urbanization and landscape on gut microbiomes in white-crowned sparrows. Microb. Ecol. https://doi.org/10.1007/s00248-020-01569-8 (2020).Article 
    PubMed 

    Google Scholar 
    Cox, L. M. et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell https://doi.org/10.1016/j.cell.2014.05.052 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Knutie, S. A., Wilkinson, C. L., Kohl, K. D. & Rohr, J. R. Early-life disruption of amphibian microbiota decreases later-life resistance to parasites. Nat. Commun. 8, 1–8 (2017).CAS 
    Article 

    Google Scholar 
    Sudyka, J., Di Lecce, I., Wojas, L., Rowiński, P. & Szulkin, M. Nest-boxes alter the reproductive ecology of urban cavity-nesters in a species-dependent way. https://doi.org/10.32942/OSF.IO/WP9MN.
    Maziarz, M., Broughton, R. K. & Wesołowski, T. Microclimate in tree cavities and nest-boxes: Implications for hole-nesting birds. For. Ecol. Manag. https://doi.org/10.1016/j.foreco.2017.01.001 (2017).Article 

    Google Scholar 
    Thompson, M. J., Capilla-Lasheras, P., Dominoni, D. M., Réale, D. & Charmantier, A. Phenotypic variation in urban environments: mechanisms and implications. Trends Ecol. Evol. 37, 171–182 (2022).CAS 
    Article 

    Google Scholar 
    Salmón, P. et al. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat. Commun. 12, 1–14 (2021).ADS 
    Article 

    Google Scholar 
    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. https://doi.org/10.1186/s13059-014-0550-8 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sackey, B. A., Mensah, P., Collison, E. & Sakyi-Dawson, E. Campylobacter, Salmonella, Shigella and Escherichia coli in live and dressed poultry from metropolitan Accra. Int. J. Food Microbiol. https://doi.org/10.1016/S0168-1605(01)00595-5 (2001).Article 
    PubMed 

    Google Scholar 
    Benskin, C. M. W. H., Wilson, K., Jones, K. & Hartley, I. R. Bacterial pathogens in wild birds: A review of the frequency and effects of infection. Biol. Rev. https://doi.org/10.1111/j.1469-185X.2008.00076.x (2009).Article 
    PubMed 

    Google Scholar 
    Hansell, M. & Overhill, R. Bird nests and construction behaviour. Bird Nests Constr. Behav. https://doi.org/10.1017/cbo9781139106788 (2000).Article 

    Google Scholar 
    Siddiqui, S. H., Khan, M., Kang, D., Choi, H. W. & Shim, K. Meta-analysis and systematic review of the thermal stress response: Gallus gallus domesticus show low immune responses during heat stress. Front. Physiol. 13, 31 (2022).Article 

    Google Scholar 
    Sepulveda, J. & Moeller, A. H. The effects of temperature on animal gut microbiomes. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.00384 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kohl, K. D. & Yahn, J. Effects of environmental temperature on the gut microbial communities of tadpoles. Environ. Microbiol. https://doi.org/10.1111/1462-2920.13255 (2016).Article 
    PubMed 

    Google Scholar 
    Teyssier, A. et al. Diet contributes to urban-induced alterations in gut microbiota: Experimental evidence from a wild passerine. Proc. R. Soc. B Biol. Sci. https://doi.org/10.1098/rspb.2019.2182 (2020).Article 

    Google Scholar 
    Benskin, C. M. W. H., Rhodes, G., Pickup, R. W., Wilson, K. & Hartley, I. R. Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2010.04892.x (2010).Article 
    PubMed 

    Google Scholar 
    Garrett, W. S. et al. Enterobacteriaceae Act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe https://doi.org/10.1016/j.chom.2010.08.004 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Videvall, E. et al. Early-life gut dysbiosis linked to juvenile mortality in ostriches. BMC Microbiome 8, 1–13 (2020).Article 

    Google Scholar 
    Hooper, L. V. & MacPherson, A. J. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol. https://doi.org/10.1038/nri2710 (2010).Article 
    PubMed 

    Google Scholar 
    Borre, Y. E. et al. Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends Mol. Med. https://doi.org/10.1016/j.molmed.2014.05.002 (2014).Article 
    PubMed 

    Google Scholar 
    Jones, E. L. & Leather, S. R. Invertebrates in urban areas: A review. Eur. J. Entomol. https://doi.org/10.14411/eje.2012.060 (2012).Article 

    Google Scholar 
    Wilkin, T. A., King, L. E. & Sheldon, B. C. Habitat quality, nestling diet, and provisioning behaviour in great tits Parus major. J. Avian Biol. https://doi.org/10.1111/j.1600-048X.2009.04362.x (2009).Article 

    Google Scholar 
    Pollock, C. J., Capilla-Lasheras, P., McGill, R. A. R., Helm, B. & Dominoni, D. M. Integrated behavioural and stable isotope data reveal altered diet linked to low breeding success in urban-dwelling blue tits (Cyanistes caeruleus). Sci. Rep. https://doi.org/10.1038/s41598-017-04575-y (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Davidson, G. L. et al. Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird. Sci. Rep. https://doi.org/10.1038/s41598-020-77256-y (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bodawatta, K. H. et al. Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets. Anim. Microbiome 2021(3), 1–14 (2021).
    Google Scholar 
    Baniel, A. et al. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. Microbiome 9, 1–20 (2021).Article 

    Google Scholar 
    Sullam, K. E. et al. Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2012.05552.x (2012).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martiny, J. B. H. et al. Microbial biogeography: Putting microorganisms on the map. Nat. Rev. Microbiol. https://doi.org/10.1038/nrmicro1341 (2006).Article 
    PubMed 

    Google Scholar 
    Lucass, C., Eens, M. & Müller, W. When ambient noise impairs parent-offspring communication. Environ. Pollut. https://doi.org/10.1016/j.envpol.2016.03.015 (2016).Article 
    PubMed 

    Google Scholar 
    Kight, C. R. & Swaddle, J. P. How and why environmental noise impacts animals: An integrative, mechanistic review. Ecol. Lett. https://doi.org/10.1111/j.1461-0248.2011.01664.x (2011).Article 
    PubMed 

    Google Scholar 
    Cui, B., Gai, Z., She, X., Wang, R. & Xi, Z. Effects of chronic noise on glucose metabolism and gut microbiota-host inflammatory homeostasis in rats. Sci. Rep. https://doi.org/10.1038/srep36693 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Campo, J. L., Gil, M. G. & Dávila, S. G. Effects of specific noise and music stimuli on stress and fear levels of laying hens of several breeds. Appl. Anim. Behav. Sci. https://doi.org/10.1016/j.applanim.2004.08.028 (2005).Article 

    Google Scholar 
    Injaian, A. S., Taff, C. C. & Patricelli, G. L. Experimental anthropogenic noise impacts avian parental behaviour, nestling growth and nestling oxidative stress. Anim. Behav. https://doi.org/10.1016/j.anbehav.2017.12.003 (2018).Article 

    Google Scholar 
    Cui, B. et al. Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: Implications for Alzheimer’s disease. J. Neuroinflammation https://doi.org/10.1186/s12974-018-1223-4 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wei, L. et al. Constant light exposure alters gut microbiota and promotes the progression of steatohepatitis in high fat diet rats. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.01975 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chatelain, M. et al. Replicated, urban-driven exposure to metallic trace elements in two passerines. Sci. Rep. 11, 1–10 (2021).Article 

    Google Scholar 
    Chatelain, M. et al. Urban metal pollution explains variation in reproductive outputs in great tits and blue tits. Sci. Total Environ. 776, 145966 (2021).ADS 
    CAS 
    Article 

    Google Scholar 
    Rosenfeld, C. S. Gut dysbiosis in animals due to environmental chemical exposures. Front. Cell. Infect. Microbiol. 7, 396 (2017).Article 

    Google Scholar 
    Sommer, F. & Bäckhed, F. The gut microbiota-masters of host development and physiology. Nat. Rev. Microbiol. https://doi.org/10.1038/nrmicro2974 (2013).Article 
    PubMed 

    Google Scholar 
    Tomiałojć, L. & Wesołowski, T. Diversity of the Białowieza forest avifauna in space and time. J. Ornithol. https://doi.org/10.1007/s10336-003-0017-2 (2004).Article 

    Google Scholar 
    Corsini, M. et al. Growing in the city: Urban evolutionary ecology of avian growth rates. Evol. Appl. https://doi.org/10.1111/eva.13081 (2021).Article 
    PubMed 

    Google Scholar 
    Teyssier, A., Lens, L., Matthysen, E. & White, J. Dynamics of gut microbiota diversity during the early development of an avian host: Evidence from a cross-foster experiment. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01524 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tremblay, I., Thomas, D., Blondel, J., Perret, P. & Lambrechts, M. M. The effect of habitat quality on foraging patterns, provisioning rate and nestling growth in Corsican Blue Tits Parus caeruleus. Ibis (Lond 1859). 147, 17–24 (2005).Article 

    Google Scholar 
    Corsini, M., Marrot, P. & Szulkin, M. Quantifying human presence in a heterogeneous urban landscape. Behav. Ecol. https://doi.org/10.1093/beheco/arz128 (2019).Article 

    Google Scholar 
    Corsini, M., Dubiec, A., Marrot, P. & Szulkin, M. Humans and tits in the city: Quantifying the effects of human presence on great tit and blue tit reproductive trait variation. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2017.00082 (2017).Article 

    Google Scholar 
    Kyba, C. C. M. et al. High-resolution imagery of earth at night: New sources, opportunities and challenges. Remote Sens. https://doi.org/10.3390/rs70100001 (2015).Article 

    Google Scholar 
    Maraci, Ö. et al. The gut microbial composition is species-specific and individual-specific in two species of estrildid finches, the Bengalese finch and the zebra finch. Front. Microbiol. https://doi.org/10.3389/fmicb.2021.619141 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Engel, K. et al. Individual- and species-specific skin microbiomes in three different estrildid finch species revealed by 16S amplicon sequencing. Microb. Ecol. https://doi.org/10.1007/s00248-017-1130-8 (2017).Article 
    PubMed 

    Google Scholar 
    Magoč, T. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics https://doi.org/10.1093/bioinformatics/btr507 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal https://doi.org/10.14806/ej.17.1.200 (2011).Article 

    Google Scholar 
    Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01541-09 (2009).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics https://doi.org/10.1093/bioinformatics/btq461 (2010).Article 
    PubMed 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. https://doi.org/10.1093/nar/gks1219 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2020).
    Google Scholar 
    Clarke, K. R., Gorley, R., Somerfield, P. & Warwick, R. Change in Marine Communities: an Approach to Statistical Analysis and Interpretation 3rd edn (Prim. Plymouth, 2014).Shannon, C. E. The mathematical theory of communication. MD Comput. https://doi.org/10.2307/410457 (1997).Article 
    PubMed 

    Google Scholar 
    Faith, D. P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. https://doi.org/10.1016/0006-3207(92)91201-3 (1992).Article 

    Google Scholar 
    Bates, D., Mächler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. https://doi.org/10.18637/jss.v067.i01 (2015).Article 

    Google Scholar 
    Fox, J. et al. The car Package. R (2012).Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. https://doi.org/10.1111/j.2041-210x.2009.00001.x (2010).Article 

    Google Scholar 
    DHARMa: Residual diagnostics for hierarchical (multi-level/mixed) regression models. https://cran.r-project.org/web/packages/DHARMa/vignettes/DHARMa.html.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).Book 

    Google Scholar 
    McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE https://doi.org/10.1371/journal.pone.0061217 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B https://doi.org/10.1111/j.2517-6161.1995.tb02031.x (1995).Article 
    MATH 

    Google Scholar 
    Whittaker, R. H. Vegetation of the Siskiyou mountains Oregon and California. Ecol. Monogr. https://doi.org/10.2307/1948435 (1960).Article 

    Google Scholar 
    Paulson, J. metagenomeSeq: Statistical analysis for sparse high-throughput sequencing. Bioconductor.Jp (2014).Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. https://doi.org/10.2307/1942268 (1957).Article 

    Google Scholar 
    Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01996-06 (2007).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Oksanen, J. et al. Package ‘vegan’ Title Community Ecology Package Version 2.5-6. cran.ism.ac.jp (2019).Anderson, M. J. & Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. https://doi.org/10.1046/j.1442-9993.2001.01070.x (2001).Article 

    Google Scholar 
    Clarke, K. R. & Ainsworth, M. A method of linking multivariate community structure to environmental variables. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps092205 (1993).Article 

    Google Scholar 
    QGIS Development Team. QGIS Geographic Information System (Open Source Geospatial Foundation, 2019).
    Google Scholar  More

  • in

    Expanding ocean food production under climate change

    United Nations. World Population Prospects: The 2017 Revision, Key Findings and Advance Tables. Working Paper No. ESA/P/WP/248 (UN-DESA, 2017).Costello, C. et al. The future of food from the sea. Nature 588, 95–100 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    IPCC. IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (2019).FAO. Mapping Supply and Demand for Animal-Source Foods to 2030 (2011).Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    DeFries, R. S., Rudel, T., Uriarte, M. & Hansen, M. Deforestation driven by urban population growth and agricultural trade in the twenty-first century. Nat. Geosci. 3, 178–181 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    Rockström, J. et al. Future water availability for global food production: the potential of green water for increasing resilience to global change. Water Resour. Res. 45, W00A12 (2009).Article 

    Google Scholar 
    IPCC. IPCC Special Report on Climate Change and Land (2019).Poore, J. & Nemecek, T. Reducing food’s environmental impacts through producers and consumers. Science 360, 987–992 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture 2020: Sustainability in Action (2020).Bryndum‐Buchholz, A. et al. Twenty-first-century climate change impacts on marine animal biomass and ecosystem structure across ocean basins. Glob. Change Biol. 25, 459–472 (2019).ADS 
    Article 

    Google Scholar 
    Cheung, W. W. L., Dunne, J., Sarmiento, J. L. & Pauly, D. Integrating ecophysiology and plankton dynamics into projected maximum fisheries catch potential under climate change in the Northeast Atlantic. ICES J. Mar. Sci. 68, 1008–1018 (2011).Article 

    Google Scholar 
    Froehlich, H. E., Gentry, R. R. & Halpern, B. S. Global change in marine aquaculture production potential under climate change. Nat. Ecol. Evol. 2, 1745–1750 (2018).PubMed 
    Article 

    Google Scholar 
    Handisyde, N., Telfer, T. C. & Ross, L. G. Vulnerability of aquaculture-related livelihoods to changing climate at the global scale. Fish Fish. 18, 466–488 (2017).Article 

    Google Scholar 
    Szuwalski, C. S. & Hollowed, A. B. Climate change and non-stationary population processes in fisheries management. ICES J. Mar. Sci. 73, 1297–1305 (2016).Article 

    Google Scholar 
    Pinsky, M. L. et al. Preparing ocean governance for species on the move. Science 360, 1189–1191 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Gaines, S. D. et al. Improved fisheries management could offset many negative effects of climate change. Sci. Adv. 4, eaao1378 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Free, C. M. et al. Realistic fisheries management reforms could mitigate the impacts of climate change in most countries. PLoS ONE 15, e0224347 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Clapp, J. Food self-sufficiency: making sense of it, and when it makes sense. Food Policy 66, 88–96 (2017).Article 

    Google Scholar 
    Barange, M., Bahri, T., Beveridge, M. & Cochrane, K. L. Impacts of Climate Change on Fisheries and Aquaculture: Synthesis of Current Knowledge, Adaptation and Mitigation Options. Fisheries and Aquaculture Technical Paper No. 627 (FAO, 2018).Lester, S. E. et al. Marine spatial planning makes room for offshore aquaculture in crowded coastal waters. Nat. Commun. 9, 945 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cottrell, R. S., Blanchard, J. L., Halpern, B. S., Metian, M. & Froehlich, H. E. Global adoption of novel aquaculture feeds could substantially reduce forage fish demand by 2030. Nat. Food 1, 301–308 (2020).Article 

    Google Scholar 
    Hua, K. et al. The future of aquatic protein: implications for protein sources in aquaculture diets. One Earth 1, 316–329 (2019).ADS 
    Article 

    Google Scholar 
    Chavanne, H. et al. A comprehensive survey on selective breeding programs and seed market in the European aquaculture fish industry. Aquacult. Int. 24, 1287–1307 (2016).Article 

    Google Scholar 
    Troell, M., Jonell, M. & Henriksson, P. J. G. Ocean space for seafood. Nat. Ecol. Evol. 1, 1224–1225 (2017).PubMed 
    Article 

    Google Scholar 
    European Union. Commission Regulation (EC) No 710/2009 of 5 August 2009 Amending Regulation (EC) No 889/2008 laying down detailed rules for the implementation of Council Regulation (EC) No 834/2007, as regards laying down detailed rules on organic aquaculture animal and seaweed production. http://data.europa.eu/eli/reg/2009/710/oj (2009).Golden, C. D. et al. Aquatic foods to nourish nations. Nature 598, 315–320 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Davies, I. P. et al. Governance of marine aquaculture: pitfalls, potential, and pathways forward. Mar. Policy 104, 29–36 (2019).Article 

    Google Scholar 
    Gentry, R. R. et al. Exploring the potential for marine aquaculture to contribute to ecosystem services. Rev. Aquacult. 12, 499–512 (2020).Article 

    Google Scholar 
    Troell, M. et al. Ecological engineering in aquaculture — potential for integrated multi-trophic aquaculture (IMTA) in marine offshore systems. Aquaculture 297, 1–9 (2009).Article 

    Google Scholar 
    Froehlich, H. E., Jacobsen, N. S., Essington, T. E., Clavelle, T. & Halpern, B. S. Avoiding the ecological limits of forage fish for fed aquaculture. Nat. Sustain. 1, 298–303 (2018).Article 

    Google Scholar 
    Øverland, M., Mydland, L. T. & Skrede, A. Marine macroalgae as sources of protein and bioactive compounds in feed for monogastric animals. J. Sci. Food Agric. 99, 13–24 (2019).PubMed 
    Article 
    CAS 

    Google Scholar 
    Besson, M. et al. Environmental impacts of genetic improvement of growth rate and feed conversion ratio in fish farming under rearing density and nitrogen output limitations. J. Clean. Prod. 116, 100–109 (2016).Article 

    Google Scholar 
    Froehlich, H. E., Runge, C. A., Gentry, R. R., Gaines, S. D. & Halpern, B. S. Comparative terrestrial feed and land use of an aquaculture-dominant world. Proc. Natl Acad. Sci. USA 115, 5295–5300 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aguilar-Manjarrez, J., Soto, D., Brummett, R. E. Aquaculture Zoning, Site Selection and Area Management under the Ecosystem Approach to Aquaculture (FAO, 2017).Soto, D. et al. In Impacts Of Climate Change on Fisheries and Aquaculture: Synthesis of Current Knowledge, Adaptation and Mitigation Options Ch. 26 (FAO, 2018).Darwin, C. The Variation of Animals and Plants Under Domestication (John Murray, 1868).Gjedrem, T., Robinson, N. & Rye, M. The importance of selective breeding in aquaculture to meet future demands for animal protein: a review. Aquaculture 350–353, 117–129 (2012).Article 

    Google Scholar 
    Antonello, J. et al. Estimates of heritability and genetic correlation for body length and resistance to fish pasteurellosis in the gilthead sea bream (Sparus aurata L.). Aquaculture 298, 29–35 (2009).Article 

    Google Scholar 
    Saillant, E., Dupont-Nivet, M., Haffray, P. & Chatain, B. Estimates of heritability and genotype–environment interactions for body weight in sea bass (Dicentrarchus labrax L.) raised under communal rearing conditions. Aquaculture 254, 139–147 (2006).Article 

    Google Scholar 
    Klinger, D. H., Levin, S. A. & Watson, J. R. The growth of finfish in global open-ocean aquaculture under climate change. Proc. R. Soc. B 284, 20170834 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Salayo, N. D., Perez, M. L., Garces, L. R. & Pido, M. D. Mariculture development and livelihood diversification in the Philippines. Mar. Policy 36, 867–881 (2012).Article 

    Google Scholar 
    Boyce, D. G., Lotze, H. K., Tittensor, D. P., Carozza, D. A. & Worm, B. Future ocean biomass losses may widen socioeconomic equity gaps. Nat. Commun. 11, 2235 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sumaila, U. R. et al. Benefits of the Paris Agreement to ocean life, economies, and people. Sci. Adv. 5, eaau3855 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    United Nations. Transforming Our World: The 2030 Agenda for Sustainable Development (United Nations, 2017).Hilborn, R. et al. Effective fisheries management instrumental in improving fish stock status. Proc. Natl Acad. Sci. USA 117, 2218–2224 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Free, C. M. et al. Impacts of historical warming on marine fisheries production. Science 363, 979–983 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Costello, C. et al. Global fishery prospects under contrasting management regimes. Proc. Natl Acad. Sci. USA 113, 5125–5129 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ye, Y. & Gutierrez, N. L. Ending fishery overexploitation by expanding from local successes to globalized solutions. Nat. Ecol. Evol. 1, 0179 (2017).Article 

    Google Scholar 
    Leape, J. et al. Technology, Data and New Models for Sustainably Managing Ocean Resources (World Resources Institute, 2020).Anderson, C. R. et al. Scaling up from regional case studies to a global harmful algal bloom observing system. Front. Mar. Sci. 6, 250 (2019).Article 

    Google Scholar 
    Dunn, D. C., Maxwell, S. M., Boustany, A. M. & Halpin, P. N. Dynamic ocean management increases the efficiency and efficacy of fisheries management. Proc. Natl Acad. Sci. USA 113, 668–673 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    FAO. Aquaculture Development: 7. Aquaculture Governance and Sector Development (2017).Oyinlola, M. A., Reygondeau, G., Wabnitz, C. C. C., Troell, M. & Cheung, W. W. L. Global estimation of areas with suitable environmental conditions for mariculture species. PLoS ONE 13, e0191086 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Jackson, A. Fish in-fish out ratio explained. Aquacult. Eur. 34, 5–10 (2009).
    Google Scholar 
    Tacon, A. G. J. & Metian, M. Feed matters: satisfying the feed demand of aquaculture. Rev. Fish. Sci. Aquacult. 23, 1–10 (2015).Article 

    Google Scholar 
    Tacon, A. G. J. & Metian, M. Global overview on the use of fish meal and fish oil in industrially compounded aquafeeds: trends and future prospects. Aquaculture 285, 146–158 (2008).CAS 
    Article 

    Google Scholar 
    World Bank. Population, Total (2020); https://data.worldbank.org/indicator/SP.POP.TOTLEdwards, P., Zhang, W., Belton, B. & Little, D. C. Misunderstandings, myths and mantras in aquaculture: its contribution to world food supplies has been systematically over reported. Mar. Policy 106, 103547 (2019).Article 

    Google Scholar 
    Roberts, P. Conversion Factors for Estimating the Equivalent Live Weight of Fisheries Products (The Food and Agriculture Organization of the United Nations, 1998).R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).Kaschner, K. et al. AquaMaps: Predicted Range Maps for Aquatic Species https://www.aquamaps.org/ (2019).García Molinos, J. et al. Climate velocity and the future global redistribution of marine biodiversity. Nat. Clim. Change 6, 83–88 (2016).ADS 
    Article 

    Google Scholar 
    Cashion, T., Le Manach, F., Zeller, D. & Pauly, D. Most fish destined for fishmeal production are food-grade fish. Fish Fish. 18, 837–844 (2017).Article 

    Google Scholar 
    Froehlich, H. E., Gentry, R. R. & Halpern, B. S. Synthesis and comparative analysis of physiological tolerance and life-history growth traits of marine aquaculture species. Aquaculture 460, 75–82 (2016).Article 

    Google Scholar 
    Thorson, J. T., Munch, S. B., Cope, J. M. & Gao, J. Predicting life history parameters for all fishes worldwide. Ecol. Appl. 27, 2262–2276 (2017).PubMed 
    Article 

    Google Scholar 
    Froese, R. & Pauly, D. FishBase http://www.fishbase.org (2021).Palomares, M. & Pauly, D. SeaLifeBase http://www.sealifebase.org (2019).FAO. Cultured Aquatic Species (2019).Dunne, J. P. et al. GFDL’s ESM2 global coupled climate–carbon Earth system models. Part I: physical formulation and baseline simulation characteristics. J. Clim. 25, 6646–6665 (2012).ADS 
    Article 

    Google Scholar 
    Dunne, J. P. et al. GFDL’s ESM2 global coupled climate–carbon Earth system models. Part II: carbon system formulation and baseline simulation characteristics. J. Clim. 26, 2247–2267 (2013).ADS 
    Article 

    Google Scholar 
    Song, Z. et al. Centuries of monthly and 3-hourly global ocean wave data for past, present, and future climate research. Sci. Data 7, 226 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gentry, R. R. et al. Mapping the global potential for marine aquaculture. Nat. Ecol. Evol. 1, 1317–1324 (2017).PubMed 
    Article 

    Google Scholar 
    Barton, A. et al. Impacts of coastal acidification on the Pacific Northwest shellfish industry and adaptation strategies implemented in response. Oceanography 25, 146–159 (2015).Article 

    Google Scholar 
    Froehlich, H. E., Smith, A., Gentry, R. R. & Halpern, B. S. Offshore aquaculture: I know it when I see it. Front. Mar. Sci. 4, 154 (2017).Article 

    Google Scholar 
    World Bank. Adjusted Net National Income per Capita (Current US$) (2019); https://data.worldbank.org/indicator/NY.ADJ.NNTY.PC.CDWorld Bank. Pump Price for Diesel Fuel (US$ per liter) (2019); https://data.worldbank.org/indicator/EP.PMP.DESL.CDPiburn, J. wbstats: programmatic access to the World Bank API. R package v.1.0.4 https://cran.r-project.org/web/packages/wbstats/index.html (2018).Rubino, M. (ed.) Offshore Aquaculture in the United States: Economic Considerations, Implications & Opportunities NOAA Technical Memorandum NMFS F/SPO-103 (US Department of Commerce, 2008).Jackson, A. & Newton, R. Project to Model the Use of Fisheries By-products in the Production of Marine Ingredients, with Special Reference to the Omega 3 Fatty Acids EPA and DHA (Institute Of Aquaculture, University Of Stirling And IFFO, 2016). More

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    A global reptile assessment highlights shared conservation needs of tetrapods

    We used the IUCN Red List criteria34,35 and methods developed in other global status-assessment efforts36,37 to assess 10,078 reptile species for extinction risk. We additionally include recommended Red List categories for 118 turtle species38, for a total of 10,196 species covered, representing 89% of the 11,341 described reptile species as of August 202039.Data compilationWe compiled assessment data primarily through regional in-person and remote (that is, through phone and email) workshops with species experts (9,536 species) and consultation with IUCN Species Survival Commission Specialist Groups and stand-alone Red List Authorities (442 species, primarily marine turtles, terrestrial and freshwater turtles, iguanas, sea snakes, mainland African chameleons and crocodiles). We conducted 48 workshops between 2004 and 2019 (Supplementary Table 1). Workshop participants provided information to complete the required species assessment fields (geographical distribution, population abundance and trends, habitat and ecological requirements, threats, use and trade, literature) and draw a distribution map. We then applied the Red List criteria34 to this information to assign a Red List category: extinct, extinct in the wild, critically endangered, endangered, vulnerable, near threatened, least concern and data deficient. Threatened species are those categorized as critically endangered, endangered and vulnerable.TaxonomyWe used The Reptile Database39 as a taxonomic standard, diverging only to follow well-justified taxonomic standards from the IUCN Species Survival Commission40. We could not revisit new descriptions for most regions after the end of the original assessment, so the final species list is not fully consistent with any single release of The Reptile Database.Distribution mapsWhere data allowed, we developed distribution maps in Esri shapefile format using the IUCN mapping guidelines41 (1,003 species). These maps are typically broad polygons that encompass all known localities, with provisions made to show obvious discontinuity in areas of unsuitable habitat. Each polygon is coded according to species’ presence (extant, possibly extant or extinct) and origin (native, introduced or reintroduced)41. For some regions covered in workshops (Caucasus, Southeast Asia, much of Africa, Australia and western South America), we collaborated with the Global Assessment of Reptile Distributions (GARD) (http://www.gardinitiative.org/) to provide contributing experts with a baseline species distribution map for review. Although refined maps were returned to the GARD team, not all of these maps have been incorporated into the GARD.Habitat preferencesWhere known, species habitats were coded using the IUCN Habitat Classification Scheme (v.3.1) (https://www.iucnredlist.org/resources/habitat-classification-scheme). Species were assigned to all habitat classes in which they are known to occur. Where possible, habitat suitability (suitable, marginal or unknown) and major importance (yes or no) was recorded. Habitat data were available for 9,484 reptile species.ThreatsAll known historical, current and projected (within 10 years or 3 generations, whichever is the longest; generation time estimated, when not available, from related species for which it is known; generation time recorded for 76.3% of the 186 species categorized as threatened under Red List criteria A and C1, the only criteria using generation length) threats were coded using the IUCN Threats Classification Scheme v.3.2 (https://www.iucnredlist.org/resources/threat-classification-scheme), which follows a previously published study42. Where possible, the scope (whole ( >90%), majority (50–90%), minority (30%), rapid ( >20%), slow but notable ( More

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    Variations in leaf water status and drought tolerance of dominant tree species growing in multi-aged tropical forests in Thailand

    Stibig, H. J., Achard, F., Carboni, S., Raši, R. & Miettinen, J. Change in tropical forest cover of Southeast Asia from 1990 to 2010. Biogeosciences 11, 247–258. https://doi.org/10.5194/bg-11-247-2014 (2014).ADS 
    Article 

    Google Scholar 
    Wilcove, D. S., Giam, X., Edwards, D. P., Fisher, B. & Koh, L. P. Navjot’s nightmare revisited: Logging, agriculture, and biodiversity in Southeast Asia. Trends Ecol. Evol. 28, 531–540. https://doi.org/10.1016/j.tree.2013.04.005 (2013).Article 
    PubMed 

    Google Scholar 
    Zeng, Z. et al. Highland cropland expansion and forest loss in Southeast Asia in the twenty-first century. Nat. Geosci. 11, 556–562. https://doi.org/10.1038/s41561-018-0166-9 (2018).ADS 
    CAS 
    Article 

    Google Scholar 
    Imai, N., Furukawa, T., Tsujino, R., Kitamura, S. & Yumoto, T. Correction: Factors affecting forest area change in Southeast Asia during 1980–2010. PLoS ONE 13, e0199908. https://doi.org/10.1371/journal.pone.0199908 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Allen, C. D. et al. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For. Ecol. Manag. 259, 660–684. https://doi.org/10.1016/j.foreco.2009.09.001 (2010).Article 

    Google Scholar 
    McDowell, N. G. et al. Multi-scale predictions of massive conifer mortality due to chronic temperature rise. Nat. Clim. Change 6, 295–300. https://doi.org/10.1038/nclimate2873 (2015).ADS 
    Article 

    Google Scholar 
    Reichstein, M. et al. Climate extremes and the carbon cycle. Nature 500, 287–295. https://doi.org/10.1038/nature12350 (2013).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Barbeta, A. et al. The combined effects of a long-term experimental drought and an extreme drought on the use of plant-water sources in a Mediterranean forest. Global Change Biol. 21, 1213–1225. https://doi.org/10.1111/gcb.12785 (2015).ADS 
    Article 

    Google Scholar 
    Mueller, R. C. et al. Differential tree mortality in response to severe drought: Evidence for long-term vegetation shifts. J. Ecol. 93, 1085–1093. https://doi.org/10.1111/j.1365-2745.2005.01042.x (2005).Article 

    Google Scholar 
    Carnicer, J. et al. Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought. Proc. Natl. Acad. Sci. USA 108, 1474–1478. https://doi.org/10.1073/pnas.1010070108 (2011).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shaw, J. D., Steed, B. E. & DeBlander, L. T. Forest Inventory and Analysis (FIA) annual inventory answers the question: What is happening to pinyon-juniper woodlands?. J. For. 103, 280–285 (2005).
    Google Scholar 
    Lebrija-Trejos, E., Pérez-García, E. A., Meave, J. A., Poorter, L. & Bongers, F. Environmental changes during secondary succession in a tropical dry forest in Mexico. J. Trop. Ecol. 27, 477–489. https://doi.org/10.1017/s0266467411000253 (2011).Article 

    Google Scholar 
    Lee, Y. K. et al. Differences of tree species composition and microclimate between a mahogany(swietenia macrophyllaking) plantation and a secondary forest in Mt. Makiling, Philippines. For. Sci. Technol. 2, 1–12. https://doi.org/10.1080/21580103.2006.9656293 (2006).CAS 
    Article 

    Google Scholar 
    Lebrija-Trejos, E., Perez-Garcia, E. A., Meave, J. A., Bongers, F. & Poorter, L. Functional traits and environmental filtering drive community assembly in a species-rich tropical system. Ecology 91, 386–398. https://doi.org/10.1890/08-1449.1 (2010).Article 
    PubMed 

    Google Scholar 
    Heithecker, T. D. & Halpern, C. B. Edge-related gradients in microclimate in forest aggregates following structural retention harvests in western Washington. For. Ecol. Manag. 248, 163–173. https://doi.org/10.1016/j.foreco.2007.05.003 (2007).Article 

    Google Scholar 
    Marthews, T. R., Burslem, D. F. R. P., Paton, S. R., Yangüez, F. & Mullins, C. E. Soil drying in a tropical forest: Three distinct environments controlled by gap size. Ecol. Model. 216, 369–384. https://doi.org/10.1016/j.ecolmodel.2008.05.011 (2008).Article 

    Google Scholar 
    Pineda-Garcia, F., Paz, H. & Meinzer, F. C. Drought resistance in early and late secondary successional species from a tropical dry forest: The interplay between xylem resistance to embolism, sapwood water storage and leaf shedding. Plant Cell Environ. 36, 405–418. https://doi.org/10.1111/j.1365-3040.2012.02582.x (2013).Article 
    PubMed 

    Google Scholar 
    Bretfeld, M., Ewers, B. E. & Hall, J. S. Plant water use responses along secondary forest succession during the 2015–2016 El Nino drought in Panama. New Phytol. 219, 885–899. https://doi.org/10.1111/nph.15071 (2018).Article 
    PubMed 

    Google Scholar 
    Matheny, A. M. et al. Contrasting strategies of hydraulic control in two codominant temperate tree species. Ecohydrology https://doi.org/10.1002/eco.1815 (2016).Article 

    Google Scholar 
    Pineda-Garcia, F., Paz, H., Meinzer, F. C. & Angeles, G. Exploiting water versus tolerating drought: Water-use strategies of trees in a secondary successional tropical dry forest. Tree Physiol. 36, 208–217. https://doi.org/10.1093/treephys/tpv124 (2016).Article 
    PubMed 

    Google Scholar 
    Powell, T. L. et al. Differences in xylem and leaf hydraulic traits explain differences in drought tolerance among mature Amazon rainforest trees. Global Change Biol. 23, 4280–4293. https://doi.org/10.1111/gcb.13731 (2017).ADS 
    Article 

    Google Scholar 
    Ruiz-Benito, P. et al. Climate- and successional-related changes in functional composition of European forests are strongly driven by tree mortality. Global Change Biol. 23, 4162–4176. https://doi.org/10.1111/gcb.13728 (2017).ADS 
    Article 

    Google Scholar 
    Choat, B. et al. Triggers of tree mortality under drought. Nature 558, 531–539. https://doi.org/10.1038/s41586-018-0240-x (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Sevanto, S., McDowell, N. G., Dickman, L. T., Pangle, R. & Pockman, W. T. How do trees die? A test of the hydraulic failure and carbon starvation hypotheses. Plant Cell Environ. 37, 153–161. https://doi.org/10.1111/pce.12141 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    McDowell, N. et al. Mechanisms of plant survival and mortality during drought: Why do some plants survive while others succumb to drought?. New Phytol. 178, 719–739. https://doi.org/10.1111/j.1469-8137.2008.02436.x (2008).Article 
    PubMed 

    Google Scholar 
    Rowland, L. et al. Death from drought in tropical forests is triggered by hydraulics not carbon starvation. Nature 528, 119–122. https://doi.org/10.1038/nature15539 (2015).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Lazar, T., Taiz, L. & Zeiger, E. Plant physiology. 3rd edn. Ann. Bot. 91, 750–751. https://doi.org/10.1093/aob/mcg079 (2003).Article 
    PubMed Central 

    Google Scholar 
    Steppe, K. The potential of the tree water potential. Tree Physiol. 38, 937–940. https://doi.org/10.1093/treephys/tpy064 (2018).Article 
    PubMed 

    Google Scholar 
    Johnson, D., Katul, G. G. & Domec, J. C. Catastrophic hydraulic failure and tipping points in plants. Plant Cell Environ. (2022).Adams, H. D. et al. A multi-species synthesis of physiological mechanisms in drought-induced tree mortality. Nat. Ecol. Evol. 1, 1285–1291. https://doi.org/10.1038/s41559-017-0248-x (2017).Article 
    PubMed 

    Google Scholar 
    Skelton, R. P., West, A. G. & Dawson, T. E. Predicting plant vulnerability to drought in biodiverse regions using functional traits. Proc. Natl. Acad. Sci. USA 112, 5744–5749. https://doi.org/10.1073/pnas.1503376112 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Domec, J.-C. et al. Conversion of natural forests to managed forest plantations decreases tree resistance to prolonged droughts. For. Ecol. Manag. 355, 58–71. https://doi.org/10.1016/j.foreco.2015.04.012 (2015).Article 

    Google Scholar 
    Maherali, H., Pockman, W. T. & Jackson, R. B. Adaptive variation in the vulnerability of woody plants to xylem cavitation. Ecology 85, 2184–2199. https://doi.org/10.1890/02-0538 (2004).Article 

    Google Scholar 
    Barros, F. V. et al. Hydraulic traits explain differential responses of Amazonian forests to the 2015 El Nino-induced drought. New Phytol. 223, 1253–1266. https://doi.org/10.1111/nph.15909 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bittencourt, P. R. L. et al. Amazonia trees have limited capacity to acclimate plant hydraulic properties in response to long-term drought. Global Change Biol. 26, 3569–3584. https://doi.org/10.1111/gcb.15040 (2020).ADS 
    Article 

    Google Scholar 
    Nolf, M. et al. Stem and leaf hydraulic properties are finely coordinated in three tropical rain forest tree species. Plant Cell Environ. 38, 2652–2661. https://doi.org/10.1111/pce.12581 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Trueba, S. et al. Vulnerability to xylem embolism as a major correlate of the environmental distribution of rain forest species on a tropical island. Plant, Cell Environ. 40, 277–289. https://doi.org/10.1111/pce.12859 (2017).CAS 
    Article 

    Google Scholar 
    Zhu, S. D., Chen, Y. J., Fu, P. L. & Cao, K. F. Different hydraulic traits of woody plants from tropical forests with contrasting soil water availability. Tree Physiol. 37, 1469–1477. https://doi.org/10.1093/treephys/tpx094 (2017).Article 
    PubMed 

    Google Scholar 
    Chen, Y. J. et al. Physiological regulation and efficient xylem water transport regulate diurnal water and carbon balances of tropical lianas. Funct. Ecol. 31, 306–317. https://doi.org/10.1111/1365-2435.12724 (2016).Article 

    Google Scholar 
    Tan, F.-S. et al. Hydraulic safety margins of co-occurring woody plants in a tropical karst forest experiencing frequent extreme droughts. Agr. Forest Meteorol. https://doi.org/10.1016/j.agrformet.2020.108107 (2020).Article 

    Google Scholar 
    Markesteijn, L., Iraipi, J., Bongers, F. & Poorter, L. Seasonal variation in soil and plant water potentials in a Bolivian tropical moist and dry forest. J. Trop. Ecol. 26, 497–508. https://doi.org/10.1017/s0266467410000271 (2010).Article 

    Google Scholar 
    Mitchell, P. J., Veneklaas, E. J., Lambers, H. & Burgess, S. S. Leaf water relations during summer water deficit: Differential responses in turgor maintenance and variation in leaf structure among different plant communities in south-western Australia. Plant Cell Environ. 31, 1791–1802. https://doi.org/10.1111/j.1365-3040.2008.01882.x (2008).Article 
    PubMed 

    Google Scholar 
    Baltzer, J. L., Davies, S. J., Bunyavejchewin, S. & Noor, N. S. M. The role of desiccation tolerance in determining tree species distributions along the Malay-Thai Peninsula. Funct. Ecol. 22, 221–231. https://doi.org/10.1111/j.1365-2435.2007.01374.x (2008).Article 

    Google Scholar 
    Kursar, T. A. et al. Tolerance to low leaf water status of tropical tree seedlings is related to drought performance and distribution. Funct. Ecol. 23, 93–102. https://doi.org/10.1111/j.1365-2435.2008.01483.x (2009).Article 

    Google Scholar 
    Engelbrecht, B. M. J., Tyree, M. T. & Kursar, T. A. Visual assessment of wilting as a measure of leaf water potential and seedling drought survival. J. Trop. Ecol. 23, 497–500. https://doi.org/10.1017/s026646740700421x (2007).Article 

    Google Scholar 
    Blackman, C. J. et al. Drought response strategies and hydraulic traits contribute to mechanistic understanding of plant dry-down to hydraulic failure. Tree Physiol. 39, 910–924. https://doi.org/10.1093/treephys/tpz016 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bucci, S. J. et al. Mechanisms contributing to seasonal homeostasis of minimum leaf water potential and predawn disequilibrium between soil and plant water potential in Neotropical savanna trees. Trees 19, 296–304. https://doi.org/10.1007/s00468-004-0391-2 (2004).Article 

    Google Scholar 
    Prado, C. H. B. A., Wenhui, Z., Cardoza Rojas, M. H. & Souza, G. M. Seasonal leaf gas exchange and water potential in a woody cerrado species community. Braz. J. Plant Physiol. 16, 7–16. https://doi.org/10.1590/s1677-04202004000100002 (2004).Article 

    Google Scholar 
    Fetcher, N., Oberbauer, S. F. & Strain, B. R. Vegetation effects on microclimate in lowland tropical forest in Costa Rica. Int. J. Biometeorol. 29, 145–155. https://doi.org/10.1007/bf02189035 (1985).ADS 
    Article 

    Google Scholar 
    McCarthy, J. Gap dynamics of forest trees: A review with particular attention to boreal forests. Environ. Rev. 9, 1–59. https://doi.org/10.1139/a00-012 (2001).Article 

    Google Scholar 
    Zhu, S.-D. & Cao, K.-F. Hydraulic properties and photosynthetic rates in co-occurring lianas and trees in a seasonal tropical rainforest in southwestern China. Plant Ecol. 204, 295–304. https://doi.org/10.1007/s11258-009-9592-5 (2009).Article 

    Google Scholar 
    Sperry, J. S., Hacke, U. G., Oren, R. & Comstock, J. P. Water deficits and hydraulic limits to leaf water supply. Plant Cell Environ. 25, 251–263. https://doi.org/10.1046/j.0016-8025.2001.00799.x (2002).Article 
    PubMed 

    Google Scholar 
    Choat, B., Sack, L. & Holbrook, N. M. Diversity of hydraulic traits in nine Cordia species growing in tropical forests with contrasting precipitation. New Phytol. 175, 686–698. https://doi.org/10.1111/j.1469-8137.2007.02137.x (2007).Article 
    PubMed 

    Google Scholar 
    Vinya, R. et al. Xylem cavitation vulnerability influences tree species’ habitat preferences in miombo woodlands. Oecologia 173, 711–720. https://doi.org/10.1007/s00442-013-2671-2 (2013).ADS 
    Article 
    PubMed 

    Google Scholar 
    Vander Willigen, C., Sherwin, H. W. & Pammenter, N. W. Xylem hydraulic characteristics of subtropical trees from contrasting habitats grown under identical environmental conditions. New Phytol. 145, 51–59. https://doi.org/10.1046/j.1469-8137.2000.00549.x (2000).Article 

    Google Scholar 
    Domec, J. C. et al. Diurnal and seasonal variation in root xylem embolism in neotropical savanna woody species: Impact on stomatal control of plant water status. Plant Cell Environ. 29, 26–35. https://doi.org/10.1111/j.1365-3040.2005.01397.x (2006).CAS 
    Article 
    PubMed 

    Google Scholar 
    Barnard, D. M. et al. Climate-related trends in sapwood biophysical properties in two conifers: Avoidance of hydraulic dysfunction through coordinated adjustments in xylem efficiency, safety and capacitance. Plant Cell Environ. 34, 643–654. https://doi.org/10.1111/j.1365-3040.2010.02269.x (2011).Article 
    PubMed 

    Google Scholar 
    Rosner, S., Heinze, B., Savi, T. & Dalla-Salda, G. Prediction of hydraulic conductivity loss from relative water loss: New insights into water storage of tree stems and branches. Physiol. Plant. 165, 843–854. https://doi.org/10.1111/ppl.12790 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Markesteijn, L., Poorter, L., Paz, H., Sack, L. & Bongers, F. Ecological differentiation in xylem cavitation resistance is associated with stem and leaf structural traits. Plant Cell Environ. 34, 137–148. https://doi.org/10.1111/j.1365-3040.2010.02231.x (2011).Article 
    PubMed 

    Google Scholar 
    Cartwright, J. M., Littlefield, C. E., Michalak, J. L., Lawler, J. J. & Dobrowski, S. Z. Topographic, soil, and climate drivers of drought sensitivity in forests and shrublands of the Pacific Northwest, USA. Sci. Rep. 10, 18486. https://doi.org/10.1038/s41598-020-75273-5 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Choat, B., Ball, M. C., Luly, J. G. & Holtum, J. A. M. Hydraulic architecture of deciduous and evergreen dry rainforest tree species from north-eastern Australia. Trees 19, 305–311. https://doi.org/10.1007/s00468-004-0392-1 (2004).Article 

    Google Scholar 
    Krober, W., Zhang, S., Ehmig, M. & Bruelheide, H. Linking xylem hydraulic conductivity and vulnerability to the leaf economics spectrum–a cross-species study of 39 evergreen and deciduous broadleaved subtropical tree species. PLoS ONE 9, e109211. https://doi.org/10.1371/journal.pone.0109211 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brockelman, W. Y., Nathalang, A. & Maxwell, J. F. Mo Singto Forest Dynamics Plot: Flora and Ecology (National Science and Technology Development Agency, 2017).
    Google Scholar 
    Zhang, Q. W., Zhu, S. D., Jansen, S., Cao, K. F. & McCulloh, K. Topography strongly affects drought stress and xylem embolism resistance in woody plants from a karst forest in Southwest China. Funct. Ecol. 35, 566–577. https://doi.org/10.1111/1365-2435.13731 (2020).Article 

    Google Scholar 
    Ishida, A. et al. Seasonal variations of gas exchange and water relations in deciduous and evergreen trees in monsoonal dry forests of Thailand. Tree Physiol. 30, 935–945. https://doi.org/10.1093/treephys/tpq025 (2010).Article 
    PubMed 

    Google Scholar 
    Nardini, A., Battistuzzo, M. & Savi, T. Shoot desiccation and hydraulic failure in temperate woody angiosperms during an extreme summer drought. New Phytol. 200, 322–329. https://doi.org/10.1111/nph.12288 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Choat, B. et al. Global convergence in the vulnerability of forests to drought. Nature 491, 752–755. https://doi.org/10.1038/nature11688 (2012).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Brodribb, T. J. Progressing from “functional” to mechanistic traits. New Phytol. 215, 9–11. https://doi.org/10.1111/nph.14620 (2017).Article 
    PubMed 

    Google Scholar 
    Oliveira, R. S. et al. Embolism resistance drives the distribution of Amazonian rainforest tree species along hydro-topographic gradients. New Phytol. 221, 1457–1465. https://doi.org/10.1111/nph.15463 (2019).Article 
    PubMed 

    Google Scholar 
    Popradit, A. et al. Anthropogenic effects on a tropical forest according to the distance from human settlements. Sci. Rep. 5, 14689. https://doi.org/10.1038/srep14689 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hérault, B. & Gourlet-Fleury, S. In Climate Change and Agriculture Worldwide (ed. Torquebiau, E.) 183–196 (Springer, 2016).Chapter 

    Google Scholar 
    Elliott, S. et al. Selecting framework tree species for restoring seasonally dry tropical forests in northern Thailand based on field performance. For. Ecol. Manag. 184, 177–191. https://doi.org/10.1016/s0378-1127(03)00211-1 (2003).Article 

    Google Scholar 
    Vieira, D. L. M. & Scariot, A. Principles of natural regeneration of tropical dry forests for restoration. Restor. Ecol. 14, 11–20. https://doi.org/10.1111/j.1526-100X.2006.00100.x (2006).Article 

    Google Scholar 
    Hérault, B. & Piponiot, C. Key drivers of ecosystem recovery after disturbance in a neotropical forest. For. Ecosyst. 5, 2. https://doi.org/10.1186/s40663-017-0126-7 (2018).Article 

    Google Scholar 
    Davies, S. J. et al. ForestGEO: Understanding forest diversity and dynamics through a global observatory network. Biol. Conserv. 253, 108907. https://doi.org/10.1016/j.biocon.2020.108907 (2021).Article 

    Google Scholar 
    Chanthorn, W. et al. Viewing tropical forest succession as a three-dimensional dynamical system. Theor. Ecol. 9, 163–172. https://doi.org/10.1007/s12080-015-0278-4 (2015).Article 

    Google Scholar 
    Chanthorn, W., Hartig, F. & Brockelman, W. Y. Structure and community composition in a tropical forest suggest a change of ecological processes during stand development. For. Ecol. Manag. 404, 100–107. https://doi.org/10.1016/j.foreco.2017.08.001 (2017).Article 

    Google Scholar 
    Rodtassana, C. et al. Different responses of soil respiration to environmental factors across forest stages in a Southeast Asian forest. Ecol. Evol. 11, 15430–15443. https://doi.org/10.1002/ece3.8248 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tor-ngern, P. et al. Variation of leaf-level gas exchange rates and leaf functional traits of dominant trees across three successional stages in a Southeast Asian tropical forest. For. Ecol. Manag. https://doi.org/10.1016/j.foreco.2021.119101 (2021).Article 

    Google Scholar 
    Zhu, S. D., Song, J. J., Li, R. H. & Ye, Q. Plant hydraulics and photosynthesis of 34 woody species from different successional stages of subtropical forests. Plant Cell Environ. 36, 879–891. https://doi.org/10.1111/pce.12024 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Martin-StPaul, N. K. et al. How reliable are methods to assess xylem vulnerability to cavitation? The issue of “open vessel” artifact in oaks. Tree Physiol. 34, 894–905. https://doi.org/10.1093/treephys/tpu059 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Ennajeh, M., Simoes, F., Khemira, H. & Cochard, H. How reliable is the double-ended pressure sleeve technique for assessing xylem vulnerability to cavitation in woody angiosperms?. Physiol. Plant. 142, 205–210. https://doi.org/10.1111/j.1399-3054.2011.01470.x (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pérez-Harguindeguy, N. et al. Corrigendum to: New handbook for standardised measurement of plant functional traits worldwide. Aust. J. Bot. 64, 715–716. https://doi.org/10.1071/bt12225_co (2016).Article 

    Google Scholar 
    Ewers, F. W. & Fisher, J. B. Techniques for measuring vessel lengths and diameters in stems of woody plants. Am. J. Bot. 76, 645–656. https://doi.org/10.1002/j.1537-2197.1989.tb11360.x (1989).Article 

    Google Scholar 
    Gao, H. et al. Vessel-length determination using silicone and air injection: Are there artifacts?. Tree Physiol. 39, 1783–1791. https://doi.org/10.1093/treephys/tpz064 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Sperry, J. S. & Saliendra, N. Z. Intra- and inter-plant variation in xylem cavitation in Betula occidentalis. Plant Cell Environ. 17, 1233–1241. https://doi.org/10.1111/j.1365-3040.1994.tb02021.x (1994).Article 

    Google Scholar 
    Melcher, P. J. et al. Measurements of stem xylem hydraulic conductivity in the laboratory and field. Methods Ecol. Evol. 3, 685–694. https://doi.org/10.1111/j.2041-210X.2012.00204.x (2012).Article 

    Google Scholar 
    Edwards, W. R. N. & Jarvis, P. G. Relations between water content, potential and permeability in stems of conifers. Plant Cell Environ. 5, 271–277. https://doi.org/10.1111/1365-3040.ep11572656 (1982).Article 

    Google Scholar 
    Sperry, J. S. & Ikeda, T. Xylem cavitation in roots and stems of Douglas-fir and white fir. Tree Physiol. 17, 275–280. https://doi.org/10.1093/treephys/17.4.275 (1997).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pammenter, N. W. & Vander Willigen, C. A mathematical and statistical analysis of the curves illustrating vulnerability of xylem to cavitation. Tree Physiol. 18, 589–593. https://doi.org/10.1093/treephys/18.8-9.589 (1998).Article 
    PubMed 

    Google Scholar 
    Domec, J.-C. & Gartner, B. L. Cavitation and water storage capacity in bole xylem segments of mature and young Douglas-fir trees. Trees 15, 204–214. https://doi.org/10.1007/s004680100095 (2001).Article 

    Google Scholar  More

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    Impact of disabled circadian clock on yellow fever mosquito Aedes aegypti fitness and behaviors

    Bell-Pedersen, D., Cassone, V. M., Earnest, D. J., Golden, S. S. & Hardin, P. E. Circadian rhythms from multiple oscillators: Lessons from diverse organisms. Nat. Rev. Drug Discov. 4, 121–130 (2005).Article 
    CAS 

    Google Scholar 
    Taylor, B. & Jones, M. D. The circadian rhythm of flight activity in the mosquito Aedes aegypti (L.): The phase-setting effects of light-on and light-off. J. Exp. Biol. 51, 59–70 (1969).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jones, M. D. R. The programming of circadian flight-activity in relation to mating and the gonotrophic cycle in the mosquito. Physiol. Entomol. 6, 307–313 (1981).Article 

    Google Scholar 
    Lee, H., Yang, Y., Liu, Y., Teng, H. & Sauman, I. Circadian control of permethrin-resistance in the mosquito Aedes aegypti. Physiol. Entomol. 56, 1219–1223 (2010).
    Google Scholar 
    Ptitsyn, A. A. et al. Rhythms and synchronization patterns in gene expression in the Aedes aegypti mosquito. BMC Genom. 12, 153 (2011).CAS 
    Article 

    Google Scholar 
    Rund, S. S. C., Hou, T. Y., Ward, S. M., Collins, F. H. & Duf, G. E. Genome-wide profiling of diel and circadian gene expression in the malaria vector Anopheles gambiae. Proc. Natl. Acad. Sci. USA. 108, 419–444 (2011).Article 

    Google Scholar 
    Rund, S. S. C., Gentile, J. E. & Duffield, G. E. Extensive circadian and light regulation of the transcriptome in the malaria mosquito Anopheles gambiae. BMC Genom. 14, 218 (2013).CAS 
    Article 

    Google Scholar 
    Leming, M. T., Rund, S. S. C., Behura, S. K., Duffield, G. E. & O’Tousa, J. E. A database of circadian and diel rhythmic gene expression in the yellow fever mosquito Aedes aegypti. BMC Genom. 15, 1–9 (2014).Article 
    CAS 

    Google Scholar 
    Faria, N. R. et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546, 406–410 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Araujo, M. S., Guo, F. & Rosbash, M. Video recording can conveniently assay mosquito locomotor activity. Sci. Rep. 10, 1–9 (2020).Article 
    CAS 

    Google Scholar 
    Lima-Camara, T. N. et al. Dengue infection increases the locomotor activity of Aedes aegypti females. PLoS ONE 6, 1–5 (2011).Article 
    CAS 

    Google Scholar 
    Das, S. & Dimopoulos, G. Molecular analysis of photic inhibition of blood-feeding in Anopheles gambiae. BMC Physiol. 19, 1–19 (2008).
    Google Scholar 
    Gentile, C. et al. Circadian clock of Aedes aegypti: Effects of blood-feeding, insemination and RNA interference. Mem. Inst. Oswaldo Cruz 108, 80–87 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Meireles-filho, A. C. A. & Kyriacou, C. P. Circadian rhythms in insect disease vectors. Mem. Inst. Oswaldo Cruz 108, 48–58 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yuan, Q., Metterville, D., Briscoe, A. D. & Reppert, S. M. Insect cryptochromes: Gene duplication and loss define diverse ways to construct insect circadian clocks. Mol. Biol. Evol. 24, 948–955 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gentile, C., Rivas, G. B. S., Meireles-Filho, A. C. A., Lima, J. B. P. & Peixoto, A. A. Circadian expression of clock genes in two mosquito disease vectors: Cry2 is different. J. Biol. Rhythms 24, 444–451 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, Y., Markert, M. J., Groves, S. C., Hardin, P. E. & Merlin, C. Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity. Proc. Natl. Acad. Sci. USA. 114, E7516–E7525 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Matthews, B. J. et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 563, 501–507 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Baylies, M. K., Bargiello, T. A., Jackson, F. R. & Young, M. W. Changes in abundance or structure of the per gene product can alter periodicity of the Drosophila clock. Nature 48, 1986–1988 (1987).
    Google Scholar 
    Sehgal, A., Price, J. L., Man, B. & Young, M. W. Loss of circadian behavioral rhythms and per RNA oscillations in the Drosophila mutant timeless. Science 263, 1603–1606 (1994).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Allada, R., White, N. E., So, W. V., Hall, J. C. & Rosbash, M. A mutant Drosophila homolog of mammalian clock disrupts circadian rhythms and transcription of period and timeless. Cell 93, 791–804 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rutila, J. E., Maltseva, O. & Rosbash, M. The timSL mutant affects a restricted portion of the drosophila melanogaster circadian cycle. J. Biol. Rhythms 13, 380–392 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rund, S. S. C. et al. Daily rhythms in antennal protein and olfactory sensitivity in the malaria mosquito Anopheles gambiae. Sci. Rep. 3, 1–9 (2013).Article 

    Google Scholar 
    Meireles-Filho, A. C. A. et al. The biological clock of an hematophagous insect: Locomotor activity rhythms, circadian expression and downregulation after a blood meal. FEBS Lett. 580, 2–8 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Tallon, A. K., Hill, S. R. & Ignell, R. Sex and age modulate antennal chemosensory-related genes linked to the onset of host seeking in the yellow-fever mosquito, Aedes aegypti. FEBS Lett. https://doi.org/10.1038/s41598-018-36550-6 (2019).Article 

    Google Scholar 
    Hug, N., Longman, D. & Cáceres, J. F. Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res. 44, 1483–1495 (2015).Article 

    Google Scholar 
    Hardin, P. E. Molecular genetic analysis of circadian timekeeping in Drosophila. Adv. Genet. 74, 147 (2011).
    Google Scholar 
    Tauber, E., Roe, H., Costa, R., Hennessy, J. M. & Kyriacou, C. P. Temporal mating isolation driven by a behavioral gene in Drosophila. Curr. Biol. 13, 140–145 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rutila, J. E. et al. Cycle is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell 93, 805–814 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lin, F.-J., Song, W., Meyer-Bernstein, E., Naidoo, N. & Sehgal, A. Photic signaling by cryptochrome in the Drosophila circadian system. Mol. Cell. Biol. 21, 7287–7294 (2001).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yadav, P., Thandapani, M. & Sharma, V. K. Interaction of light regimes and circadian clocks modulate timing of pre-adult developmental events in Drosophila. BMC Dev. Biol. 14, 1–12 (2014).Article 
    CAS 

    Google Scholar 
    Jones, M. & Reiter, P. Entrainment of the pupation and adult activity rhythms during development in the mosquito Anopheles gambiae. Nature 254, 242–244 (1968).ADS 
    Article 

    Google Scholar 
    Nayar, J. K. The pupation rhythm in Aedes taeniorhynchus (Diptera: Culicidae). II. Ontogenetic timing, rate of development, and endogenous diurnal rhythm of pupation. Ann. Entomol. Soc. Am. 60, 946–971 (1967).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nijhout, H. F. et al. The developmental control of size in insects. Wiley Interdiscip. Rev. Dev. Biol. 3, 113–134 (2014).PubMed 
    Article 

    Google Scholar 
    Kaneko, M., Hamblen, M. J. & Hall, J. C. Involvement of the period gene in developmental time-memory: Effect of the per(Short) mutation on phase shifts induced by light pulses delivered to Drosophila larvae. J. Biol. Rhythms 15, 13–30 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Srivastava, M., James, A., Varma, V., Sharma, V. K. & Sheeba, V. Environmental cycles regulate development time via circadian clock mediated gating of adult emergence. BMC Dev. Biol. 18, 1–10 (2018).Article 
    CAS 

    Google Scholar 
    Duffield, G. E. et al. Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr. Biol. 12, 551–557 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Menon, A., Varma, V. & Sharma, V. K. Rhythmic egg-laying behaviour in virgin females of fruit flies Drosophila melanogaster. Chronobiol. Int. 31, 433–441 (2014).PubMed 
    Article 

    Google Scholar 
    Kyriacou, C. P., Oldroyd, M., Wood, J., Sharp, M. & Hill, M. Clock mutations alter developmental timing in drosophila. Heredity 64, 395–401 (1990).PubMed 
    Article 

    Google Scholar 
    Allada, R. & Chung, B. Y. Circadian organization of behavior and physiology in Drosophila. Annu. Rev. Physiol. 72, 605–624 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lima-Camara, T. N., Lima, J. B. P., Bruno, R. V. & Peixoto, A. A. Effects of insemination and blood-feeding on locomotor activity of Aedes albopictus and Aedes aegypti (Diptera: Culicidae) females under laboratory conditions. Parasit. Vectors 7, 1–8 (2014).Article 

    Google Scholar 
    Krishnan, B., Dryer, S. E. & Hardin, P. E. Circadian rhythms in olfactory responses of Drosophila melanogaster. Nature 400, 375–378 (1999).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Delventhal, R. et al. Dissection of central clock function in Drosophila through cell-specific CRISPR-mediated clock gene disruption. Elife 8, 48305 (2019).Article 

    Google Scholar 
    Nayar, J. K. & Sauerman, D. M. The effect of light regimes on the circadian rhythm of flight activity in the mosquito Aedes taeniorhynchus. J. Exp. Biol. 54, 745–756 (1971).CAS 
    PubMed 
    Article 

    Google Scholar 
    Granados-Fuentes, D., Tseng, A. & Herzog, E. D. A circadian clock in the olfactory bulb controls olfactory responsivity. J. Neurosci. 26, 12219–12225 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Eilerts, D. F., Vandergiessen, M., Bose, E. A. & Broxton, K. Odor-specific daily rhythms in the olfactory sensitivity and behavior of Aedes aegypti mosquitoes. Insects 9, 147 (2018).PubMed Central 
    Article 

    Google Scholar 
    Tanoue, S., Krishnan, P., Krishnan, B., Dryer, S. E. & Hardin, P. E. Circadian clocks in antennal neurons are necessary and sufficient for olfaction rhythms in Drosophila. Curr. Biol. 14, 638–649 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wang, G. et al. Clock genes and environmental cues coordinate Anopheles pheromone synthesis, swarming, and mating. Science 371, 411–415 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Sakai, T. & Ishida, N. Circadian rhythms of female mating activity governed by clock genes in Drosophila. Proc. Natl. Acad. Sci. USA. 98, 9221–9225 (2001).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Petersen, G., Hall, J. C. & Rosbash, M. The period gene of Drosophila carries species-specific behavioral instructions. EMBO J. 7, 3939–3947 (1988).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cabrera, M. & Jaffe, K. An aggregation pheromone modulates lekking behavior in the vector mosquito Aedes aegypti (Diptera: Culicidae). J. Am. Mosq. Control Assoc. 23, 1–10 (2007).PubMed 
    Article 

    Google Scholar 
    Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M. & Valen, E. CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, 401–407 (2014).Article 
    CAS 

    Google Scholar 
    Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: A web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272–W276 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bassett, A. R., Tibbit, C., Ponting, C. P. & Liu, J. L. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4, 220–228 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhu, H. et al. The two CRYs of the butterfly. Curr. Biol. 15, 730 (2005).Article 
    CAS 

    Google Scholar 
    McDonald, M. J., Rosbash, M. & Emery, P. Wild-type circadian rhythmicity is dependent on closely spaced e boxes in the Drosophila timeless promoter. Mol. Cell. Biol. 21, 1207–1217 (2001).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chang, D. C. & Reppert, S. M. A novel c-terminal domain of drosophila PERIOD inhibits dCLOCK:CYCLE-mediated transcription. Curr. Biol. 13, 654–658 (2003).Article 
    CAS 

    Google Scholar  More

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    Synergistic use of siderophores and weak organic ligands during zinc transport in the rhizosphere controlled by pH and ion strength gradients

    Speciation models, conditional and intrinsic stability constants and EDH model parametersThe complete set of analytical results for the Zn(II)/ligand systems, including conditional stability constants (logβ) for the formation of hydrolysed Zn(II)–ligand complexes, of zinc hydroxide complexes and of Zn(II)–ligand complexes as well as acidity constants for citrate and DFOB at different ionic strength in NaCl and T = 298.1 K are reported in Table 1 and SI Table 2. Also shown are the values for the optimised parameter C and the intrinsic association constants (logβ0). SI Table 1 lists all the reactions included in the speciation models used to fit the potentiometric titrations and SI Fig. 2 shows single crystal X-ray structures for some of the proposed structures including ZnH2Cit2, Zn2Cit2(H2O)2 and ZnCit22− taken from the Cambridge Crystallographic Data Base. Figure 3 displays the experimentally determined conditional Zn(II)–ligand stability constants and the corresponding EDH model from this study. Also shown are logb values from the literature for [Zn(HCit)] and [Zn(Cit)]− for the Zn(II)/Cit system and [Zn(H2DFOB)]+, [Zn(HDFOB)] and [Zn(DFOB)]− for the Zn(II)/DFOB system. Examples of titration curves and manually fitted models along with the speciation model considered and the experimental conditions are included in the supporting information (see SI Figs. 3 and 4). Only models that fitted the experimental data with sigma values below 5 were considered. Examples of Hyperquad files showing titrations and model fits for Zn(II)/Cit and Zn(II)/DFOB systems and of Excel calculation files for the application of the EDH model to the Zn(II)/DFOB experimental data set, including error calculation for C and logβ0 are uploaded to the Zenodo repository (https://doi.org/10.5281/zenodo.4548162). Errors reported for measured logβ and calculated (modelled) logβ0 and C values have no detectable effect on subsequent speciation calculations. The errors reported on C are slightly larger than in comparable studies22, however, a sensitivity analysis on the two Zn(II)–ligand species with the largest relative error on C found that logβ0 remains within its error range even when logβ0 was recalculated for the maximum and minimum possible C values. The stability constant we report for specific Zn(II)–L complexes at specific ion strengths are in line with literature reports (Fig. 3). For example, the logβ for the formation of [Zn(Cit)]− in 0.15 mol dm−3 NaCl shows good agreement with the value reported by Cigala and co-workers in 0.15 mol dm−3 NaCl; 4.79 vs. 4.7126. We note, however, also significant variations within reported conditional logβ values as seen Fig. 3, with published values for the formation of [Zn(HCit)] and [Zn(Cit)]− in different 1:1 electrolytes differing over two orders of magnitudes. This highlights the analytical challenges associated with accurate and precise logβ determinations of low affinity metal–ligand complexes, in low ion strength solutions33.Figure 3Experimental Zn(II)–ligand conditional stability constants (logβ) for (a) citrate and (b) DFOB at 0.05, 0.15, 0.3, 0.5 and 1 mol dm−3 in NaCl solution (open circles) determined using potentiometric titrations. For each species, the Extended Debye-Hückel (EDH) model has been parameterised using the experimental data (see Table 1 for C and logβ0) and the corresponding model is shown as a solid line. Literature data is included in the figure for comparison (closed circles) from Cigala et al. (2015, NaNO3 and NaCl), Capone et al. (1986, KNO3), Daniele et al. (1988, KNO3), Field et al. (1975, KNO3), Matsushima et al. (1963, NaCl) and Li et al. 1959, NaCl) for the Zn–H–Cit system and from Schijf et al. (2015, NaClO4), Farkas et al. (1997, KCl) and Hernlem et al. (1996, KNO3) for the Zn-H-DFOB system. Note the large variability reported for the Zn–Cit system at 0.1 and 0.15 mol dm−3. We find good agreement with the data published by Sammartano and co-workers26,69.Full size imageThe final speciation scheme with the best statistical fits and with chemically sensible species are given in Table 1. From the eight Zn-Cit species initially considered (SI Table 1), the inclusion of five species resulted in model fits with sigma values below 5. For the Zn(II)/Cit system, the dominant species are [Zn(Cit)]−, [Zn(HCit)], and [Zn2(Cit)2(OH)2]4−. We report also the presence of a [Zn(Cit)(OH)3]4− complex above pH 9 in significant amounts ( > 20%) and we confirm the presence of [Zn(Cit)2]4− if citrate is present in large excess26,31. The presence of [Zn(Cit)]−, [Zn(HCit)] and [Zn(Cit)2]4− were confirmed in pH 6 solutions by mass spectrometry. To confirm the presence of [Zn(Cit)(OH)3]4−, further investigations are warranted. SI Fig. 5 shows the species distributions in the Zn(II)–Cit system with different Zn:L molar ratios (1:1, 1:2 and 1:10) and different concentrations (between 10–6 and 10–3 for Zn and 10–5 and 10–3 for citrate). We find that [Zn(Cit)]− dominates (i.e., formation relative to total Zn is above 50%) between pH 5 and 7.5, [Zn2(Cit)2(OH)2]4− dominates between pH 7.5 and 10 and [Zn(Cit)(OH)3]4− dominates at pH values above 10. We find the formation of [Zn(Cit)2]4− only at Zn:Cit molar ratio of 1:10 and [Zn] and [L] concentrations of 10–4 and 10–3 mol dm−3, respectively. The species [Zn(Cit)(OH)]2− and Zn(Cit)(OH))2]3− possibly form at higher pH but were excluded from the final model. We noted that for titrations of solutions with Zn:Cit molar ratios below 1:3, it was not possible to refine the stepwise stability constant (logK) for [Zn(Cit)2]4− to within ± 0.09 log units, indicating that it is an unstable species that forms at negligible concentrations. The stability constants for zinc complexation with citrate decrease with increasing ionic strength. Table 1 shows that the most significant change is seen between 0.05 and 0.15 mol dm−3 NaCl, where there is approximately a 0.5 to 1.5 log unit change. In dilute solutions, stability constants are sensitive to small increases in ionic strength because changes in the effective concentration (activity) of ions are large.For the Zn(II)–DFOB system, all the stability constants measured during this study are in good agreement with those reported in the literature50,51,53. For example, the stability constant we report for [Zn(HDFOB)] in 0.5 mol dm−3 NaCl is 19.34. This is within ~ 0.5 log units of the stability constant reported by Schijf and co-workers in 0.7 mol dm−3 NaClO4 solutions53. The speciation scheme we report differs slightly from that predicted by Schijf based on a three-step model. Our model does not include the bidentate species [Zn(H3DFOB)]2+, the weakest and least stable Zn(II)–DFOB species. In Table 1, we report stability constants for hexadentate [Zn(DFOB)]− and [Zn(HDFOB)] and tetradentate [Zn(H2DFOB)]+. We observe that as the denticity of the complex increases, so does the strength of the stability constant. The stepwise stability constant (K) differs by approximately 2 log units between the formation of the three different DFOB:Zn:H species (7.75, 9.88, 11.67, see Table 1). DFOB complexation of Zn(II) shows the same pattern of ionic strength dependence as citrate, with the greatest decrease of logβ occurring between 0.05 and 0.15 mol dm−3 NaCl, the region of most importance to the rhizosphere.The absolute decrease in [ZnL] and [Zn(HL)] stability constants between 0.05 and 0.15 mol dm−3 is approximately equal for citrate and DFOB species, average 1.58 vs. 1.73, respectively. This is explained by the effect of ionic strength primarily depending on the charge of the ions involved and free citrate and DFOB having the same electrostatic charge (−3). The ionic strength dependent parameter C shows no systematic change for neither citrate nor DFOB species. The good agreement between literature50,51,52,54,68,69,70 and our speciation models as well as the conditional logβ and pKa values validates the use of a single analytical method for the determination of the LEP. We note that the proposed formation of the trihydroxy Zn(II) citrate complex at pH above 10, needs to be investigated in greater detail using supplementary techniques. However, the formation of this species is not relevant for the pH range of interest in our study. As discussed below the main prevailing species in solution are those of 1:1:0 and 2:2:−2 stoichiometry for Zn:Cit:H.Figure 4 shows intrinsic stability constants for the formation of [Zn(Cit)]− and [Zn(HCit)] determined (i) using the Davies equation and the conditional association constants determined at different ionic strengths and (ii) fitting the parameterised EDH equation to the full ionic strength dataset. We find statistically significant (p  More

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    The EU needs a nutrient directive

    Sutton, M. A. et al. The European Nitrogen Assessment: Sources, Effects and Policy Perspectives (Cambridge Univ. Press, 2011).Withers, P. J. A. & Haygarth, P. M. Agriculture, phosphorus and eutrophication: A European perspective. Soil Use Manag. 23, 1–4 (2007).Article 

    Google Scholar 
    Heffer, P. Assessment of Fertilizer Use by Crop at the Global Level (IFA, 2008).Wassen, M. J., Schrader, J., van Dijk, J. & Eppinga, M. B. Phosphorus fertilization is eradicating the niche of northern Eurasia’s threatened plant species. Nat. Ecol. Evol. 5, 67–73 (2021).Article 

    Google Scholar 
    Penuelas, J., Janssens, I. A., Ciais, P., Obersteiner, M. & Sardans, J. Anthropogenic global shifts in biospheric N and P concentrations and ratios and their impacts on biodiversity, ecosystem productivity, food security, and human health. Glob. Change Biol. 26, 1962–1985 (2020).Article 

    Google Scholar 
    Stokstad, E. Nitrogen crisis threatens Dutch environment — and economy. Science 366, 1180–1181 (2019).Article 

    Google Scholar 
    Dentener, F. et al. Nitrogen and sulfur deposition on regional and global scales: A multimodel evaluation. Global Biogeochem. Cycles 20, GB4003 (2006).Article 

    Google Scholar 
    Garske, B., Stubenrauch, J. & Ekardt, F. Sustainable phosphorus management in European agricultural and environmental law. RECIEL 29, 107–117 (2020).Article 

    Google Scholar 
    A Farm to Fork Strategy for a Fair, Healthy and Environmentally-friendly Food System (COM(2020) 381 final: European Commission, 2020); https://knowledge4policy.ec.europa.eu/publication/communication-com2020381-farm-fork-strategy-fair-healthy-environmentally-friendly-food_en More