More stories

  • in

    eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity

    Notomi, T. et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. https://doi.org/10.1093/nar/28.12.e63 (2000).Article 

    Google Scholar 
    Nagamine, K., Hase, T. & Notomi, T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell. Probes 16, 223–229. https://doi.org/10.1006/mcpr.2002.0415 (2002).CAS 
    Article 

    Google Scholar 
    Nagamine, K., Watanabe, K., Ohtsuka, K., Hase, T. & Notomi, T. Loop-mediated isothermal amplification reaction using a nondenatured template. Clin. Chem. 47, 1742–1743 (2001).CAS 
    Article 

    Google Scholar 
    Thai, H. T. C. et al. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus. J. Clin. Microbiol. 42, 1956–1961. https://doi.org/10.1128/jcm.42.5.1956-1961.2004 (2004).CAS 
    Article 

    Google Scholar 
    Geojith, G., Dhanasekaran, S., Chandran, S. P. & Kenneth, J. Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting. J. Microbiol. Methods 84, 71–73. https://doi.org/10.1016/j.mimet.2010.10.015 (2011).CAS 
    Article 

    Google Scholar 
    Saengsawang, N. et al. Development of a fluorescent distance-based paper device using loop-mediated isothermal amplification to detect Escherichia coli in urine. Analyst 145, 8077–8086. https://doi.org/10.1039/d0an01306d (2020).CAS 
    Article 

    Google Scholar 
    Yoshikawa, R. et al. Development and evaluation of a rapid and simple diagnostic assay for COVID-19 based on loop-mediated isothermal amplification. Plos Neglect. Trop. Dis. 14, 14. https://doi.org/10.1371/journal.pntd.000885 (2021).Article 

    Google Scholar 
    Kim, J. et al. Development and evaluation of a multiplex loop-mediated isothermal amplification (LAMP) assay for differentiation of Mycobacterium tuberculosis and non-tuberculosis mycobacterium in clinical samples. PLoS ONE 16, 11. https://doi.org/10.1371/journal.pone.0244753 (2021).CAS 
    Article 

    Google Scholar 
    Hongjaisee, S. et al. Rapid visual detection of hepatitis C virus using a reverse transcription loop-mediated isothermal ampli fi cation assay. Int. J. Infect. Dis. 102, 440–445. https://doi.org/10.1016/j.ijid.2020.10.082 (2021).CAS 
    Article 

    Google Scholar 
    Niessen, L. & Vogel, R. F. Detection of Fusarium graminearum DNA using a loop-mediated isothermal amplification (LAMP) assay. Int. J. Food Microbiol. 140, 183–191. https://doi.org/10.1016/j.ijfoodmicro.2010.03.036 (2010).CAS 
    Article 

    Google Scholar 
    Ren, W. C., Liu, N. & Li, B. H. Development and application of a LAMP method for rapid detection of apple blotch caused by Marssonina coronaria. Crop Prot. 141, 6. https://doi.org/10.1016/j.cropro.2020.105452 (2021).CAS 
    Article 

    Google Scholar 
    Kong, G. H. et al. Detection of Peronophythora litchii on lychee by loop-mediated isothermal amplification assay. Crop Prot. 139, 6. https://doi.org/10.1016/j.cropro.2020.105370 (2021).CAS 
    Article 

    Google Scholar 
    Zhou, Q. J. et al. Simultaneous detection of multiple bacterial and viral aquatic pathogens using a fluorogenic loop-mediated isothermal amplification-based dual-sample microfluidic chip. J. Fish Dis. https://doi.org/10.1111/jfd.13325 (2020).Article 

    Google Scholar 
    Huang, H. L. et al. Molecular method for rapid detection of the red tide dinoflagellate Karenia mikimotoi in the coastal region of Xiangshan Bay, China. J. Microbiol. Methods 168, 7. https://doi.org/10.1016/j.mimet.2019.105801 (2020).CAS 
    Article 

    Google Scholar 
    Sridapan, T. et al. Rapid detection of Clostridium perfringens in food by loop-mediated isothermal amplification combined with a lateral flow biosensor. PLoS ONE 16, 14. https://doi.org/10.1371/journal.pone.0245144 (2021).CAS 
    Article 

    Google Scholar 
    Xiong, X. et al. Using real time fluorescence loop-mediated isothermal amplification for rapid species authentication of Atlantic salmon (Salmo salar). J. Food Compos. Anal. 95, 7. https://doi.org/10.1016/j.jfca.2020.103659 (2021).CAS 
    Article 

    Google Scholar 
    Huang, C. G., Hsu, J. C., Haymer, D. S., Lin, G. C. & Wu, W. J. Rapid identification of the Mediterranean fruit fly (Diptera: Tephritidae) by loop-mediated isothermal amplification. J. Econ. Entomol. 102, 1239–1246 (2009).CAS 
    Article 

    Google Scholar 
    Ide, T., Kanzaki, N., Ohmura, W. & Okabe, K. Molecular identification of an invasive wood-boring insect Lyctus brunneus (Coleoptera: Bostrichidae: Lyctinae) using frass by loop-mediated isothermal amplification and nested PCR assays. J. Econ. Entomol. 109, 1410–1414. https://doi.org/10.1093/jee/tow030 (2016).CAS 
    Article 

    Google Scholar 
    Stainton, K., Hall, J., Budge, G. E., Boonham, N. & Hodgetts, J. Rapid molecular methods for in-field and laboratory identification of the yellow-legged Asian hornet (Vespa velutina nigrithorax). J. Appl. Entomol. 142, 610–616. https://doi.org/10.1111/jen.12506 (2018).CAS 
    Article 

    Google Scholar 
    Agarwal, A., Cunningham, J. P., Valenzuela, I. & Blacket, M. J. A diagnostic LAMP assay for the destructive grapevine insect pest, phylloxera (Daktulosphaira vitifoliae). Sci. Rep. 10, 10. https://doi.org/10.1038/s41598-020-77928-9 (2020).CAS 
    Article 

    Google Scholar 
    Rizzo, D. et al. Molecular identification of Anoplophora glabripennis (Coleoptera: Cerambycidae) from frass by loop-mediated isothermal amplification. J. Econ. Entomol. 113, 2911–2919. https://doi.org/10.1093/jee/toaa206 (2020).CAS 
    Article 

    Google Scholar 
    Hsieh, C. H., Wang, H. Y., Chen, Y. F. & Ko, C. C. Loop-mediated isothermal amplification for rapid identification of biotypes B and Q of the globally invasive pest Bemisia tabaci, and studying population dynamics. Pest Manag. Sci. 68, 1206–1213. https://doi.org/10.1002/ps.3298 (2012).CAS 
    Article 

    Google Scholar 
    Williams, M. R. et al. Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp. PLoS ONE 12, 18. https://doi.org/10.1371/journal.pone.0186462 (2017).CAS 
    Article 

    Google Scholar 
    Ponting, S., Tomkies, V. & Stainton, K. Rapid identification of the invasive small hive beetle (Aethina tumida) using LAMP. Pest Manag. Sci. 77, 1476–1481. https://doi.org/10.1002/ps.6168 (2020).CAS 
    Article 

    Google Scholar 
    Davis, C. N. et al. Rapid detection of Galba truncatula in water sources on pasture-land using loop-mediated isothermal amplification for control of trematode infections. Parasites Vectors 13, 11. https://doi.org/10.1186/s13071-020-04371-0 (2020).CAS 
    Article 

    Google Scholar 
    Carvalho, J. et al. Faster monitoring of the invasive alien species (IAS) Dreissena polymorpha in river basins through isothermal amplification. Sci. Rep. 11, 10. https://doi.org/10.1038/s41598-021-89574-w (2021).CAS 
    Article 

    Google Scholar 
    Treguier, A. et al. Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds. J. Appl. Ecol. 51, 871–879. https://doi.org/10.1111/1365-2664.12262 (2014).CAS 
    Article 

    Google Scholar 
    Cai, W. et al. Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site. PLoS ONE https://doi.org/10.1371/journal.pone.0177724 (2017).Article 

    Google Scholar 
    Wilcox, T. M. et al. Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis. Biol. Conserv. 194, 209–216. https://doi.org/10.1016/j.biocon.2015.12.023 (2016).Article 

    Google Scholar 
    Hunter, M. E., Ferrante, J. A., Meigs-Friend, G. & Ulmer, A. Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques. Sci. Rep. https://doi.org/10.1038/s41598-019-40977-w (2019).Article 

    Google Scholar 
    Twardochleb, L. A., Olden, J. D. & Larson, E. R. A global meta-analysis of the ecological impacts of nonnative crayfish. Freshw. Sci. 32, 1367–1382. https://doi.org/10.1899/12-203.1 (2013).Article 

    Google Scholar 
    Andruszkiewicz, A. E., Zhang, W. G. & Govindarajan, A. F. Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes. Environ. DNA 3, 492–514. https://doi.org/10.1002/edn3.141 (2021).Article 

    Google Scholar 
    Stedtfeld, R. D. et al. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomed. Microdev. 17, 89. https://doi.org/10.1007/s10544-015-9994-1 (2015).CAS 
    Article 

    Google Scholar 
    Koloren, Z., Sotiriadou, I. & Karanis, P. Investigations and comparative detection of Cryptosporidium species by microscopy, nested PCR and LAMP in water supplies of Ordu, Middle Black Sea, Turkey. Ann. Trop. Med. Parasitol. 105, 607–615. https://doi.org/10.1179/2047773211y.0000000011 (2011).CAS 
    Article 

    Google Scholar 
    Sabike, I. I. et al. Use of direct LAMP screening of broiler fecal samples for Campylobacter jejuni and Campylobacter coli in the positive flock identification strategy. Front. Microbiol. 7, 1582. https://doi.org/10.3389/fmicb.2016.01582 (2016).Article 

    Google Scholar 
    Gahlawat, S. K., Ellis, A. E. & Collet, B. A sensitive loop-mediated isothermal amplification (LAMP) method for detection of Renibacterium salmoninarum, causative agent of bacterial kidney disease in salmonids. J. Fish Dis. 32, 491–497. https://doi.org/10.1111/j.1365-2761.2009.01005.x (2009).CAS 
    Article 

    Google Scholar 
    Levy, J. et al. Methods for rapid and effective PCR-based detection of ‘Candidatus Liberibacter solanacearum’ from the insect vector Bactericera cockerelli: Streamlining the DNA extraction/purification process. J. Econ. Entomol. 106, 1440–1445. https://doi.org/10.1603/ec12419 (2013).CAS 
    Article 

    Google Scholar 
    Kaneko, H., Kawana, T., Fukushima, E. & Suzutani, T. Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J. Biochem. Biophys. Methods 70, 499–501. https://doi.org/10.1016/j.jbbm.2006.08.008 (2007).CAS 
    Article 

    Google Scholar 
    Curtis, A. N., Tiemann, J. S., Douglass, S. A., Davis, M. A. & Larson, E. R. High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability. Divers. Distrib. 27, 1918–1931. https://doi.org/10.1111/ddi.13196 (2020).Article 

    Google Scholar 
    Mauvisseau, Q. et al. Environmental DNA as an efficient tool for detecting invasive crayfishes in freshwater ponds. Hydrobiologia 805, 163–175. https://doi.org/10.1007/s10750-017-3288-y (2018).CAS 
    Article 

    Google Scholar 
    RStudioTeam. Boston (ed. PBC) (2020).Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).Book 

    Google Scholar  More

  • in

    Potential negative effects of ocean afforestation on offshore ecosystems

    Bach, L. T. et al. Testing the climate intervention potential of ocean afforestation using the Great Atlantic Sargassum Belt. Nat. Commun. 12, 2556 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    N‘Yeurt, A. D. R., Chynoweth, D. P., Capron, M. E., Stewart, J. R. & Hasan, M. A. Negative carbon via ocean afforestation. Process Saf. Environ. Prot. 90, 467–474 (2012).Article 
    CAS 

    Google Scholar 
    Duarte, C. M., Bruhn, A. & Krause-Jensen, D. A seaweed aquaculture imperative to meet global sustainability targets. Nat. Sustain. 5, 185–193 (2022).Article 

    Google Scholar 
    Woody, T. Seaweed ‘forests’ can help fight climate change. National Geographic https://www.nationalgeographic.co.uk/environment-and-conservation/2019/08/seaweed-forests-can-help-fight-climate-change (2019).Godin, M. The ocean farmers trying to save the world with seaweed. Time https://time.com/5848994/seaweed-climate-change-solution/ (2020).Marshall, M. Kelp is coming: how seaweed could prevent catastrophic climate change. New Scientist https://www.newscientist.com/article/mg24632821-100-kelp-is-coming-how-seaweed-could-prevent-catastrophic-climate-change/ (2020).Bever, F. ‘Run the oil industry in reverse’: fighting climate change by farming kelp. NPR https://www.npr.org/2021/03/01/970670565/run-the-oil-industry-in-reverse-fighting-climate-change-by-farming-kelp (2021).Running Tide. https://www.runningtide.com/ (2022).IPCC: Summary for Policymakers. In Global Warming of 1.5 °C (eds Masson-Delmotte, V. et al.) (WMO, 2018).IPCC: Summary for Policymakers. In Climate Change 2021: The Physical Science Basis (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press) (in the press).GESAMP. High Level Review of a Wide Range of Proposed Marine Geoengineering Techniques (eds Boyd, P. W. & Vivian, C. M. G.) GESAMP Working Group 41 (International Maritime Organization, 2019).Boyd, P. & Vivian, C. Should we fertilize oceans or seed clouds? No one knows. Nature 570, 155–157 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Law, C. S. Predicting and monitoring the impact of large-scale iron fertilisation on marine trace gas emissions. Mar. Ecol. Prog. Ser. 364, 283–288 (2008).CAS 
    Article 

    Google Scholar 
    Russell, L. M. et al. Ecosystem impacts of geoengineering: a review for developing a science plan. Ambio 41, 350–369 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Costello, C., Fries, L. & Gaines, S. Transformational opportunities in ocean-based food & nutrition. Zenodo https://zenodo.org/record/4646319#.YkBFxhPMLAw (2021).Jouffray, J.-B., Blasiak, R., Norström, A. V., Österblom, H. & Nyström, M. The blue acceleration: the trajectory of human expansion into the ocean. One Earth 2, 43–54 (2020).Article 

    Google Scholar 
    Cullen, J. J. & Boyd, P. W. Predicting and verifying the intended and uninterested consequence of large-scale iron fertilization. Mar. Ecol. Prog. Ser. 364, 295–301 (2008).CAS 
    Article 

    Google Scholar 
    Bach, L. T., Gill, S. J., Rickaby, R. E. M., Gore, S. & Renforth, P. CO2 removal with enhanced weathering and ocean alkalinity enhancement: potential risks and co-benefits for marine pelagic ecosystems. Front. Clim. https://doi.org/10.3389/fclim.2019.00007 (2019).Moore, C. M. et al. Processes and patterns of oceanic nutrient limitation. Nat. Geosci. 6, 701–710 (2013).CAS 
    Article 

    Google Scholar 
    Suchet, P. A., Probst, J.-L. & Ludwig, L. Worldwide distribution of continental rock lithology: implications for the atmospheric/soil CO2 uptake by continental weathering and alkalinity river transport to the oceans. Glob. Biogeochem. Cycles 17, 1038 (2003).
    Google Scholar 
    Macreadie, P. I. et al. The future of blue carbon science. Nat. Commun. 10, 3998 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Fraser, C. I., Nikula, R. & Waters, J. M. Oceanic rafting by a coastal community. Proc. Biol. Sci. 278, 649–655 (2011).PubMed 

    Google Scholar 
    Fraser, C. I., Davies, I. D., Bryant, D. & Waters, J. M. How disturbance and dispersal influence intraspecific structure. J. Ecol. 106, 1298–1306 (2018).Article 

    Google Scholar 
    Fraser, C. I. et al. Antarctica’s ecological isolation will be broken by storm-driven dispersal and warming. Nat. Clim. Change 8, 704–708 (2018).Article 

    Google Scholar 
    Chung, I. K., Beardall, J., Mehta, S., Sahoo, D. & Stojkovic, S. Using marine macroalgae for carbon sequestration: a critical appraisal. J. Appl. Phycol. 23, 877–886 (2011).CAS 
    Article 

    Google Scholar 
    Krause-Jensen, D. & Duarte, C. M. Substantial role of macroalgae in marine carbon sequestration. Nat. Geosci. 9, 737–742 (2016).CAS 
    Article 

    Google Scholar 
    Hurd, C. L. et al. Forensic carbon accounting: assessing the role of seaweeds for carbon sequestration. J. Phycol., https://doi.org/10.1111/jpy.13249 (2022).Stripe commits $8M to six new carbon removal companies. Stripe https://stripe.com/newsroom/news/spring-21-carbon-removal-purchases (2021).General application. Stripe https://github.com/stripe/carbon-removal-source-materials/blob/master/Project%20Applications/Spring2021/Running%20Tide%20-%20Stripe%20Spring21%20CDR%20Purchase%20Application.pdf (2021).Coston-Clements, L. Utilization of the Sargassum Habitat by Marine Invertebrates and Vertebrates: a Review. NOAA Technical Memorandum NMFS-SEFSC, 296 (U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southeast Fisheries Science Center & Beaufort Laboratory, 1991).Egan, S. et al. The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol. Rev. 37, 462–476 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Califano, G., Kwantes, M., Abreu, M. H., Costa, R. & Wichard, T. Cultivating the macroalgal holobiont: effects of integrated multi-trophic aquaculture on the microbiome of Ulva rigida (Chlorophyta)Front. Mar. Sci. 7, 52 (2020).Article 

    Google Scholar 
    Selvarajan, R. et al. Distribution, interaction and functional profiles of epiphytic bacterial communities from the rocky intertidal seaweeds, South Africa. Sci. Rep. 9, 19835 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bonthond, G. et al. The role of host promiscuity in the invasion process of a seaweed holobiont. ISME J. 15, 1668–1679 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, M. et al. The great Atlantic Sargassum belt. Science 365, 83–87 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Johns, E. M. et al. The establishment of a pelagic Sargassum population in the tropical Atlantic: biological consequences of a basin-scale long distance dispersal event. Prog. Oceanogr. 182, 102269 (2020).Article 

    Google Scholar 
    Martiny, A. C. et al. Biogeochemical controls of surface ocean phosphate. Sci. Adv. 5, eaax0341 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zehr, J. P. & Capone, D. G. Changing perspectives in marine nitrogen fixation. Science 368, eaay9514 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Harrison, P. J., Druehl, L. D., Lloyd, K. E. & Thompson, P. A. Nitrogen uptake kinetics in three year-classes of Laminaria groenlandica (Laminariales: Phaeophyta). Mar. Biol. 93, 29–35 (1986).CAS 
    Article 

    Google Scholar 
    Hurd, C. L. & Dring, M. L. Phosphate uptake by intertidal algae in relation to zonation and season. Mar. Biol. 107, 281–289 (1990).Article 

    Google Scholar 
    Ohtake, M. et al. Growth and nutrient uptake characteristics of Sargassum macrocarpum cultivated with phosphorus-replete wastewater. Aquat. Bot. 163, 103208 (2020).Article 

    Google Scholar 
    MacFarlane, J. J. & Raven, J. A. C, N and P nutrition of Lemanea mamillosa Kütz. (Batrachospermales, Rhodophyta) in the Dighty Burn, Angus, U.K. Plant Cell Environ. 13, 1–13 (1990).CAS 
    Article 

    Google Scholar 
    Wu, J., Keller, D. P. & Oschlies, A. Carbon dioxide removal via macroalgae open-ocean mariculture and sinking: an Earth system modeling study. Preprint at Earth System Dynamics Discuss https://doi.org/10.5194/esd-2021-104 (2022).Kwiatkowski, L. et al. Twenty-first century ocean warming, acidification, deoxygenation, and upper-ocean nutrient and primary production decline from CMIP6 model projections. Biogeosciences 17, 3439–3470 (2020).CAS 
    Article 

    Google Scholar 
    Chapman, A. R. O. & Craigie, J. S. Seasonal growth in Laminaria longicruris: relations with dissolved inorganic nutrients and internal reserves of nitrogen. Mar. Biol. 40, 197–205 (1977).CAS 
    Article 

    Google Scholar 
    Dutkiewicz, S., Scott, J. R. & Follows, M. J. Winners and losers: ecological and biogeochemical changes in a warming ocean. Glob. Biogeochem. Cycles 27, 463–477 (2013).CAS 
    Article 

    Google Scholar 
    Thomas, M. K. et al. Temperature–nutrient interactions exacerbate sensitivity to warming in phytoplankton. Glob. Change Biol. 2, 3269–3280 (2017).Article 

    Google Scholar 
    Lapointe, B. E. et al. Nutrient content and stoichiometry of pelagic Sargassum reflects increasing nitrogen availability in the Atlantic Basin. Nat. Commun. 12, 3060 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Fan, W. et al. A sea trial of enhancing carbon removal from Chinese coastal waters by stimulating seaweed cultivation through artificial upwelling. Appl. Ocean Res. 101, 102260 (2020).Article 

    Google Scholar 
    Karl, D. M. & Letelier, R. M. Nitrogen fixation-enhanced carbon sequestration in low nitrate, low chlorophyll seascapes. Mar. Ecol. Prog. Ser. 364, 257–268 (2008).CAS 
    Article 

    Google Scholar 
    Oschlies, A. S., Pahlow, M., Yool, A. & Matear, R. Climate engineering by artificial ocean upwelling: channelling the sorcerer’s apprentice. Geophys. Res. Lett. 37, L04701 (2010).Article 
    CAS 

    Google Scholar 
    Thornton, D. C. O. Dissolved organic matter (DOM) release by phytoplankton in the contemporary and future ocean. Eur. J. Phycol. 49, 20–46 (2014).CAS 
    Article 

    Google Scholar 
    Morán, X. A. G., Sebastián, M., Pedrós-Alió, C. & Estrada, M. Response of Southern Ocean phytoplankton and bacterioplankton production to short-term experimental warming. Limnol. Oceanogr. 51, 1791–1800 (2006).Article 

    Google Scholar 
    Marañón, E., Cermeño, P., Fernández, E., Rodríguez, J. & Zabala, L. Significance and mechanisms of photosynthetic production of dissolved organic carbon in a coastal eutrophic ecosystem. Limnol. Oceanogr. 49, 1652–1666 (2004).Article 

    Google Scholar 
    Paine, E. R., Schmid, M., Boyd, P. W., Diaz-Pulido, G. & Hurd, C. L. Rate and fate of dissolved organic carbon release by seaweeds: a missing link in the coastal ocean carbon cycle. J. Phycol. 57, 1375–1391 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Brylinsky, M. Release of dissolved organic matter by some marine macrophytes. Mar. Biol. 39, 213–220 (1977).Article 

    Google Scholar 
    Sieburth, J. M. Studies on algal substances in the sea. III. The production of extracellular organic matter by littoral marine algae. J. Exp. Mar. Biol. Ecol. 3, 290–309 (1969).CAS 
    Article 

    Google Scholar 
    Hanson, R. B. Pelagic Sargassum community metabolism: carbon and nitrogen. J. Exp. Mar. Biol. Ecol. 29, 107–118 (1977).CAS 
    Article 

    Google Scholar 
    Zark, M., Riebesell, U. & Dittmar, T. Effects of ocean acidification on marine dissolved organic matter are not detectable over the succession of phytoplankton blooms. Sci. Adv. 1, e1500531 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Zhang, Y., Liu, X., Wang, M. & Qin, B. Compositional differences of chromophoric dissolved organic matter derived from phytoplankton and macrophytes. Org. Geochem. 55, 26–37 (2013).Article 
    CAS 

    Google Scholar 
    Hulatt, C. J., Thomas, D. N., Bowers, D. G., Norman, L. & Zhang, C. Exudation and decomposition of chromophoric dissolved organic matter (CDOM) from some temperate macroalgae. Estuar. Coast. Shelf Sci. 84, 147–153 (2009).CAS 
    Article 

    Google Scholar 
    Liu, S., Trevathan-Tackett, S. M., Ewers Lewis, C. J., Huang, X. & Macreadie, P. I. Macroalgal blooms trigger the breakdown of seagrass blue carbon. Environ. Sci. Technol. 54, 14750–14760 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Vieira, H. C. et al. Ocean warming may enhance biochemical alterations induced by an invasive seaweed exudate in the mussel Mytilus galloprovincialis. Toxics 9, 121 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brooks, S. D. & Thornton, D. C. O. Marine aerosols and clouds. Ann. Rev. Mar. Sci. 10, 289–313 (2018).PubMed 
    Article 

    Google Scholar 
    Lewis, M. R., Carr, M.-E., Feldman, G. C., Esaias, W. & McClain, C. Influence of penetrating solar radiation on the heat budget of the equatorial Pacific Ocean. Nature 347, 543–545 (1990).Article 

    Google Scholar 
    Morel, A. Optical modeling of the upper ocean in relation to its biogenous matter content (case-I waters). J. Geophys. Res. 93, 10749–10768 (1988).Article 

    Google Scholar 
    Park, J.-Y., Kug, J.-S., Bader, J., Rolph, R. & Kwon, M. Amplified Arctic warming by phytoplankton under greenhouse warming. Proc. Natl Acad. Sci. USA 112, 5921–5926 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Denaro, G. et al. Dynamics of two picophytoplankton groups in Mediterranean Sea: analysis of the deep chlorophyll maximum by a stochastic advection-reaction-diffusion model. PLoS ONE 8, e66765 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kavanaugh, M. T. et al. Experimental assessment of the effects of shade on an intertidal kelp: do phytoplankton blooms inhibit growth of open-coast macroalgae? Limnol. Oceanogr. 54, 276–288 (2009).Article 

    Google Scholar 
    Omand, M. M., Steinberg, D. K. & Stamies, K. Cloud shadows drive vertical migrations of deep-dwelling marine life. Proc. Natl Acad. Sci. USA 118, e2022977118 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bach, L. T. & Boyd, P. W. Seeking natural analogs to fast-forward the assessment of marine CO2 removal. Proc. Natl Acad. Sci. USA 118, e2106147118 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    van Donk, E. & van de Bund, W. J. Impact of submerged macrophytes including charophytes on phyto- and zooplankton communities: allelopathy versus other mechanisms. Aquat. Bot. 72, 261–274 (2002).Article 

    Google Scholar 
    Jin, Q., Dong, S. & Wang, C. Allelopathic growth inhibition of Prorocentrum micans (Dinophyta) by Ulva pertusa and Ulva linza (Chlorophyta) in laboratory cultures. Eur. J. Phycol. 40, 31–37 (2005).Article 

    Google Scholar 
    Wallace, R. B. & Gobler, C. J.Factors controlling blooms of microalgae and macroalgae (Ulva rigida) in a eutrophic, urban estuary: Jamaica Bay, NY, USA. Estuaries Coast 38, 519–533 (2015).CAS 
    Article 

    Google Scholar 
    Tang, Y. Z. & Gobler, C. J. The green macroalga, Ulva lactuca, inhibits the growth of seven common harmful algal bloom species via allelopathy. Harmful Algae 10, 480–488 (2011).Article 

    Google Scholar 
    Cagle, S. E., Roelke, D. L. & Muhl, R. W. Allelopathy and micropredation paradigms reconcile with system stoichiometry. Ecosphere 12, e03372 (2021).Article 

    Google Scholar 
    Hein, M., Pedersen, M. F. & Sand-Jensen, K. Size-dependent nitrogen uptake in micro- and macroalgae. Mar. Ecol. Prog. Ser. 118, 247–253 (1995).Article 

    Google Scholar 
    Stevens, C. L., Hurd, C. L. & Smith, M. J. Water motion relative to subtidal kelp fronds. Limnol. Oceanogr. 46, 668–678 (2001).Article 

    Google Scholar 
    Raut, Y., Morando, M. & Capone, D. G. Diazotrophic macroalgal associations with living and decomposing Sargassum. Front. Microbiol. 9, 3127 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Villareal, T. A., Woods, S., Moore, J. K. & CulverRymsza, K. Vertical migration of Rhizosolenia mats and their significance to NO3− fluxes in the central North Pacific gyre. J. Plankton Res. 18, 1103–1121 (1996).Article 

    Google Scholar 
    Gachon, C. M. M., Sime-Ngando, T., Strittmatter, M., Chambouvet, A. & Kim, G. H. Algal diseases: spotlight on a black box. Trends Plant Sci. 15, 633–640 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sánchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol. 30, 143–157 (2022).PubMed 
    Article 
    CAS 

    Google Scholar 
    Thiel, M. & Gutow, L. in Oceanography and Marine Biology: an Annual Review Vol. 43 (eds Gibson, R. et al.) 279–418 (Taylor & Francis, 2005).Rech, S., Borrell Pichs, Y. J. & García-Vazquez, E. Anthropogenic marine litter composition in coastal areas may be a predictor of potentially invasive rafting fauna. PLoS ONE 13, e0191859 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Food and Agriculture Organization (FAO) of the United Nations. The State of World Fisheries and Aquaculture 2020: Sustainability in Action (FAO, 2020).Schell, J. M., Goodwin, D. S. & Siuda, A. N. S. Recent Sargassum inundation events in the Caribbean: shipboard observations reveal dominance of a previously rare form. Oceanography 28, 8–10 (2015).Article 

    Google Scholar 
    Rodríguez-Martínez, R. E. et al. Element concentrations in pelagic Sargassum along the Mexican Caribbean coast in 2018–2019. Peer J. 8, e8667 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Flannery, T. How farming giant seaweed can feed fish and fix the climate. The Conversation Trust https://theconversation.com/how-farming-giant-seaweed-can-feed-fish-and-fix-the-climate-81761 (2017).GESAMP. Methodology for the Evaluation of Ballast Water Management Systems Using Active Substances. GESAMP No. 101 (eds Linders, J. & Dock, A.) (International Maritime Organization, 2019).Lenton, A., Boyd, P. W., Thatcher, M. & Emmerson, K. M. Foresight must guide geoengineering research and development. Nat. Clim. Change 9, 342 (2019).Article 

    Google Scholar 
    Sumaila, U. R. Financing a sustainable ocean economy. Nat. Commun. 12, 3259 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rockström, J. et al. Planetary boundaries: exploring the safe operating space for humanity. Ecol. Soc. 14, 32 (2009).Article 

    Google Scholar 
    Rech, S., Salmina, S., Borrell Pichs, Y. J. & García-Vazquez, E. Dispersal of alien invasive species on anthropogenic litter from European mariculture areas. Mar. Pollut. Bull. 131, 10–16 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Therriault, T. W. et al. The invasion risk of species associated with Japanese tsunami marine debris in Pacific North America and Hawaii. Mar. Pollut. Bull. 132, 82–89 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Miller, J. A., Carlton, J. T., Chapman, J. W., Geller, J. B. & Ruiz, G. M. Transoceanic dispersal of the mussel Mytilus galloprovincialis on Japanese tsunami marine debris: an approach for evaluating rafting of a coastal species at sea. Mar. Pollut. Bull. 132, 60–69 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Carlton, J. T. et al. Tsunami-driven rafting: transoceanic species dispersal and implications for marine biogeography. Science 357, 1402–1406 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hunt, G. L. Jr et al. Advection in polar and sub-polar environments: impacts on high latitude marine ecosystems. Prog. Oceanogr. 149, 40–81 (2016).Article 

    Google Scholar 
    Hallegraeff, G. M. & Bolch, C. J. Transport of dinoflagellate cysts in ship’s ballast water: implications for plankton biogeography and aquaculture. J. Plankton Res. 14, 1067–1084 (1992).Article 

    Google Scholar 
    Russell, L. K., Hepburn, C. D., Hurd, C. L. & Stuart, M. D. The expanding range of Undaria pinnatifida in southern New Zealand: distribution, dispersal mechanisms and the invasion of wave-exposed environments. Biol. Invasions 10, 103–115 (2008).Article 

    Google Scholar 
    Uwai, S. et al. Genetic diversity in Undaria pinnatifida (Laminariales, Phaeophyceae) deduced from mitochondria genes—origins and succession of introduced populations. Phycologia 45, 687–695 (2006).Article 

    Google Scholar  More

  • in

    Evaluation of hair cortisol as an indicator of long-term stress responses in dogs in an animal shelter and after subsequent adoption

    Beerda, B., Schilder, M. B. H., Van Hooff, J. A., De Vries, H. W. & Mol, J. A. Chronic stress in dogs subjected to social and spatial restriction I. Behavioral responses. Physiol. Behav. 66, 233–242 (1999).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rooney, N. J., Gaines, S. A. & Bradshaw, J. W. Behavioural and glucocorticoid responses of dogs (Canis familiaris) to kennelling: investigating mitigation of stress by prior habituation. Physiol. Behav. 92, 847–854. https://doi.org/10.1016/j.physbeh.2007.06.011 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stephen, J. M. & Ledger, R. A. A longitudinal evaluation of urinary cortisol in kennelled dogs Canis familiaris. Physiol. Behav. 87, 911–916. https://doi.org/10.1016/j.physbeh.2006.02.015 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Mills, D., Karagiannis, C., Zulch, H. Stress its effects on health and behavior. Vet. Clin. North Am. Small Anim. Pract. 44, 525–541 (2014).Mormède, P. et al. Exploration of the hypothalamic–pituitary–adrenal function as a tool to evaluate animal welfare. Physiol. Behav. 92, 317–339 (2007).PubMed 
    Article 

    Google Scholar 
    Hennessy, M. B. Using hypothalamic–pituitary–adrenal measures for assessing and reducing the stress of dogs in shelters: A review. Appl. Anim. Behav. Sci. 149, 1–12 (2013).Article 

    Google Scholar 
    Cobb, M. L., Iskandarani, K., Chinchilli, V. M. & Dreschel, N. A. A systematic review and meta-analysis of salivary cortisol measurement in domestic canines. Domest. Anim. Endocrinol. 57, 31–42 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wester, V. L. & van Rossum, E. F. Clinical applications of cortisol measurements in hair. Eur. J. Endocrinol. 173, M1–M10 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Heimbürge, S., Kanitz, E. & Otten, W. The use of hair cortisol for the assessment of stress in animals. Gen. Comp. Endocrinol. 270, 10–17 (2019).PubMed 
    Article 

    Google Scholar 
    Meyer, J. S. & Novak, M. A. Minireview: hair cortisol: A novel biomarker of hypothalamic-pituitary-adrenocortical activity. Endocrinology 153, 4120–4127 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Khoury, J. E., Bosquet Enlow, M., Plamondon, A. & Lyons-Ruth, K. The association between adversity and hair cortisol levels in humans: A meta-analysis. Psychoneuroendocrinology 103, 104–117 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Davenport, M. D., Tiefenbacher, S., Lutz, C. K., Novak, M. A. & Meyer, J. S. Analysis of endogenous cortisol concentrations in the hair of rhesus macaques. Gen. Comp. Endocrinol. 147, 255–261 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Greff, M. J. E. et al. Hair cortisol analysis: An update on methodological considerations and clinical applications. Clin. Biochem. 63, 1–9 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    del Rosario, G. et al. Effects of adrenocorticotropic hormone challenge and age on hair cortisol concentrations in dairy cattle. Can. J. Vet. Res. 75, 216–221 (2011).
    Google Scholar 
    Macbeth, B. J., Cattet, M., Stenhouse, G. B., Gibeau, M. L. & Janz, D. M. Hair cortisol concentration as a noninvasive measure of long-term stress in free-ranging grizzly bears (Ursus arctos): considerations with implications for other wildlife. Can. J. Zool. 88, 935–949 (2010).CAS 
    Article 

    Google Scholar 
    Accorsi, P. A. et al. Cortisol determination in hair and faeces from domestic cats and dogs. Gen. Comp. Endocrinol. 155, 398–402 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bennett, A. & Hayssen, V. Measuring cortisol in hair and saliva from dogs: coat color and pigment differences. Domest. Anim. Endocrinol. 39, 171–180 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bryan, H. M., Adams, A. G., Invik, R. M., Wynne-Edwards, K. E. & Smits, J. E. Hair as a meaningful measure of baseline cortisol levels over time in dogs. J. Am. Assoc. Lab. Anim. Sci. 52, 189–196 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Siniscalchi, M., McFarlane, J. R., Kauter, K. G., Quaranta, A. & Rogers, L. J. Cortisol levels in hair reflect behavioural reactivity of dogs to acoustic stimuli. Res. Vet. Sci. 94, 49–54 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Stella, J., Shreyer, T., Ha, J. & Croney, C. Improving canine welfare in commercial breeding (CB) operations: Evaluating rehoming candidates. Appl. Anim. Behav. Sci. 220, 104861. https://doi.org/10.1016/j.applanim.2019.104861 (2019).Article 

    Google Scholar 
    Nicholson, S. L. & Meredith, J. E. Should stress management be part of the clinical care provided to chronically ill dogs?. J. Vet. Behav. 10, 489–495 (2015).Article 

    Google Scholar 
    Maxwell, N., Buchanan, C. & Evans, N. Hair cortisol concentrations, as a measure of chronic activity within the hypothalamic-pituitary-adrenal axis, is elevated in dogs farmed for meat, relative to pet dogs South Korea. Anim. Welf. 28, 389–395 (2019).Article 

    Google Scholar 
    Roth, L. S., Faresjö, Å, Theodorsson, E., Jensen, P. Hair cortisol varies with season and lifestyle and relates to human interactions in German shepherd dogs. Sci. Rep. 6, 19631; https://doi.org/10.1038/srep19631 (2016).Packer, R. M. et al. What can we learn from the hair of the dog? Complex effects of endogenous and exogenous stressors on canine hair cortisol. PLoS ONE 14, e0216000. https://doi.org/10.1371/journal.pone.0216000 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sundman, A. et al. Long-term stress levels are synchronized in dogs and their owners. Sci. Rep. 9, 7391; https://doi.org/10.1038/s41598-019-43851-x (2019).Höglin, A. et al. Long-term stress in dogs is related to the human-dog relationship and personality traits. Sci. Rep. 11, 8612; https://doi.org/10.1038/s41598-021-88201-y (2021).Bowland, G. B. et al. Fur color and nutritional status predict hair cortisol concentrations of dogs in Nicaragua. Front. Vet. Sci. 7, 565346. https://doi.org/10.3389/fvets.2020.565346 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Veronesi, M. C. et al. Coat and claws as new matrices for noninvasive long-term cortisol assessment in dogs from birth up to 30 days of age. Theriogenology 84, 791–796 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Davenport, M. D., Lutz, C. K., Tiefenbacher, S., Novak, M. A. & Meyer, J. S. A rhesus monkey model of self-injury: Effects of relocation stress on behavior and neuroendocrine function. Biol. Psychiatry 63, 990–996 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    van der Laan, J. E., Vinke, C. M., van der Borg, J. A. M. & Arndt, S. S. Restless nights? Nocturnal activity as a useful indicator of adaptability of shelter housed dogs. Appl. Anim. Behav. Sci. 241, 105377. https://doi.org/10.1016/j.applanim.2021.105377 (2021).Article 

    Google Scholar 
    Pollinger, J. P. et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898–902 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Voith, V. L., Ingram, E., Mitsouras, K. & Irizarry, K. Comparison of adoption agency breed identification and DNA breed identification of dogs. J. Appl. Anim. Welf. Sci. 12, 253–262 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gunter, L. M., Barber, R. T. & Wynne, C. D. L. A canine identity crisis: Genetic breed heritage testing of shelter dogs. PLoS ONE 13, e0202633. https://doi.org/10.1371/journal.pone.0202633 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pinheiro, J., Bates, D., DebRoy, S. & Sarkar, D., R Core Team. Nlme: linear and nonlinear mixed effects models. R package version 3. 1–148 (2020).Protopopova, A. & Gunter, L. Adoption and relinquishment interventions at the animal shelter: a review. Anim. Welf. 26, 35–48 (2017).Article 

    Google Scholar 
    Müntener, T., Doherr, M. G., Guscetti, F., Suter, M. M. & Welle, M. M. The canine hair cycle – a guide for the assessment of morphological and immunohistochemical criteria. Vet. Dermatol. 22, 383–395 (2011).PubMed 
    Article 

    Google Scholar 
    Wennig, R. Potential problems with the interpretation of hair analysis results. Forensic Sci. Int. 107, 5–12 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Heimbürge, S., Kanitz, E., Tuchscherer, A. & Otten, W. Within a hair’s breadth – Factors influencing hair cortisol levels in pigs and cattle. Gen. Comp. Endocrinol. 288, 113359. https://doi.org/10.1016/j.ygcen.2019.113359 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Diaz, S. F., Torres, S. M., Dunstan, R. W. & Lekcharoensuk, C. An analysis of canine hair re-growth after clipping for a surgical procedure. Vet. Dermatol. 15, 25–30 (2004).PubMed 
    Article 

    Google Scholar 
    Zeugswetter, F., Bydzovsky, N., Kampner, D. & Schwendenwein, I. Tailored reference limits for urine corticoid:creatinine ratio in dogs to answer distinct clinical questions. Vet. Rec. 167, 997–1001 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jones, S. et al. Use of accelerometers to measure stress levels in shelter dogs. J. Appl. Anim. Welf. Sci. 17, 18–28 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gunter, L. M., Feuerbacher, E. N., Gilchrist, R. J. & Wynne, C. D. Evaluating the effects of a temporary fostering program on shelter dog welfare. PeerJ 7, e6620. https://doi.org/10.7717/peerj.6620 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Van den Brom, W. E. & Biewenga, W. J. Assessment of glomerular filtration rate in normal dogs: analysis of the 51Cr-EDTA clearance and its relation to several endogenous parameters of glomerular filtration. Res. Vet. Sci. 30, 152–157 (1981).PubMed 
    Article 

    Google Scholar 
    Sandri, M., Colussi, A., Perrotta, M. G. & Stefanon, B. Salivary cortisol concentration in healthy dogs is affected by size, sex, and housing context. J. Vet. Behav. 10, 302–306 (2015).Article 

    Google Scholar 
    Haase, C. G., Long, A. K. & Gillooly, J. F. Energetics of stress: linking plasma cortisol levels to metabolic rate in mammals. Biol. Lett. 12, 20150867. https://doi.org/10.1098/rsbl.2015.0867 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Garnier, F., Benoit, E., Virat, M., Ochoa, R. & Delatour, P. Adrenal cortical response in clinically normal dogs before and after adaptation to a housing environment. Lab. Anim. 24, 40–43 (1990).CAS 
    PubMed 
    Article 

    Google Scholar 
    Beerda, B. et al. Chronic stress in dogs subjected to social and spatial restriction. II. Hormonal and immunological responses. Physiol. Behav. 66, 243–254 (1999).Rincón-Cortés, M., Herman, J. P., Lupien, S., Maguire, J. & Shansky, R. M. Stress: Influence of sex, reproductive status and gender. Neurobiol. Stress 10, 100155. https://doi.org/10.1016/j.ynstr.2019.100155 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oyola, M. G. & Handa, R. J. Hypothalamic–pituitary–adrenal and hypothalamic–pituitary–gonadal axes: sex differences in regulation of stress responsivity. Stress 20, 476–494 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Willen, R. M., Mutwill, A., MacDonald, L. J., Schiml, P. A. & Hennessy, M. B. Factors determining the effects of human interaction on the cortisol levels of shelter dogs. Appl. Anim. Behav. Sci. 186, 41–48 (2017).Article 

    Google Scholar 
    Protopopova, A. Effects of sheltering on physiology, immune function, behavior, and the welfare of dogs. Physiol. Behav. 159, 95–103 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Mesarcova, L., Kottferova, J., Skurkova, L., Leskova, L. & Kmecova, N. Analysis of cortisol in dog hair-a potential biomarker of chronic stress: a review. Vet. Med. (Praha) 62, 363–376 (2017).CAS 
    Article 

    Google Scholar 
    Neumann, A. et al. Predicting hair cortisol levels with hair pigmentation genes: a possible hair pigmentation bias. Sci. Rep. 7, 8529 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Romero, L. M. & Beattie, U. K. Common myths of glucocorticoid function in ecology and conservation. J. Exp. Zool. A. Ecol. Integr. Physiol. https://doi.org/10.1002/jez.2459 (2021).PubMed 
    Article 

    Google Scholar 
    Heimbürge, S., Kanitz, E., Tuchscherer, A. & Otten, W. Is it getting in the hair? – Cortisol concentrations in native, regrown and segmented hairs of cattle and pigs after repeated ACTH administrations. Gen. Comp. Endocrinol. 295, 113534. https://doi.org/10.1016/j.ygcen.2020.113534 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Van Ockenburg, S. L. et al. The relationship between 63 days of 24-h urinary free cortisol and hair cortisol levels in 10 healthy individuals. Psychoneuroendocrinology 73, 142–147 (2016).PubMed 
    Article 

    Google Scholar 
    Short, S. J. et al. Correspondence between hair cortisol concentrations and 30-day integrated daily salivary and weekly urinary cortisol measures. Psychoneuroendocrinology 71, 12–18 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mack, Z. & Fokidis, H. B. A novel method for assessing chronic cortisol concentrations in dogs using the nail as a source. Domest. Anim. Endocrinol. 59, 53–57 (2017).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Heterogeneous effects of climatic conditions on Andean bean landraces and cowpeas highlight alternatives for crop management and conservation

    A summary describing all plant architecture, flower, fruit, and yield, and phenological traits for each of the thirteen Phaseolus sp. and Vigna sp. landraces in the open field and the greenhouse conditions is provided in Supporting Tables S3, S4 and S5. Main effects Kruskal–Wallis tests are summarised in Table 1, and the interactions between treatment conditions (open field and greenhouse) and species, and landrace and climatic background are summarised in Table 2.Table 1 Main effects Kruskal–Wallis H tests for treatment (open field vs greenhouse conditions), species, landrace, and climatic background of the landraces.Full size tableTable 2 Kruskal–Wallis H tests for the interactions between treatment (open field and greenhouse) and species, landrace, or the climatic background.Full size tableI. Plant architecturePlants under high temperatures and low humidity in the greenhouse exhibited significant higher overall mean rank values than field plants for stem diameter, the degree of branch orientation, composite sheet length and width, and the terminal leaflet length. The size of the angle of the base of the terminal leaflet, however, was bigger in the field (Supporting Tables S3 and Table 1). There were overall significant differences for species and landrace for all studied characters (Table 1). The Kruskal–Wallis analyses of the interactions between treatment (open field vs greenhouse conditions) and species, climatic background, and landrace were significant for all the traits (p-value  More

  • in

    Home range size and habitat quality affect breeding success but not parental investment in barn owl males

    Stearns, S. C. The Evolution of Life Histories (Oxford University, 1992).
    Google Scholar 
    Roff, D. A., Mostowy, S. & Fairbairn, D. J. The evolution of trade-offs: Testing predictions on response to selection and environmental variation. Evolution (N. Y.). 56, 84–95 (2002).
    Google Scholar 
    Lack, D. The Significance of Clutch-size. Ibis (Lond. 1859). 89, 302–352 (1947).Article 

    Google Scholar 
    Drent, R. H. & Daan, S. The prudent parent: Energetic adjustments in avian breeding. Adrea 68, 225–263 (1980).
    Google Scholar 
    Harshman, L. G. & Zera, A. J. The cost of reproduction: The devil in the details. Trends Ecol. Evol. 22, 80–86 (2007).Article 

    Google Scholar 
    Dijkstra, C., Daan, S. & Tinbergen, J. M. Family planning in the Kestrel (Falco Tinnunculus): The ultimate control of covariation of laying date and clutch size. Behaviour 114, 83–116 (1990).Article 

    Google Scholar 
    Cox, R. M. et al. Experimental evidence for physiological costs underlying the trade-off between reproduction and survival. Funct. Ecol. 24, 1262–1269 (2010).Article 

    Google Scholar 
    Marshall, K. E. & Sinclair, B. J. Repeated stress exposure results in a survival-reproduction trade-off in Drosophila melanogaster. Proc. R. Soc. B Biol. Sci. 277, 963–969 (2010).Article 

    Google Scholar 
    Rivalan, P. et al. Trade-off between current reproductive effort and delay to next reproduction in the leatherback sea turtle. Oecologia 145, 564–574 (2005).ADS 
    Article 

    Google Scholar 
    Perrins, C. M. Population Fluctuations and Clutch-Size in the Great Tit, Parus major. J. Anim. Ecol. 34, 601 (1965).Article 

    Google Scholar 
    Walker, R. S., Gurven, M., Burger, O. & Hamilton, M. J. The trade-off between number and size of offspring in humans and other primates. Proc. R. Soc. B Biol. Sci. 275, 827–833 (2008).Article 

    Google Scholar 
    Williams, G. C. Natural selection, the costs of reproduction, and a refinement of Lack’s principle. Am. Nat. 100, 687–690 (1966).Article 

    Google Scholar 
    Charnov, E. L. & Krebs, J. R. On clutch-size and fitness. Ibis (Lond. 1859). 116, 217–219 (1974).Article 

    Google Scholar 
    Ricklefs, R. E. On the evolution of reproductive strategies in birds: Reproductive effort. Am. Nat. 111, 453–478 (1977).Article 

    Google Scholar 
    Martin, T. E. Food as a limit on breeding birds: A life-history perspective. Annu. Rev. Ecol. Syst. 18, 435–487 (1987).Article 

    Google Scholar 
    Santangeli, A., Hakkarainen, H., Laaksonen, T. & Korpimäki, E. Home range size is determined by habitat composition but feeding rate by food availability in male Tengmalm’s owls. Anim. Behav. 83, 1115–1123 (2012).Article 

    Google Scholar 
    Kouba, M., Bartoš, L., Sindelář, J. & St’astny, K. Alloparental care and adoption in Tengmalm’s Owl (Aegolius funereus). J. Ornithol. 158, 185–191 (2017).Article 

    Google Scholar 
    Redpath, S. M. Habitat fragmentation and the individual: Tawny owls Strix aluco in woodland patches. J. Anim. Ecol. 64, 652 (1995).Article 

    Google Scholar 
    Bruun, M. & Smith, H. G. Landscape composition affects habitat use and foraging flight distances in breeding European starlings. Biol. Conserv. 114, 179–187 (2003).Article 

    Google Scholar 
    Frey-Roos, F., Brodmann, P. A. & Reyer, H. U. Relationships between food resources, foraging patterns, and reproductive success in the water pipit, Anthus sp. Spinoletta. Behav. Ecol. 6, 287–295 (1995).Article 

    Google Scholar 
    Saïd, S. et al. What shapes intra-specific variation in home range size? A case study of female roe deer. Oikos 118, 1299–1306 (2009).Article 

    Google Scholar 
    Van Beest, F. M., Rivrud, I. M., Loe, L. E., Milner, J. M. & Mysterud, A. What determines variation in home range size across spatiotemporal scales in a large browsing herbivore?. J. Anim. Ecol. 80, 771–785 (2011).Article 

    Google Scholar 
    Hakkarainen, H., Koivunen, V. & Korpimäki, E. Reproductive success and parental effort of Tengmalm’s owls: Effects of spatial and temporal variation in habitat quality. Ecoscience 4, 35–42 (1997).Article 

    Google Scholar 
    Kittle, A. M. et al. Wolves adapt territory size, not pack size to local habitat quality. J. Anim. Ecol. 84, 1177–1186 (2015).Article 

    Google Scholar 
    Trembley, 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 (2004).Article 

    Google Scholar 
    Turcotte, Y. & Desrochers, A. Landscape-dependent response to predation risk by forest birds. Oikos 100, 614–618 (2003).Article 

    Google Scholar 
    Hinsley, S. A., Rothery, P. & Bellamy, P. E. Influence of woodland area on breeding success in great tits parus major and blue tits Parus caeruleus. J. Avian Biol. 30, 271 (1999).Article 

    Google Scholar 
    Hinam, H. L. & Clair, C. C. S. High levels of habitat loss and fragmentation limit reproductive success by reducing home range size and provisioning rates of Northern saw-whet owls. Biol. Conserv. 141, 524–535 (2008).Article 

    Google Scholar 
    Daan, S., Deerenberg, C. & Dijkstra, C. Increased daily work precipitates natural death in the Kestrel. J. Anim. Ecol. 65, 539 (1996).Article 

    Google Scholar 
    Slagsvold, T., Sandvik, J., Rofstad, G., Lorentsen, O. & Husby, M. On the adaptive value of intraclutch egg-size variation in birds. Auk 101, 685–697 (1984).Article 

    Google Scholar 
    Tripet, F., Richner, H. & Tripet, F. Host responses to ectoparasites: Food compensation by parent blue tits. Oikos 78, 557 (1997).Article 

    Google Scholar 
    Budden, A. E. & Beissinger, S. R. Resource allocation varies with parental sex and brood size in the asynchronously hatching green-rumped parrotlet (Forpus passerinus). Behav. Ecol. Sociobiol. 63, 637–647 (2009).Article 

    Google Scholar 
    Bókony, V. et al. Stress response and the value of reproduction: Are birds prudent parents?. Am. Nat. 173, 589–598 (2009).Article 

    Google Scholar 
    McGinley, M. A., Temme, D. H. & Geber, M. A. Parental investment in offspring in variable environments: Theoretical and empirical considerations. Am. Nat. 130, 370–398 (1987).Article 

    Google Scholar 
    Ghalambor, C. K. & Martin, T. E. Fecundity-survival trade-offs and parental risk-taking in birds. Science (80-.). 292, 494–497 (2001).ADS 
    CAS 
    Article 

    Google Scholar 
    Caro, S. M., Griffin, A. S., Hinde, C. A. & West, S. A. Unpredictable environments lead to the evolution of parental neglect in birds. Nat. Commun. 7, 1–10 (2016).Article 

    Google Scholar 
    Roulin, A. Barn Owls: Evolution and Ecology (Cambridge University Press, 2020).
    Google Scholar 
    Romano, A., Séchaud, R. & Roulin, A. Global biogeographical patterns in the diet of a cosmopolitan avian predator. J. Biogeogr. 47, 1467–1481 (2020).Article 

    Google Scholar 
    Arlettaz, R., Krähenbühl, M., Almasi, B., Roulin, A. & Schaub, M. Wildflower areas within revitalized agricultural matrices boost small mammal populations but not breeding Barn Owls. J. Ornithol. 151, 553–564 (2010).Article 

    Google Scholar 
    Hindmarch, S., Elliott, J. E., Mccann, S. & Levesque, P. Habitat use by barn owls across a rural to urban gradient and an assessment of stressors including, habitat loss, rodenticide exposure and road mortality. Landsc. Urban Plan. 164, 132–143 (2017).Article 

    Google Scholar 
    Castañeda, X. A., Huysman, A. E. & Johnson, M. D. Barn Owls select uncultivated habitats for hunting in a winegrape growing region of California. Ornithol. Appl. 123, 1–15 (2021).
    Google Scholar 
    Séchaud, R. et al. Behaviour-specific habitat selection patterns of breeding barn owls. Mov. Ecol. 9, 18 (2021).Article 

    Google Scholar 
    Roulin, A., Ducrest, A.-L. & Dijkstra, C. Effect of brood size manipulations on parents and offspring in the barn owl Tyto alba. Ardea 87, 91–100 (1999).
    Google Scholar 
    Béziers, P. & Roulin, A. Double brooding and offspring desertion in the barn owl Tyto alba. J. Avian Biol. 47, 235–244 (2016).Article 

    Google Scholar 
    Laaksonen, T., Hakkarainen, H. & Korpimäki, E. Lifetime reproduction of a forest-dwelling owl increases with age and area of forests. Proc. R. Soc. B Biol. Sci. 271, 10058 (2004).Article 

    Google Scholar 
    Bryant, D. M. Energy expenditure and body mass changes as measures of reproductive costs in birds. Funct. Ecol. 2, 23 (1988).Article 

    Google Scholar 
    Merilä, J. & Wiggins, D. A. Mass loss in breeding blue tits: The role of energetic stress. J. Anim. Ecol. 66, 452 (1997).Article 

    Google Scholar 
    Frey, C., Sonnay, C., Dreiss, A. & Roulin, A. Habitat, breeding performance, diet and individual age in Swiss Barn Owls (Tyto alba). J. Ornithol. 152, 279–290 (2010).Article 

    Google Scholar 
    Aschwanden, J., Holzgang, O. & Jenni, L. Importance of ecological compensation areas for small mammals in intensively farmed areas. Wildlife Biol. 13, 150–158 (2007).Article 

    Google Scholar 
    Roulin, A. Tyto alba Barn Owl. BWP Updat. 4, 115–138 (2002).
    Google Scholar 
    Calabrese, J. M., Fleming, C. H. & Gurarie, E. ctmm: An R package for analyzing animal relocation data as a continuous-time stochastic process. Methods Ecol. Evol. 7, 1124–1132 (2016).Article 

    Google Scholar 
    Fleming, C. H. et al. Rigorous home range estimation with movement data: A new autocorrelated kernel density estimator. Ecology 96, 1182–1188 (2015).CAS 
    Article 

    Google Scholar 
    Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).Article 

    Google Scholar 
    Taylor, I. Barn Owls: Predator-Prey Relationships and Conservation (Cambridge University Press, 1994).
    Google Scholar 
    van den Brink, V., Dreiss, A. N. & Roulin, A. Melanin-based coloration predicts natal dispersal in the barn owl, Tyto alba. Anim. Behav. 84, 805–812 (2012).Article 

    Google Scholar 
    Dreiss, A. N. & Roulin, A. Divorce in the barn owl: Securing a compatible or better mate entails the cost of re-pairing with a less ornamented female mate. J. Evol. Biol. 27, 1114–1124 (2014).CAS 
    Article 

    Google Scholar 
    Garriga, J., Palmer, J. R. B., Oltra, A. & Bartumeus, F. Expectation-maximization binary clustering for behavioural annotation. PLoS One 11, e0151984 (2016).Article 

    Google Scholar 
    San-Jose, L. M. et al. Differential fitness effects of moonlight on plumage colour morphs in barn owls. Nat. Ecol. Evol. 3, 1331–1340 (2019).Article 

    Google Scholar 
    Bracis, C., Bildstein, K. L. & Mueller, T. Revisitation analysis uncovers spatio-temporal patterns in animal movement data. Ecography (Cop.) 41, 1801–1811 (2018).Article 

    Google Scholar 
    Bates, D., Mächler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    Lüdecke, D. Data Visualization for Statistics in Social Science [R package sjPlot version 2.8.9]. (2021).Rutz, C. & Bijlsma, R. G. Food-limitation in a generalist predator. Proc. R. Soc. B Biol. Sci. 273, 2069–2076 (2006).Article 

    Google Scholar 
    Altmann, S. A. The impact of locomotor energetics on mammalian foraging. J. Zool. 211, 215–225 (1987).Article 

    Google Scholar 
    Evens, R. et al. Proximity of breeding and foraging areas affects foraging effort of a crepuscular, insectivorous bird. Sci. Rep. 8, 1–11 (2018).
    Google Scholar 
    Pfeiffer, T. & Meyburg, B. U. GPS tracking of Red Kites (Milvus milvus) reveals fledgling number is negatively correlated with home range size. J. Ornithol. 156, 963–975 (2015).Article 

    Google Scholar 
    Romano, A. et al. Nestling sex and plumage color predict food allocation by barn swallow parents. Behav. Ecol. 27, 1198–1205 (2016).Article 

    Google Scholar 
    Bryant, D. M. & Tatner, P. Hatching asynchrony, sibling competition and siblicide in nestling birds: Studies of swiftlets and bee-eaters. Anim. Behav. 39, 657–671 (1990).Article 

    Google Scholar 
    Mock, D. W. & Parker, G. A. Advantages and disadvantages of egret and heron brood reduction. Evolution (N. Y.). 40, 459–470 (1986).
    Google Scholar 
    Stenning, M. J. Hatching asynchrony, brood reduction and other rapidly reproducing hypotheses. Trends Ecol. Evol. 11, 243–246 (1996).CAS 
    Article 

    Google Scholar 
    Roulin, A., Colliard, C., Russier, F., Fleury, M. & Grandjean, V. Sib-sib communication and the risk of prey theft in the barn owl Tyto alba. J. Avian Biol. 39, 593–598 (2008).Article 

    Google Scholar 
    Korpimaki, E. Costs of reproduction and success of manipulated broods under varying food conditions in Tengmalm’s owl. J. Anim. Ecol. 57, 1879 (1988).
    Google Scholar 
    Tolonen, P. & Korpimäki, E. Do kestrels adjust their parental effort to current or future benefit in a temporally varying environment?. Écoscience 3, 165–172 (1996).Article 

    Google Scholar 
    Harrison, F., Barta, Z., Cuthill, I. & Székely, T. How is sexual conflict over parental care resolved? A meta-analysis. J. Evol. Biol. 22, 1800–1812 (2009).CAS 
    Article 

    Google Scholar 
    Osorno, J. L. & Székely, T. Sexual conflict and parental care in magnificent frigatebirds: Full compensation by deserted females. Anim. Behav. 68, 337–342 (2004).Article 

    Google Scholar 
    Paredes, R., Jones, I. L. & Boness, D. J. Parental roles of male and female thick-billed murres and razorbills at the Gannet Islands, Labrador. Behaviour 143, 451–481 (2006).Article 

    Google Scholar 
    Kleijn, D. et al. Mixed biodiversity benefits of agri-environment schemes in five European countries. Ecol. Lett. 9, 243–254 (2006).CAS 
    Article 

    Google Scholar 
    Zingg, S., Ritschard, E., Arlettaz, R. & Humbert, J. Y. Increasing the proportion and quality of land under agri-environment schemes promotes birds and butterflies at the landscape scale. Biol. Conserv. 231, 39–48 (2019).Article 

    Google Scholar  More

  • in

    Indoor green wall affects health-associated commensal skin microbiota and enhances immune regulation: a randomized trial among urban office workers

    Rook, G. A. W. Review series on helminths, immune modulation and the hygiene hypothesis: The broader implications of the hygiene hypothesis. Immunology 126, 3–11 (2009).CAS 
    Article 

    Google Scholar 
    Von Hertzen, L., Hanski, I. & Haahtela, T. Natural immunity. Biodiversity loss and inflammatory diseases are two global megatrends that might be related. EMBO Rep. 12, 1089–1093 (2011).Article 

    Google Scholar 
    Von Hertzen, L. & Haahtela, T. Disconnection of man and the soil: Reason for the asthma and atopy epidemic?. J. Allergy Clin. Immunol. 117, 334–344 (2006).Article 

    Google Scholar 
    Hanski, I. et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc. Natl. Acad. Sci. U. S. A. 109, 8334–8339 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    Haahtela, T. et al. Immunological resilience and biodiversity for prevention of allergic diseases and asthma. Allergy Eur. J. Allergy Clin. Immunol. https://doi.org/10.1111/all.14895 (2021).Article 

    Google Scholar 
    Rook, G. A. W. et al. Mycobacteria and other environmental organisms as immunomodulators for immunoregulatory disorders. Springer Semin. Immunopathol. 25, 237–255 (2004).CAS 
    Article 

    Google Scholar 
    Fyhrquist, N. et al. Acinetobacter species in the skin microbiota protect against allergic sensitization and inflammation. J. Allergy Clin. Immunol. 134, 1301-1309.e11 (2014).CAS 
    Article 

    Google Scholar 
    Ottman, N. et al. Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model. J. Allergy Clin. Immunol. 143, 1198-1206.e12 (2019).CAS 
    Article 

    Google Scholar 
    Nurminen, N. et al. Nature-derived microbiota exposure as a novel immunomodulatory approach. Fut. Microbiol. 13, 737–744 (2018). CAS 
    Article 

    Google Scholar 
    Shaffer, M. & Lozupone, C. Prevalence and source of fecal and oral bacteria on infant, child, and adult hands. mSystems 3, 1–12 (2018).Article 

    Google Scholar 
    Grönroos, M. et al. Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota. MicrobiologyOpen https://doi.org/10.1002/mbo3.645 (2019).Article 

    Google Scholar 
    Roslund, M. I. et al. Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Sci. Adv. 6, 7–105 (2020).Article 

    Google Scholar 
    Roslund, M. I. et al. Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children. Environ. Int. 157, 7008 (2021).Article 

    Google Scholar 
    Lax, S. et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science (80-.). 345, 1048–1052 (2014).ADS 
    CAS 
    Article 

    Google Scholar 
    Flies, E. J., Clarke, L. J., Brook, B. W. & Jones, P. Urbanisation reduces the abundance and diversity of airborne microbes-but what does that mean for our health? A systematic review. Sci. Total Environ. 738, 140337 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    Ege, M. J. et al. Exposure to environmental microorganisms and childhood asthma.. Science 364, 701–709 (2011).CAS 

    Google Scholar 
    Li, H. et al. Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China. Sci. Total Environ. 665, 61–68 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    Chase, J. et al. Geography and location are the primary drivers of office microbiome composition. mSystems 1, 1–18 (2016).
    Google Scholar 
    Danko, D. et al. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184, 3376-3393.e17 (2021).CAS 
    Article 

    Google Scholar 
    Hui, N. et al. Soil microbial communities are shaped by vegetation type and park age in cities under cold climate. Environ. Microbiol. 19, 1281–1295 (2017).Article 

    Google Scholar 
    Mhuireach, G. et al. Urban greenness influences airborne bacterial community composition. Sci. Total Environ. 571, 680–687 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Franzetti, A., Gandolfi, I., Gaspari, E., Ambrosini, R. & Bestetti, G. Seasonal variability of bacteria in fine and coarse urban air particulate matter. Appl. Microbiol. Biotechnol. 90, 745–753 (2011).CAS 
    Article 

    Google Scholar 
    Mhuireach, G., Wilson, H. & Johnson, B. R. Urban aerobiomes are influenced by season, vegetation, and individual site characteristics. EcoHealth 18, 331–344 (2021).Article 

    Google Scholar 
    Mahnert, A., Moissl-Eichinger, C. & Berg, G. Microbiome interplay: Plants alter microbial abundance and diversity within the built environment. Front. Microbiol. 6, 1–11 (2015).Article 

    Google Scholar 
    Ruokolainen, L. et al. Green areas around homes reduce atopic sensitization in children. Allergy Eur. J. Allergy Clin. Immunol. 70, 195–202 (2015).CAS 
    Article 

    Google Scholar 
    Kirjavainen, P. V. et al. Farm-like indoor microbiota in non-farm homes protects children from asthma development. Nat. Med. 25, 1089–1095 (2019).CAS 
    Article 

    Google Scholar 
    Nurminen, N. et al. Land cover of early-life environment modulates the risk of type 1 diabetes. Diabetes Care 44, 1506–1514 (2021).Article 

    Google Scholar 
    Parajuli, A. et al. Yard vegetation is associated with gut microbiota composition. Sci. Total Environ. 713, 136707 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    Köberl, M., Dita, M., Martinuz, A., Staver, C. & Berg, G. Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America. Sci. Rep. 7, 1–9 (2017).Article 

    Google Scholar 
    Delanghe, L. et al. The role of lactobacilli in inhibiting skin pathogens. Biochem. Soc. Trans. 5, 617–627. https://doi.org/10.1042/bst20200329 (2021).CAS 
    Article 

    Google Scholar 
    George, F. et al. Occurrence and dynamism of lactic acid bacteria in distinct ecological niches: A multifaceted functional health perspective. Front. Microbiol. 9, 1–15 (2018).CAS 
    Article 

    Google Scholar 
    Yu, A. O., Leveau, J. H. J. & Marco, M. L. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. Environ. Microbiol. Rep. 12, 16–29 (2020).CAS 
    Article 

    Google Scholar 
    Parajuli, A. et al. Urbanization reduces transfer of diverse environmental microbiota indoors. Front. Microbiol. 9, 1405 (2018).Article 

    Google Scholar 
    Parajuli, A. et al. The abundance of health-associated bacteria is altered in PAH polluted soils—Implications for health in urban areas?. PLoS One 7, 1–18. https://doi.org/10.1371/journal.pone.0187852 (2017).CAS 
    Article 

    Google Scholar 
    Vari, H. K. et al. Associations between land cover categories, gaseous PAH levels in ambient air and endocrine signaling predicted from gut bacterial metagenome of the elderly. Chemosphere 265, 1559 (2021).Article 

    Google Scholar 
    Orsini, F., Kahane, R., Nono-Womdim, R. & Gianquinto, G. Urban agriculture in the developing world: A review. Agron. Sustain. Dev. 33, 695–720 (2013).Article 

    Google Scholar 
    Hui, N. et al. Diverse environmental microbiota as a tool to augment biodiversity in urban landscaping materials. Front. Microbiol. 10, 1–10 (2019).CAS 
    Article 

    Google Scholar 
    Puhakka, R. et al. Greening of daycare yards with biodiverse materials affords well-being, play and environmental relationships. Int. J. Environ. Res. Public Health 16, 2948 (2019).Article 

    Google Scholar 
    Burmeister, A. R. & Marriott, I. The interleukin-10 family of cytokines and their role in the CNS. Front. Cell. Neurosci. 12, 1–13 (2018).Article 

    Google Scholar 
    Opal, S. M. & DePalo, V. A. Anti-inflammatory cytokines. Chest 117, 1162–1172 (2000).CAS 
    Article 

    Google Scholar 
    Kuwabara, T., Ishikawa, F., Kondo, M. & Kakiuchi, T. The role of IL-17 and related cytokines in inflammatory autoimmune diseases. Mediators Inflamm. 2017, 4598 (2017).Article 

    Google Scholar 
    Li, M. O., Wan, Y. Y., Sanjabi, S., Robertson, A. K. L. & Flavell, R. A. Transforming growth factor-β regulation of immune responses. Annu. Rev. Immunol. 24, 99–146 (2006).CAS 
    Article 

    Google Scholar 
    Prudhomme, G. J. & Piccirillo, C. A. The inhibitory effects of transforming growth factor-beta-1 (TGF-β1) in autoimmune diseases. J. Autoimmun. 14, 23–42 (2000).CAS 
    Article 

    Google Scholar 
    Esebanmen, G. E. & Langridge, W. H. R. The role of TGF-beta signaling in dendritic cell tolerance. Immunol. Res. 65, 987–994 (2017).CAS 
    Article 

    Google Scholar 
    Honkanen, J. et al. IL-17 immunity in human type 1 diabetes. J. Immunol. 185, 1959–1967 (2010).CAS 
    Article 

    Google Scholar 
    Torpy, F. et al. Testing the single-pass VOC removal efficiency of an active green wall using methyl ethyl ketone (MEK). Air Qual. Atmos. Heal. 11, 163–170 (2018).CAS 
    Article 

    Google Scholar 
    Roslund, M. I. et al. Endocrine disruption and commensal bacteria alteration associated with gaseous and soil PAH contamination among daycare children. Environ. Int. 130, 104894 (2019).CAS 
    Article 

    Google Scholar 
    Schloss, P. D., Gevers, D. & Westcott, S. L. Reducing the effects of PCR amplification and sequencing Artifacts on 16s rRNA-based studies. PLoS One 6, 1789 (2011).
    Google Scholar 
    Kozich, J., Westcott, S., Baxter, N., Highlander, S. & Schloss, P. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).ADS 
    CAS 
    Article 

    Google Scholar 
    Soininen, L., Grönroos, M., Roslund, M. I. & Sinkkonen, A. Long-term storage affects resource availability and occurrence of bacterial taxa linked to pollutant degradation and human health in landscaping materials. Urban For. Urban Green. 60, 1789 (2021).Article 

    Google Scholar 
    Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).Article 

    Google Scholar 
    Huse, S. M., Welch, D. M., Morrison, H. G. & Sogin, M. L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889–1898 (2010).CAS 
    Article 

    Google Scholar 
    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).CAS 
    Article 

    Google Scholar 
    Wang, Q., Garrity, G. M., Tiedje, J. M., Cole, J. R. & Al, W. E. T. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).ADS 
    CAS 
    Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing. (2020).Oksanen, J. et al. vegan: Community Ecology Package. (2019).Huang, F. L. Alternatives to multilevel modeling for the analysis of clustered data. J. Exp. Educ. 84, 175–196 (2016).Article 

    Google Scholar 
    Moen, E. L., Fricano-Kugler, C. J., Luikart, B. W. & O’Malley, A. J. Analyzing clustered data: Why and how to account for multiple observations nested within a study participant?. PLoS ONE 11, 1–17 (2016).
    Google Scholar 
    Twisk, J. et al. Different ways to estimate treatment effects in randomised controlled trials. Contemp. Clin. Trials Commun. 10, 80–85 (2018).Chapat, L., Chemin, K., Dubois, B., Bourdet-Sicard, R. & Kaiserlian, D. Lactobacillus casei reduces CD8+ T cell-mediated skin inflammation. Eur. J. Immunol. 34, 2520–2528 (2004).CAS 
    Article 

    Google Scholar 
    Kaur, K. & Rath, G. Formulation and evaluation of UV protective synbiotic skin care topical formulation. J. Cosmet. Laser Ther. 21, 332–342 (2019).Article 

    Google Scholar 
    Rong, J. et al. Skin resistance to UVB-induced oxidative stress and hyperpigmentation by the topical use of Lactobacillus helveticus NS8-fermented milk supernatant. J. Appl. Microbiol. 123, 511–523 (2017).CAS 
    Article 

    Google Scholar 
    Yuan, J. et al. Microbial volatile compounds alter the soil microbial community. Environ. Sci. Pollut. Res. 24, 22485–22493 (2017).CAS 
    Article 

    Google Scholar 
    Abis, L. et al. Reduced microbial diversity induces larger volatile organic compound emissions from soils. Sci. Rep. 10, 1–15 (2020).Article 

    Google Scholar 
    Duffy, E. & Morrin, A. Endogenous and microbial volatile organic compounds in cutaneous health and disease. TrAC Trends Anal. Chem. 111, 163–172 (2019).CAS 
    Article 

    Google Scholar 
    Lemfack, M. C. et al. Novel volatiles of skin-borne bacteria inhibit the growth of Gram-positive bacteria and affect quorum-sensing controlled phenotypes of Gram-negative bacteria. Syst. Appl. Microbiol. 39, 503–515 (2016).CAS 
    Article 

    Google Scholar 
    Ahmed, M. & Gaffen, S. L. IL-17 in obesity and adipogenesis. Cytokine Growth Factor Rev. 21, 449–453 (2010).CAS 
    Article 

    Google Scholar  More

  • in

    Tracing the path of carbon export in the ocean though DNA sequencing of individual sinking particles

    Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237.CAS 
    Article 

    Google Scholar 
    Volk T, Hoffert M. Ocean carbon pumps: analysis of relative strengths and efficiencies in ocean-driven atmospheric CO2 changes. Geophys Monogr Ser. 1985;32:99–110.
    Google Scholar 
    Boyd PW, Claustre H, Levy M, Siegel DA, Weber T. Multi-faceted particle pumps drive carbon sequestration in the ocean. Nature. 2019;568:327–35.CAS 
    Article 

    Google Scholar 
    Siegel DA, Buesseler KO, Doney SC, Sailley SF, Behrenfeld MJ, Boyd PW. Global assessment of ocean carbon export by combining satellite observations and food-web models. Glob Biogeochem Cycles. 2014;28:181–196.Henson SA, Sanders R, Madsen E, Morris PJ, Le Moigne F, Quartly GD. A reduced estimate of the strength of the ocean’s biological carbon pump. Geophys Res Lett. 2011;38:L04606.Article 

    Google Scholar 
    Boyd PW, Trull TW. Understanding the export of biogenic particles in oceanic waters: is there consensus? Prog Oceanogr. 2007;72:276–312.Article 

    Google Scholar 
    Werdell PJ, Behrenfeld MJ, Bontempi PS, Boss E, Cairns B, Davis GT, et al. The plankton, aerosol, cloud, ocean ecosystem mission: status, science, advances. Bull Am Meteorol Soc. 2019;100:1775–94.Article 

    Google Scholar 
    Picheral M, Guidi L, Stemmann L, Karl DM, Iddaoud G, Gorsky G. The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnol Oceanogr-Methods. 2010;8:462–73.Article 

    Google Scholar 
    Olson RJ, Sosik HM. A submersible imaging-in-flow instrument to analyze nano-and microplankton: imaging FlowCytobot. Limnol Oceanogr Methods. 2007;5:195–203.Article 

    Google Scholar 
    de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.Scholin C, Birch J, Jensen S, Marin R III, Massion E, Pargett D, et al. The quest to develop ecogenomic sensors: a 25-year history of the Environmental Sample Processor (ESP) as a case study. Oceanography. 2017;30:100–13.Article 

    Google Scholar 
    Cruz BN, Brozak S, Neuer S. Microscopy and DNA-based characterization of sinking particles at the Bermuda Atlantic Time-series Study station point to zooplankton mediation of particle flux. Limnol Oceanogr. 2021;66:3697–713.CAS 
    Article 

    Google Scholar 
    Amacher J, Neuer S, Lomas M. DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study. Deep Sea Res Part II Top Stud Oceanogr. 2013;93:71–83.CAS 
    Article 

    Google Scholar 
    Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol. 2015;6:469.Article 

    Google Scholar 
    Preston CM, Durkin CA, Yamahara KM DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean. Deep Sea Res Part II Top Stud Oceanogr. 2019;173:104708.Gutierrez-Rodriguez A, Stukel MR, Lopes dos Santos A, Biard T, Scharek R, Vaulot D, et al. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. ISME J. 2019;13:964–76.CAS 
    Article 

    Google Scholar 
    Boeuf D, Edwards BR, Eppley JM, Hu SK, Poff KE, Romano AE, et al. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci. 2019;116:11824.CAS 
    Article 

    Google Scholar 
    Silver MW, Gowing MM. The “particle” flux: Origins and biological components. Prog Oceanogr. 1991;26:75–113.Article 

    Google Scholar 
    Ebersbach F, Assmy P, Martin P, Schulz I, Wolzenburg S, Nöthig E-M. Particle flux characterisation and sedimentation patterns of protistan plankton during the iron fertilisation experiment LOHAFEX in the Southern Ocean. Deep Sea Res Part Oceanogr Res Pap. 2014;89:94–103.CAS 
    Article 

    Google Scholar 
    Waite A, Bienfang PK, Harrison PJ. Spring bloom sedimentation in a subarctic ecosystem. II. Succession and sedimentation. Mar Biol. 1992;114:131–8.Article 

    Google Scholar 
    Venrick E, Lange C, Reid F, Dever EP. Temporal patterns of species composition of siliceous phytoplankton flux in the Santa Barbara Basin. J Plankton Res. 2007;30:283–97.Article 

    Google Scholar 
    Waite AM, Safi KA, Hall JA, Nodder SD. Mass sedimentation of picoplankton embedded in organic aggregates. Limnol Oceanogr. 2000;45:87–97.Article 

    Google Scholar 
    Valencia B, Stukel MR, Allen AE, McCrow JP, Rabines A, Palenik B, et al. Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export. Environ Microbiol. 2021;23:6743–8.Article 

    Google Scholar 
    Scharek R, Tupas LM, Karl DM. Diatom fluxes to the deep sea in the oligotrophic North Pacific gyre at Station ALOHA. Mar Ecol Prog Ser. 1999;182:55–67.Article 

    Google Scholar 
    Beaulieu S. Accumulation and fate of phytodetritus on the sea floor. Oceanogr Mar Biol Annu Rev. 2002;40:171–232.
    Google Scholar 
    Ikenoue T, Kimoto K, Okazaki Y, Sato M, Honda MC, Takahashi K, et al. Phaeodaria: an important carrier of particulate organic carbon in the mesopelagic twilight zone of the North Pacific Ocean. Glob Biogeochem Cycles. 2019;33:1146–60.CAS 
    Article 

    Google Scholar 
    Smith KL, Ruhl HA, Huffard CL, Messié M, Kahru M. Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific. Proc Natl Acad Sci. 2018;115:12235.CAS 
    Article 

    Google Scholar 
    Durkin CA, Buesseler KO, Cetinić I, Estapa ML, Kelly RP, Omand M. A visual tour of carbon export by sinking particles. Glob Biogeochem Cycles. 2021;35:e2021GB006985.CAS 
    Article 

    Google Scholar 
    Estapa ML, Valdes J, Tradd K, Sugar J, Omand M, Buesseler K. The neutrally buoyant sediment trap: two decades of progress. J Atmospheric Ocean Technol. 2020;37:957–973.Rainville L, Pinkel R. Wirewalker: An autonomous wave-powered vertical profiler. J Atmos Ocean Technol. 2001;18:1048–51.Article 

    Google Scholar 
    Durkin CA, Estapa ML, Buesseler KO. Observations of carbon export by small sinking particles in the upper mesopelagic. Mar Chem. 2015;175:72–81.CAS 
    Article 

    Google Scholar 
    Malmstrom R RNAlater Recipe. protocols.io. https://doi.org/10.17504/protocols.io.c56y9d. Accessed 2 Oct 2018.Mackey MD, Mackey DJ, Higgins HW, Wright SW. CHEMTAX—a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton. Mar Ecol Prog Ser. 1996;144:265–83.CAS 
    Article 

    Google Scholar 
    Massana R, Murray AE, Preston CM, DeLong EF. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol. 1997;63:50.CAS 
    Article 

    Google Scholar 
    Stoeck T, Bass D, Nebel M, Christen R, Jones M, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.CAS 
    Article 

    Google Scholar 
    Penna A, Casabianca S, Guerra A, Vernesi C, Scardi M. Analysis of phytoplankton assemblage structure in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences. Mar Genomics. 2017;36:49–55.Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.CAS 
    Article 

    Google Scholar 
    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
    Article 

    Google Scholar 
    Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2012;41:D597–D604.Article 

    Google Scholar 
    Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6:90.Article 

    Google Scholar 
    Tomas CR. Identifying marine phytoplankton. Elsevier; 1997.Hasle GR, Syvertsen EE. Marine diatoms. In: Tomas CR (ed). Identifying marine phytoplankton. San Diego, CA, USA: Academic Press; 1997. pp 5–385.Godhe A, Asplund ME, Härnström K, Saravanan V, Tyagi A, Karunasagar I. Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl Environ Microbiol. 2008;74:7174–82.CAS 
    Article 

    Google Scholar 
    Smayda TJ. The suspension and sinking of phytoplankton in the sea. Oceanogr Mar Biol Annu Rev. 1970;8:353–414.
    Google Scholar 
    Sancetta C, Villareal T, Falkowski P. Massive fluxes of rhizosolenid diatoms: a common occurrence? Limnol Oceanogr. 1991;36:1452–7.Article 

    Google Scholar 
    Goldman JC. Potential role of large oceanic diatoms in new primary production. Deep Sea Res Part Oceanogr Res Pap. 1993;40:159–68.Article 

    Google Scholar 
    Kemp AE, Pike J, Pearce RB, Lange CB. The “Fall dump”—a new perspective on the role of a “shade flora” in the annual cycle of diatom production and export flux. Deep Sea Res Part II Top Stud Oceanogr. 2000;47:2129–54.Article 

    Google Scholar 
    Villareal TA, Woods S, Moore JK, CulverRymsza K. Vertical migration of Rhizosolenia mats and their significance to NO3− fluxes in the central North Pacific gyre. J Plankton Res. 1996;18:1103–21.Article 

    Google Scholar 
    Smayda TJ. Normal and accelerated sinking of phytoplankton in the sea. Mar Geol. 1971;11:105–22.Article 

    Google Scholar 
    Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada NA. DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLOS ONE. 2021;16:e0245936.CAS 
    Article 

    Google Scholar 
    Omand MM, Govindarajan R, He J, Mahadevan A. Sinking flux of particulate organic matter in the oceans: sensitivity to particle characteristics. Sci Rep. 2020;10:5582.CAS 
    Article 

    Google Scholar 
    DeVries T, Liang J-H, Deutsch C. A mechanistic particle flux model applied to the oceanic phosphorus cycle. Biogeosciences. 2014;11:5381–98.Article 

    Google Scholar 
    Siegel DA, Buesseler KO, Behrenfeld MJ, Benitez-Nelson CR, Boss E, Brzezinski MA, et al. Prediction of the export and fate of global ocean net primary production: the EXPORTS science plan. Front Mar Sci. 2016;3:22.Article 

    Google Scholar 
    NASA Ocean Biology Processing Group. MODIS-Aqua Level 3 mapped chlorophyll data version R2018.0. 2017. NASA Ocean Biology DAAC. https://doi.org/10.5067/AQUA/MODIS/L3M/CHL/2018. More

  • in

    Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle

    Brierley AS, Kingsford MJ. Impacts of climate change on marine organisms and ecosystems. Curr Biol. 2009;19:R602–14.CAS 
    Article 

    Google Scholar 
    Pecl GT, Araújo MB, Bell JD, Blanchard J, Bonebrake TC, Chen I-C, et al. Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Science. 2017;355:eaaai9214.Article 

    Google Scholar 
    Hughes TP, Barnes ML, Bellwood DR, Cinner JE, Cumming GS, Jackson JBC, et al. Coral reefs in the Anthropocene. Nature. 2017;546:82–90.CAS 
    Article 

    Google Scholar 
    Feeley KJ, Rehm EM, Machovina B. perspective: The responses of tropical forest species to global climate change: acclimate, adapt, migrate, or go extinct? Front Biogeogr. 2012;4:69–84.Article 

    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. 2008;32:723–35.CAS 
    Article 

    Google Scholar 
    Voolstra CR, Ziegler M. Adapting with microbial help: Microbiome flexibility facilitates rapid responses to environmental change. BioEssays. 2017;42:2000004.Article 

    Google Scholar 
    Webster NS, Reusch TBH. Microbial contributions to the persistence of coral reefs. ISME J. 2017;11:2167–74.Article 

    Google Scholar 
    Wilkes Walburn J, Wemheuer B, Thomas T, Copeland E, O’Connor W, Booth M, et al. Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi). Micro Biotechnol. 2019;12:275–88.CAS 
    Article 

    Google Scholar 
    Neave MJ, Rachmawati R, Xun L, Michell CT, Bourne DG, Apprill A, et al. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME J. 2016;11:186–200.Article 

    Google Scholar 
    Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CA-F, et al. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun. 2021;12:640.Article 

    Google Scholar 
    Cardini U, Bednarz VN, Naumann MS, van Hoytema N, Rix L, Foster RA, et al. Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions. Proc R Soc B: Biol Sci. 2015;282:20152257.Article 

    Google Scholar 
    Manzano-Marı NA, Coeur d’acier A, Clamens A-L, Orvain C, Cruaud C, Barbe V, et al. Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems. ISME J. 2020;14:259–73.Article 

    Google Scholar 
    Neave MJ, Michell CT, Apprill A, Voolstra CR. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci Rep. 2017;7:40579.CAS 
    Article 

    Google Scholar 
    Ding JY, Shiu JH, Chen WM, Chiang YR, Tang SL. Genomic insight into the host-endosymbiont relationship of Endozoicomonas montiporae CL-33T with its coral host. Front Microbiol. 2016;7:251.
    Google Scholar 
    Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv. 2021;7:eabg3088.CAS 
    Article 

    Google Scholar 
    Cavalcanti G, Alker A, Delherbe N, Malter KE, Shikuma NJ. The influence of bacteria on animal metamorphosis. Ann Rev Microbiol. 2020;74:137–58.CAS 
    Article 

    Google Scholar 
    Rohwer F, Seguritan V, Azam F, Knowlton N. Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser. 2002;243:1–10.Article 

    Google Scholar 
    Rädecker N, Pogoreutz C, Voolstra CR, Wiedenmann J, Wild C. Nitrogen cycling in corals: the key to understanding holobiont functioning? Trends Microbiol. 2015;23:490–7.Article 

    Google Scholar 
    Raina JB, Clode PL, Cheong S, Bougoure J, Kilburn MR, Reeder A, et al. Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria. Elife. 2017;6:e23008.Article 

    Google Scholar 
    Rädecker N, Pogoreutz C, Gegner HM, Cárdenas A, Perna G, Geißler L, et al. Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling. ISME J. 2021;16:1110–8.Article 

    Google Scholar 
    Pogoreutz C, Voolstra CR, Rädecker N, Weis V. The coral holobiont highlights the dependence of cnidarian animal hosts on their associated microbes. In: Bosch TCG, Hadfield MG, editors. Cellular Dialogues in the Holobiont. Boca Raton: CRC Press; 2020. pp. 91–118.Xiang N, Hassenrück C, Pogoreutz C, Rädecker N, Simancas-Giraldo SM, Voolstra CR, et al. Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming. Appl Environ Microbiol. 2021;88:e01886–21.
    Google Scholar 
    Nissimov J, Rosenberg E, Munn CB. Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica. FEMS Microbiol Lett. 2009;292:210–5.CAS 
    Article 

    Google Scholar 
    Pereira LB, Palermo BRZ, Carlos C, Ottoboni LMM. Diversity and antimicrobial activity of bacteria isolated from different Brazilian coral species. FEMS Microbiol Lett. 2017;364:fnx164.Article 

    Google Scholar 
    Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Micro Biotechnol. 2021;14:2025–40.CAS 
    Article 

    Google Scholar 
    Neave MJ, Apprill A, Ferrier-Pagès C, Voolstra CR. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl Microbiol Biotechnol. 2016;100:8315–24.CAS 
    Article 

    Google Scholar 
    Meyer JL, Paul VJ, Teplitski M. Community shifts in the surface microbiomes of the coral Porites astreoides with unusual lesions. PLoS One. 2014;9:e100316.Article 

    Google Scholar 
    Morrow KM, Bourne DG, Humphrey C, Botté ES, Laffy P, Zaneveld J, et al. Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges. ISME J. 2014;9:894–908.Article 

    Google Scholar 
    Roder C, Bayer T, Aranda M, Kruse M, Voolstra CR. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences. Mol Ecol. 2015;24:3501–11.Article 

    Google Scholar 
    Ziegler M, Grupstra CGB, Barreto MM, Eaton M, BaOmar J, Zubier K, et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat Commun. 2019;10:e3092.Article 

    Google Scholar 
    Pogoreutz C, Rädecker N, Cárdenas A, Gärdes A, Wild C, Voolstra CR. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol Evol. 2018;8:2240–52.Article 

    Google Scholar 
    Tandon K, Lu C-Y, Chiang P-W, Wada N, Yang S-H, Chan Y-F, et al. Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). ISME J. 2020;14:1290–303.CAS 
    Article 

    Google Scholar 
    Sweet M, Villela H, Keller-Costa T, Costa R, Romano S, Bourne DG, et al. Insights into the cultured bacterial fraction of corals. mSystems. 2021;6:e0124920.Article 

    Google Scholar 
    Ngugi DK, Ziegler M, Duarte CM, Voolstra CR. Genomic blueprint of glycine betaine metabolism in coral metaorganisms and their contribution to reef nitrogen budgets. iScience. 2020;23:101120.CAS 
    Article 

    Google Scholar 
    Weber L, Gonzalez-Díaz P, Armenteros M, Apprill A. The coral ecosphere: a unique coral reef habitat that fosters coral–microbial interactions. Limnol Oceanogr. 2019;64:2373–88.CAS 
    Article 

    Google Scholar 
    Alain K, Querellou J. Cultivating the uncultured: limits, advances and future challenges. Extremophiles. 2009;13:583–94.Article 

    Google Scholar 
    Robbins SJ, Singleton CM, Chan CX, Messer LF, Geers AU, Ying H, et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol. 2019;4:2090–2100.Article 

    Google Scholar 
    Katharios P, Seth-Smith HMB, Fehr A, Mateos JM, Qi W, Richter D, et al. Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Sci Rep. 2015;5:17609.CAS 
    Article 

    Google Scholar 
    Keller-Costa T, Eriksson D, Gonçalves JMS, Gomes NCM, Lago-Lestón A, Costa R. The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation. FEMS Microbiol Ecol. 2017;93. https://doi.org/10.1093/femsec/fix143.Neave MJ, Michell CT, Apprill A, Voolstra CR. Whole-genome sequences of three symbiotic Endozoicomonas strains. Genome Announc. 2014;2:e00802–14.Article 

    Google Scholar 
    Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One. 2008;3:e2836.Article 

    Google Scholar 
    Bayer T, Neave MJ, Alsheikh-Hussain A, Aranda M, Yum LK, Mincer T, et al. The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria. App Environ Microbiol. 2013;79:4759–62.CAS 
    Article 

    Google Scholar 
    Pogoreutz C, Gore MA, Perna G, Millar C, Nestler R, Ormond RF, et al. Similar bacterial communities on healthy and injured skin of black tip reef sharks. Anim Microbiome. 2019;1:9.Article 

    Google Scholar 
    Pogoreutz C, Voolstra CR. Isolation, culturing, and cryopreservation of Endozoicomonas (Gammaproteobacteria: Oceanospirillales: Endozoicomonadaceae) from reef-building corals. 2018. https://doi.org/10.17504/protocols.io.t2aeqae.Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. Chichester: John Wiley & Sons; 1991. pp. 115–75.Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.CAS 
    Article 

    Google Scholar 
    Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.CAS 
    Article 

    Google Scholar 
    Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722–36.CAS 
    Article 

    Google Scholar 
    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.CAS 
    Article 

    Google Scholar 
    Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206–14.CAS 
    Article 

    Google Scholar 
    Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444.Article 

    Google Scholar 
    Sheu S-Y, Lin K-R, Hsu M-Y, Sheu D-S, Tang S-L, Chen W-M. Endozoicomonas acroporae sp. nov., isolated from Acropora coral. Int J Syst Evol Microbiol. 2017;67:3791–7.CAS 
    Article 

    Google Scholar 
    Appolinario LR, Tschoeke DA, Rua CPJ, Venas T, Campeão ME, Amaral GRS, et al. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach. Antonie Van Leeuwenhoek. 2016;109:431–8.Article 

    Google Scholar 
    Hyun DW, Shin NR, Kim MS, Oh SJ, Kim PS, Whon TW, et al. Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. Int J Syst Evol Microbiol. 2014;64:2312–8.CAS 
    Article 

    Google Scholar 
    Schreiber L, Kjeldsen KU, Funch P, Jensen J, Obst M, López-Legentil S, et al. Endozoicomonas are specific, facultative symbionts of sea squirts. Front Microbiol. 2016;7:1042.Article 

    Google Scholar 
    Miller IJ, Weyna TR, Fong SS, Lim-Fong GE, Kwan JC. Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. Sci Rep. 2016;6:34362.CAS 
    Article 

    Google Scholar 
    Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 2013;14:60.Article 

    Google Scholar 
    Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ. 2016; 4:e1900v1.Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238.Article 

    Google Scholar 
    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.CAS 
    Article 

    Google Scholar 
    Rambaut, A FigTree. Tree Figure Drawing Tool. http://tree.bio.ed.ac.uk/software/figtree/ 2009.Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.CAS 
    Article 

    Google Scholar 
    Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36:2251–2.CAS 
    Article 

    Google Scholar 
    Kanehisa M, Sato Y. KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 2020;29:28–35.CAS 
    Article 

    Google Scholar 
    UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47:D506–D515.Article 

    Google Scholar 
    Cook CB, Davy SK. Are free amino acids responsible for the ‘host factor’ effects on symbiotic zooxanthellae in extracts of host tissue? Hydrobiologia. 2001;461:71–78.Article 

    Google Scholar 
    Davy S, Cook C. The relationship between nutritional status and carbon flux in the zooxanthellate sea anemone Aiptasia pallida. Mar Biol. 2001;139:999–1005.CAS 
    Article 

    Google Scholar 
    Wiśniewski JR, Zougman A, Mann M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res. 2009;8:5674–8.Article 

    Google Scholar 
    Tyanova S, Mann M, Cox J. MaxQuant for in-depth analysis of large SILAC datasets. Methods Mol Biol. 2014;1188:351–64.Article 

    Google Scholar 
    Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26:1367–72.CAS 
    Article 

    Google Scholar 
    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
    Article 

    Google Scholar 
    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–D596.Article 

    Google Scholar 
    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
    Article 

    Google Scholar 
    Andrews S, Krueger F, Segonds-Pichon A, Biggins L, Krueger C, Wingett S. FastQC. 2010. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.Bushnell B. BBTools software package. 2014;578:579. https://sourceforge.net/projects/bbmap/.Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.CAS 
    Article 

    Google Scholar 
    Love M, Anders S, Huber W. Differential analysis of count data–the DESeq2 package. Genome Biol. 2014;15:10–1186.Article 

    Google Scholar 
    Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286–93.CAS 
    Article 

    Google Scholar 
    Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13:731–40.CAS 
    Article 

    Google Scholar 
    Schwämmle V, Hagensen CE, Rogowska-Wrzesinska A, Jensen ON. PolySTest: robust statistical testing of proteomics data with missing values improves detection of biologically relevant features. Mol Cell Proteom. 2020;19:1396–408.Article 

    Google Scholar 
    Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47:D442–D450.CAS 
    Article 

    Google Scholar 
    Alexa A, Rahnenfuhrer J. Others. topGO: enrichment analysis for gene ontology. R package version. 2010;2:2010.
    Google Scholar 
    Walter W, Sánchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31:2912–4.CAS 
    Article 

    Google Scholar 
    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.CAS 
    Article 

    Google Scholar 
    Schulz F, Martijn J, Wascher F, Lagkouvardos I, Kostanjšek R, Ettema TJG, et al. A Rickettsiales symbiont of amoebae with ancient features. Environ Microbiol. 2016;18:2326–42.CAS 
    Article 

    Google Scholar 
    Klinges JG, Rosales SM, McMinds R, Shaver EC. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. ISME J. 2019;13:2938–53.Article 

    Google Scholar 
    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.Article 

    Google Scholar 
    Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, et al. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS One. 2013;8:e76096.CAS 
    Article 

    Google Scholar 
    Pereira-Marques J, Hout A, Ferreira RM, Weber M, Pinto-Ribeiro I, van Doorn L-J, et al. Impact of host DNA and sequencing depth on the taxonomic resolution of whole metagenome sequencing for microbiome analysis. Front Microbiol. 2019;10:1277.Article 

    Google Scholar 
    Nie L, Wu G, Culley DE, Scholten JCM, Zhang W. Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit Rev Biotechnol. 2007;27:63–75.CAS 
    Article 

    Google Scholar 
    Bathke J, Konzer A, Remes B, McIntosh M, Klug G. Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth. BMC Genomics. 2019;20:358.Article 

    Google Scholar 
    Masuda T, Saito N, Tomita M, Ishihama Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteom. 2009;8:2770–7.CAS 
    Article 

    Google Scholar 
    Chaban B, Hughes HV, Beeby M. The flagellum in bacterial pathogens: For motility and a whole lot more. Semin Cell Dev Biol. 2015;46:91–103.CAS 
    Article 

    Google Scholar 
    Gao C, Garren M, Penn K, Fernandez VI, Seymour JR, Thompson JR, et al. Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen. ISME J. 2021;15:3668–82.CAS 
    Article 

    Google Scholar 
    Hentschel U, Piel J, Degnan SM, Taylor MW. Genomic insights into the marine sponge microbiome. Nat Rev Microbiol. 2012;10:641–54.CAS 
    Article 

    Google Scholar 
    Jahn MT, Arkhipova K, Markert SM, Stigloher C, Lachnit T, Pita L, et al. A phage protein aids bacterial symbionts in eukaryote immune evasion. Cell Host Microbe. 2019;26:542–.e5.CAS 
    Article 

    Google Scholar 
    Nguyen MTHD, Liu M, Thomas T. Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis. Mol Ecol. 2014;23:1635–45.CAS 
    Article 

    Google Scholar 
    Pitulescu ME, Adams RH. Eph/ephrin molecules–a hub for signaling and endocytosis. Genes Dev. 2010;24:2480–92.CAS 
    Article 

    Google Scholar 
    Toth J, Cutforth T, Gelinas AD, Bethoney KA, Bard J, Harrison CJ. Crystal structure of an ephrin ectodomain. Dev Cell. 2001;1:83–92.CAS 
    Article 

    Google Scholar 
    Kullander K, Klein R. Mechanisms and functions of Eph and ephrin signalling. Nat Rev Mol Cell Biol. 2002;3:475–86.CAS 
    Article 

    Google Scholar 
    Duboux S, Golliard M, Muller JA, Bergonzelli G, Bolten CJ, Mercenier A, et al. Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum. Sci Rep. 2021;11:7236.CAS 
    Article 

    Google Scholar 
    Bao J, Pan G, Poncz M, Wei J, Ran M, Zhou Z. Serpin functions in host-pathogen interactions. PeerJ. 2018;6:e4557.Article 

    Google Scholar 
    Rädecker N, Pogoreutz C, Gegner HM, Cárdenas A, Roth F, Bougoure J, et al. Heat stress destabilizes symbiotic nutrient cycling in corals. Proc Natl Acad Sci USA. 2021;118:e2022653118.Article 

    Google Scholar 
    Curson AR, Todd JD, Sullivan MJ, Johnston AW. Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Reviews Microbiol. 2011;9:849–59.CAS 
    Article 

    Google Scholar 
    Pogoreutz C, Rädecker N, Cárdenas A, Gärdes A, Voolstra CR, Wild C. Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching. Glob Chang Biol. 2017;23:3838–48.Article 

    Google Scholar 
    Pogoreutz C, Rädecker N, Cárdenas A, Gärdes A, Wild C, Voolstra CR. Nitrogen fixation aligns with nifH abundance and expression in two coral trophic functional groups. Front Microbiol. 2017;8:1187.Article 

    Google Scholar 
    Falkowski PG, Dubinsky Z, Muscatine L, McCloskey L. Population control in symbiotic corals. Bioscience. 1993;43:606–11.Article 

    Google Scholar 
    Muscatine L, Cernichiari E. Assimilation of photosynthetic products of zooxanthellae by a reef coral. Biol Bull. 1969;137:506–23.CAS 
    Article 

    Google Scholar 
    Sutton DC, Hoegh-Guldberg O. Host-zooxanthella interactions in four temperate marine invertebrate symbioses: assessment of effect of host extracts on symbionts. Biol Bull. 1990;178:175–86.CAS 
    Article 

    Google Scholar 
    Wang JT, Douglas AE. Essential amino acid synthesis and nitrogen recycling in an alga–invertebrate symbiosis. Mar Biol. 1999;135:219–22.CAS 
    Article 

    Google Scholar 
    Lipschultz F, Cook C. Uptake and assimilation of 15N-ammonium by the symbiotic sea anemones Bartholomea annulata and Aiptasia pallida: conservation versus recycling of nitrogen. Mar Biol. 2002;140:489–502.CAS 
    Article 

    Google Scholar 
    Matthews JL, Oakley CA, Lutz A, Hillyer KE, Roessner U, Grossman AR, et al. Partner switching and metabolic flux in a model cnidarian–dinoflagellate symbiosis. Proc R Soc B: Biol Sci. 2018;285:20182336.CAS 
    Article 

    Google Scholar 
    Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, et al. Chemotaxis by natural populations of coral reef bacteria. ISME J. 2015;9:1764–77.Article 

    Google Scholar 
    Raina J-B, Fernandez V, Lambert B, Stocker R, Seymour JR. The role of microbial motility and chemotaxis in symbiosis. Nat Rev Microbiol. 2019;17:284–94.CAS 
    Article 

    Google Scholar 
    Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature. 2005;438:90–93.CAS 
    Article 

    Google Scholar 
    Tang YZ, Koch F, Gobler CJ. Most harmful algal bloom species are vitamin B1 and B12 auxotrophs. Proc Natl Acad Sci USA. 2010;107:20756–61.CAS 
    Article 

    Google Scholar 
    Salem H, Bauer E, Strauss AS, Vogel H, Marz M, Kaltenpoth M. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. Proc R Soc B: Biol Sci. 2014;281:20141838.Article 

    Google Scholar 
    Douglas AE. The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes. Curr Opin Insect Sci. 2017;23:65–69.Article 

    Google Scholar 
    Agostini S, Suzuki Y, Casareto BE, Nakano Y, Michio H, Badrun N. Coral symbiotic complex: Hypothesis through vitamin B12 for a new evaluation. Galaxea J Coral Reef Stud. 2009;11:1–11.Article 

    Google Scholar 
    Fitzpatrick TB, Chapman LM. The importance of thiamine (vitamin B1) in plant health: From crop yield to biofortification. J Biol Chem. 2020;295:12002–13.CAS 
    Article 

    Google Scholar 
    Bertrand EM, Allen AE. Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton. Front Microbiol. 2012;3:375.CAS 
    Article 

    Google Scholar 
    Bourne D, Iida Y, Uthicke S, Smith-Keune C. Changes in coral-associated microbial communities during a bleaching event. ISME J. 2008;2:350–63.CAS 
    Article 

    Google Scholar 
    Court SJ, Waclaw B, Allen RJ. Lower glycolysis carries a higher flux than any biochemically possible alternative. Nat Commun. 2015;6:8427.CAS 
    Article 

    Google Scholar 
    Ziegler M, Seneca FO, Yum LK, Palumbi SR, Voolstra CR. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat Commun. 2017;8:14213.CAS 
    Article 

    Google Scholar 
    Peixoto RS, Sweet M, Villela HDM, Cardoso P, Thomas T, Voolstra CR, et al. Coral probiotics: premise, promise, prospects. Annu Rev Anim Biosci. 2021;9:265–88.Article 

    Google Scholar 
    Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 2017;11:853–62.Article 

    Google Scholar 
    Santos HF, Carmo FL, Duarte G, Dini-Andreote F, Castro CB, Rosado AS, et al. Climate change affects key nitrogen-fixing bacterial populations on coral reefs. ISME J. 2014;8:2272–9.Article 

    Google Scholar  More