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    Marine phytoplankton functional types exhibit diverse responses to thermal change

    1.Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: Integrating terrestrial and cceanic components. Science 281, 237–240 (1998).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    2.Falkowski, P. G., Barber, R. T. & Smetacek, V. Biogeochemical controls and feedbacks on ocean primary production. Science 281, 200–206 (1998).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Deutsch, C. A. et al. Impacts of climate warming on terrestrial ectotherms across latitude. Proc. Natl Acad. Sci. USA 105, 6668–6672 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    4.Comte, L. & Olden, J. D. Climatic vulnerability of the world’s freshwater and marine fishes. Nat. Clim. Chang. 7, 718–722 (2017).ADS 
    Article 

    Google Scholar 
    5.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).ADS 
    CAS 
    Article 

    Google Scholar 
    6.Sarmiento, J. L. et al. Response of ocean ecosystems to climate warming. Glob. Biogeochem. Cycles 18, GB3003 (2004).ADS 
    Article 
    CAS 

    Google Scholar 
    7.Taucher, J. & Oschlies, A. Can we predict the direction of marine primary production change under global warming? Geophys. Res. Lett. 38, 1–6 (2011).Article 
    CAS 

    Google Scholar 
    8.Vallina, S. M., Cermeno, P., Dutkiewicz, S., Loreau, M. & Montoya, J. M. Phytoplankton functional diversity increases ecosystem productivity and stability. Ecol. Modell. 361, 184–196 (2017).Article 

    Google Scholar 
    9.Dutkiewicz, S. et al. Impact of ocean acidification on the structure of future phytoplankton communities. Nat. Clim. Chang. 5, 1002–1006 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    10.Laufkotter, C. et al. Drivers and uncertainties of future global marine primary production in marine ecosystem models. Biogeosciences 12, 6955–6984 (2015).ADS 
    Article 

    Google Scholar 
    11.Behrenfeld, M. J., Boss, E., Siegel, D. A. & Shea, D. M. Carbon-based ocean productivity and phytoplankton physiology from space. Glob. Biogeochem. Cycles 19, 1–14 (2005).Article 
    CAS 

    Google Scholar 
    12.Anderson, S. I. & Rynearson, T. A. Variability approaching the thermal limits can drive diatom community dynamics. Limnol. Oceanogr. 65, 1961–1973 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    13.Boyd, P. W. Physiology and iron modulate diverse responses of diatoms to a warming Southern Ocean. Nat. Clim. Chang. 9, 148–152 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    14.Thomas, M. K. & Litchman, E. Effects of temperature and nitrogen availability on the growth of invasive and native cyanobacteria. Hydrobiologia 763, 357–369 (2016).Article 

    Google Scholar 
    15.Kremer, C. T., Thomas, M. K. & Litchman, E. Temperature- and size-scaling of phytoplankton population growth rates: Reconciling the Eppley curve and the metabolic theory of ecology. Limnol. Oceanogr. 62, 1658–1670 (2017).ADS 
    Article 

    Google Scholar 
    16.Edwards, K. F., Thomas, M. K., Klausmeier, C. A. & Litchman, E. Allometric scaling and taxonomic variation in nutrient utilization traits and maximum growth rate of phytoplankton. Limnol. Oceanogr. 57, 554–566 (2012).ADS 
    Article 

    Google Scholar 
    17.Poloczanska, E. S. et al. Global imprint of climate change on marine life. Nat. Clim. Chang. 3, 919–925 (2013).ADS 
    Article 

    Google Scholar 
    18.Thomas, M. K., Kremer, C. T., Klausmeier, C. A. & Litchman, E. A global pattern of thermal adaptation in marine phytoplankton. Science 338, 1085–1088 (2012).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Righetti, D., Vogt, M., Gruber, N., Psomas, A. & Zimmermann, N. E. Global pattern of phytoplankton diversity driven by temperature and environmental variability. Sci. Adv. 5, 1–11 (2019).Article 

    Google Scholar 
    20.Barton, A. D., Irwin, A. J., Finkel, Z. V. & Stock, C. A. Anthropogenic climate change drives shift and shuffle in North Atlantic phytoplankton communities. Proc. Natl Acad. Sci. USA 113, 2964–2969 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.García Molinos, J. et al. Climate velocity and the future global redistribution of marine biodiversity. Nat. Clim. Chang. 6, 4–11 (2015).
    Google Scholar 
    22.Uitz, J., Claustre, H., Gentili, B. & Stramski, D. Phytoplankton class-specific primary production in the world’s oceans: Seasonal and interannual variability from satellite observations. Glob. Biogeochem. Cycles 24, 1–19 (2010).Article 
    CAS 

    Google Scholar 
    23.Toseland, A. et al. The impact of temperature on marine phytoplankton resource allocation and metabolism. Nat. Clim. Chang. 3, 979–984 (2013).ADS 
    CAS 
    Article 

    Google Scholar 
    24.Boyd, P. W. & Hutchins, D. A. Understanding the responses of ocean biota to a complex matrix of cumulative anthropogenic change. Mar. Ecol. Prog. Ser. 470, 125–135 (2012).ADS 
    Article 

    Google Scholar 
    25.Bopp, L. et al. Multiple stressors of ocean ecosystems in the 21st century: Projections with CMIP5 models. Biogeosciences 10, 6225–6245 (2013).ADS 
    Article 

    Google Scholar 
    26.Thomas, M. K., Kremer, C. T. & Litchman, E. Environment and evolutionary history determine the global biogeography of phytoplankton temperature traits. Glob. Ecol. Biogeogr. 25, 75–86 (2016).Article 

    Google Scholar 
    27.Angilletta, M. J. Thermal Adaptation: A Theoretical and Empirical Synthesis (Oxford University Press, 2009).28.Eppley, R. W. Temperature and phytoplankton growth in the sea. Fish. Bull. 70, 1063–1085 (1972).
    Google Scholar 
    29.Bissinger, J. E., Montagnes, D. J. S., Sharples, J. & Atkinson, D. Predicting marine phytoplankton maximum growth rates from temperature: Improving on the Eppley curve using quantile regression. Limnol. Oceanogr. 53, 487–493 (2008).ADS 
    Article 

    Google Scholar 
    30.Prowe, A. E. F., Pahlow, M., Dutkiewicz, S. & Oschlies, A. How important is diversity for capturing environmental-change responses in ecosystem models? Biogeosciences 11, 3397–3407 (2014).ADS 
    Article 

    Google Scholar 
    31.Chen, B. & Liu, H. Relationships between phytoplankton growth and cell size in surface oceans: Interactive effects of temperature, nutrients, and grazing. Limnol. Oceanogr. 55, 965–972 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    32.Barton, S. & Yvon‐Durocher, G. Quantifying the temperature dependence of growth rate in marine phytoplankton within and across species. Limnol. Oceanogr. 64, 2081–2091 (2019).ADS 
    Article 

    Google Scholar 
    33.Sherman, E., Moore, J. K., Primeau, F. & Tanouye, D. Temperature influence on phytoplankton community growth rates. Glob. Biogeochem. Cycles 30, 550–559 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    34.Alexander, H. et al. Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean. Proc. Natl Acad. Sci. USA 112, E5972–E5979 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Cermeño, P. et al. The role of nutricline depth in regulating the ocean carbon cycle. Proc. Natl Acad. Sci. USA 105, 20344–20349 (2008).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Calvo, E., Pelejero, C., Pena, L. D., Cacho, I. & Logan, G. A. Eastern Equatorial Pacific productivity and related-CO2 changes since the last glacial period. Proc. Natl Acad. Sci. USA 108, 5537–5541 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.McCabe, R. M. et al. An unprecedented coastwide toxic algal bloom linked to anomalous ocean conditions. Geophys. Res. Lett. 43, 10,366–10,376 (2016).Article 

    Google Scholar 
    38.Roberts, S. D., Van Ruth, P. D., Wilkinson, C., Bastianello, S. S. & Bansemer, M. S. Marine heatwave, harmful algae blooms and an extensive fish kill event during 2013 in South Australia. Front. Mar. Sci. 6, 1–20 (2019).CAS 
    Article 

    Google Scholar 
    39.Oliver, E. C. J. et al. Longer and more frequent marine heatwaves over the past century. Nat. Commun. 9, 1–12 (2018).CAS 
    Article 

    Google Scholar 
    40.Oliver, E. C. J. et al. Projected marine heatwaves in the 21st century and the potential for ecological impact. Front. Mar. Sci. 6, 1–12 (2019).MathSciNet 
    Article 

    Google Scholar 
    41.Keeling, P. J. The endosymbiotic origin, diversification and fate of plastids. Philos. Trans. R. Soc. B Biol. Sci. 365, 729–748 (2010).CAS 
    Article 

    Google Scholar 
    42.Yoon, H. S., Hackett, J. D., Pinto, G. & Bhattacharya, D. The single, ancient origin of chromist plastids. Proc. Natl Acad. Sci. USA 99, 15507–15512 (2002).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    43.Pinsky, M. L., Eikeset, A. M., McCauley, D. J., Payne, J. L. & Sunday, J. M. Greater vulnerability to warming of marine versus terrestrial ectotherms. Nature 569, 108–111 (2019).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    44.Sunday, J. M. et al. Thermal-safety margins and the necessity of thermoregulatory behavior across latitude and elevation. Proc. Natl Acad. Sci. USA 111, 5610–5615 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    45.Jönsson, B. F. & Watson, J. R. The timescales of global surface-ocean connectivity. Nat. Commun. 7, 1–6 (2016).Article 
    CAS 

    Google Scholar 
    46.Doblin, M. A. & van Sebille, E. Drift in ocean currents impacts intergenerational microbial exposure to temperature. Proc. Natl Acad. Sci. USA 113, 5700–5705 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Whittaker, K. & Rynearson, T. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow. Proc. Natl Acad. Sci. USA 114, 2651–2656 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    48.Ward, B. A., Cael, B. B., Collins, S. & Robert Young, C. Selective constraints on global plankton dispersal. Proc. Natl Acad. Sci. USA 118, 1–7 (2021).
    Google Scholar 
    49.Huey, R. B. & Stevenson, R. D. Integrating thermal physiology and ecology of ectotherms: A discussion of approaches. Integr. Comp. Biol. 19, 357–366 (1979).
    Google Scholar 
    50.Collins, M. et al. in Climate change 2013: The physical science basis. Contribution of working group I to the fifth assessment report of the Intergovernmental Panel on Climate Change (eds. Stocker, T. F. et al.) 1029–1136 (Cambridge University Press, 2013).51.Bopp, L., Aumont, O., Cadule, P., Alvain, S. & Gehlen, M. Response of diatoms distribution to global warming and potential implications: A global model study. Geophys. Res. Lett. 32, L19606 (2005).ADS 
    Article 
    CAS 

    Google Scholar 
    52.Ward, B. A. Temperature-correlated changes in phytoplankton community structure are restricted to polar waters. PLoS ONE 10, 1–15 (2015).
    Google Scholar 
    53.Winter, A., Henderiks, J., Beaufort, L., Rickaby, R. E. M. & Brown, C. W. Poleward expansion of the coccolithophore Emiliania huxleyi. J. Plankton Res. 36, 316–325 (2014).CAS 
    Article 

    Google Scholar 
    54.Rivero-Calle, S., Gnanadesikan, A., Del Castillo, C. E., Balch, W. M. & Guikema, S. D. Multidecadal increase in North Atlantic coccolithophores and the potential role of rising CO2. Science 350, 1533–1537 (2015).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Steinacher, M. et al. Projected 21st century decrease in marine productivity: a multi-model analysis. Biogeosciences Discuss. 7, 979–1005 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    56.Arrigo, K. R., van Dijken, G. L. & Strong, A. L. Environmental controls of marine productivity hot spots around Antarctica. J. Geophys. Res. Ocean. 120, 2813–2825 (2015).Article 

    Google Scholar 
    57.Aranguren-Gassis, M., Kremer, C. T., Klausmeier, C. A. & Litchman, E. Nitrogen limitation inhibits marine diatom adaptation to high temperatures. Ecol. Lett. 22, 1860–1869 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    58.Edwards, K. F., Thomas, M. K., Klausmeier, C. A. & Litchman, E. Phytoplankton growth and the interaction of light and temperature: A synthesis at the species and community level. Limnol. Oceanogr. 61, 1232–1244 (2016).ADS 
    Article 

    Google Scholar 
    59.Ibarbalz, F. M. et al. Global trends in marine plankton diversity across kingdoms of life. Cell 179, 1084–1097.e21 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl Acad. Sci. USA 103, 9130–9135 (2006).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    61.Padfield, D., Yvon-Durocher, G., Buckling, A., Jennings, S. & Yvon-Durocher, G. Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecol. Lett. 19, 133–142 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    62.Baker, K. G. et al. Thermal niche evolution of functional traits in a tropical marine phototroph. J. Phycol. 54, 799–810 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    63.O’Donnell, D. R. et al. Rapid thermal adaptation in a marine diatom reveals constraints and trade-offs. Glob. Chang. Biol. 24, 4554–4565 (2018).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Seong, K. A., Jeong, H. J., Kim, S., Kim, G. H. & Kang, J. H. Bacterivory by co-occurring red-tide algae, heterotrophic nanoflagellates, and ciliates. Mar. Ecol. Prog. Ser. 322, 85–97 (2006).ADS 
    Article 

    Google Scholar 
    65.Arizona Software Inc. GraphClick 3.0.2. http://www.arizona-software.ch/graphclick/ (2010).66.Norberg, J. Biodiversity and ecosystem functioning: a complex adaptive systems approach. Limnol. Oceanogr. 49, 1269–1277 (2004).ADS 
    Article 

    Google Scholar 
    67.Bolker, B. & Team, R. D. C. bbmle: Tools for general maximum likelihood estimation. https://github.com/bbolker/bbmle (2017).68.R Core Team. R: A language and environment for statistical computing. https://www.R-project.org/ (2020).69.Riahi, K. et al. RCP 8.5-A scenario of comparatively high greenhouse gas emissions. Clim. Change 109, 33–57 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    70.Koenker, R. quantreg: Quantile regression. https://cran.r-project.org/package=quantreg (2019).71.Chen, B. & Laws, E. A. Is there a difference of temperature sensitivity between marine phytoplankton and heterotrophs? Limnol. Oceanogr. 62, 806–817 (2017).ADS 
    Article 

    Google Scholar 
    72.Sal, S., Alonso-Saez, L., Bueno, J., Garcıa, F. C. & Lopez-Urrutia, A. Thermal adaptation, phylogeny, and the unimodal size scaling of marine phytoplankton growth. Limnol. Oceanogr. 60, 1212–1221 (2015).ADS 
    Article 

    Google Scholar 
    73.Koenker, R. Quantile Regression, https://doi.org/10.1017/CBO9780511754098 (Cambridge University Press, 2005).74.Tomas, C. R. et al. Identifying Marine Phytoplankton. (Academic Press, 1997).75.He, X. & Hu, F. Markov chain marginal bootstrap. J. Am. Stat. Assoc. 97, 783–795 (2002).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    76.Rynearson, T. A. Literature compilation of thermal growth rates from four phytoplankton functional types. Biological and Chemical Oceanography Data Management Office (BCO-DMO), (2021). https://doi.org/10.26008/1912/bco-dmo.839696.177.Rynearson, T. A. Estimated thermal capacities for phytoplankton strains. Biological and Chemical Oceanography Data Management Office (BCO-DMO), https://doi.org/10.26008/1912/bco-dmo.839713.1 (2021).78.Rynearson, T. A. Estimated thermal traits for phytoplankton. Biological and Chemical Oceanography Data Management Office (BCO-DMO), https://doi.org/10.26008/1912/bco-dmo.839689.1 (2021).79.Anderson, S. I. sianderson/PFT_thermal_response: Marine Phytoplankton Functional Types Exhibit Diverse Responses to Thermal Change. zenodo. https://doi.org/10.5281/zenodo.5507532 (2021).80.Buitenhuis, E. T., Pangerc, T., Franklin, D. J., Le Quéré, C. & Malin, G. Growth rates of six coccolithophorid strains as a function of temperature. Limnol. Oceanogr. 53, 1181–1185 (2008).ADS 
    Article 

    Google Scholar 
    81.Stawiarski, B., Buitenhuis, E. T. & Le Quéré, C. The physiological response of picophytoplankton to temperature and its model representation. Front. Mar. Sci. 3, 1–13 (2016).Article 

    Google Scholar  More

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    Toxicity thresholds of nine herbicides to coral symbionts (Symbiodiniaceae)

    1.Castillo, L. E., de la Cruz, E. & Ruepert, C. Ecotoxicology and pesticides in tropical aquatic ecosystems of Central America. Environ. Toxicol. Chem. 16, 41–51. https://doi.org/10.1002/etc.5620160104 (1997).Article 
    CAS 

    Google Scholar 
    2.Moreno-González, R. & León, V. Presence and distribution of current-use pesticides in surface marine sediments from a Mediterranean coastal lagoon (SE Spain). Environ. Sci. Pollut. Res. 24, 8033–8048. https://doi.org/10.1007/s11356-017-8456-0 (2017).Article 
    CAS 

    Google Scholar 
    3.Hernández-Romero, A. H., Tovilla-Hernández, C., Malo, E. A. & Bello-Mendoza, R. Water quality and presence of pesticides in a tropical coastal wetland in southern Mexico. Mar. Pollut. Bull. 48, 1130–1141. https://doi.org/10.1016/j.marpolbul.2004.01.003 (2004).Article 
    PubMed 
    CAS 

    Google Scholar 
    4.Wurl, O. & Obbard, J. P. Organochlorine pesticides, polychlorinated biphenyls and polybrominated diphenyl ethers in Singapore’s coastal marine sediments. Chemosphere 58, 925–933. https://doi.org/10.1016/j.chemosphere.2004.09.054 (2005).ADS 
    Article 
    PubMed 
    CAS 

    Google Scholar 
    5.Carvalho, F. P. et al. Organic contaminants in the marine environment of Manila Bay, Philippines. Arch. Environ. Contam. Toxicol. 57, 348–358. https://doi.org/10.1007/s00244-008-9271-x (2009).Article 
    PubMed 
    CAS 

    Google Scholar 
    6.Australian Government and Queensland Government. Reef 2050 Water Quality Improvement Plan, Monitoring Program. (Australian and Queensland Governments, 2018). https://www.reefplan.qld.gov.au/tracking-progress/paddock-to-reef/modelling-and-monitoring.7.O’Brien, D. et al. Spatial and temporal variability in pesticide exposure downstream of a heavily irrigated cropping area: Application of different monitoring techniques. J. Agric. Food Chem. 64, 3975–3989. https://doi.org/10.1021/acs.jafc.5b04710 (2016).Article 
    PubMed 
    CAS 

    Google Scholar 
    8.Warne, M. St. J., Smith, R. & Turner, R. Analysis of pesticide mixtures discharged to the lagoon of the Great Barrier Reef, Australia. Environ. Pollut. 265, 114088. https://doi.org/10.1016/j.envpol.2020.114088 (2020).Article 
    PubMed 
    CAS 

    Google Scholar 
    9.Shaw, M. et al. Monitoring pesticides in the Great Barrier Reef. Mar. Pollut. Bull. 60, 113–122. https://doi.org/10.1016/j.marpolbul.2009.08.026 (2010).Article 
    PubMed 
    CAS 

    Google Scholar 
    10.Kennedy, K. et al. The influence of a season of extreme wet weather events on exposure of the World Heritage Area Great Barrier Reef to pesticides. Mar. Pollut. Bull. 64, 1495–1507. https://doi.org/10.1016/j.marpolbul.2012.05.014 (2012).Article 
    PubMed 
    CAS 

    Google Scholar 
    11.Mercurio, P. et al. Degradation of herbicides in the tropical marine environment: Influence of light and sediment. PLoS ONE 11, e0165890. https://doi.org/10.1371/journal.pone.0165890 (2016).Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    12.Gallen, C. et al. Marine Monitoring Program: Annual report for inshore pesticide monitoring 2017–18. Report for the Great Barrier Reef Marine Park Authority. http://elibrary.gbrmpa.gov.au/jspui/handle/11017/3489. (2019).13.Smith, R. et al. Large-scale pesticide monitoring across Great Barrier Reef catchments–paddock to reef integrated monitoring, modelling and reporting program. Mar. Pollut. Bull. 65, 117–127. https://doi.org/10.1016/j.marpolbul.2011.08.010 (2012).Article 
    PubMed 
    CAS 

    Google Scholar 
    14.Oettmeier, W. Herbicide resistance and supersensitivity in photosystem II. Cell. Mol. Life Sci. 55, 1255–1277. https://doi.org/10.1007/s000180050370 (1999).Article 
    PubMed 
    CAS 

    Google Scholar 
    15.Davis, A., Lewis, S., Brodie, J. & Benson, A. The potential benefits of herbicide regulation: A cautionary note for the Great Barrier Reef catchment area. Sci. Total Environ. 490, 81–92. https://doi.org/10.1016/j.scitotenv.2014.04.005 (2014).ADS 
    Article 
    PubMed 
    CAS 

    Google Scholar 
    16.King, J., Alexander, F. & Brodie, J. Regulation of pesticides in Australia: The Great Barrier Reef as a case study for evaluating effectiveness. Agr. Ecosyst. Environ. 180, 54–67. https://doi.org/10.1016/j.agee.2012.07.001 (2013).Article 

    Google Scholar 
    17.Devlin, M. et al. Advancing our Understanding of the Source, Management, Transport and Impacts of Pesticides on the Great Barrier Reef 2011–2015. Report for the Queensland Department of Environment and Heritage Protection. (Tropical Water & Aquatic Ecosytem Research (TropWATER) Publication, James Cook University, 2015). https://www.qld.gov.au/environment/assets/documents/agriculture/sustainable-farming/reef/rp104c-pesticide-report.pdf/.18.Flores, F., Collier, C. J., Mercurio, P. & Negri, A. P. Phytotoxicity of four photosystem II herbicides to tropical seagrasses. PLoS ONE 8, e75798. https://doi.org/10.1371/journal.pone.0075798 (2013).ADS 
    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    19.Haynes, D. et al. The occurrence and impact of herbicides in the Great Barrier Reef, Australia. Reef Res. 10, 3–5 (2000).
    Google Scholar 
    20.Negri, A. P., Flores, F., Röthig, T. & Uthicke, S. Herbicides increase the vulnerability of corals to rising sea surface temperature. Limnol. Oceanogr. 56, 471–485. https://doi.org/10.4319/lo.2011.56.2.0471 (2011).ADS 
    Article 
    CAS 

    Google Scholar 
    21.Marques, J. A., Flores, F., Bianchini, A., Uthicke, S. & Negri, A. P. Acclimation history modulates effect size of calcareous algae (Halimeda opuntia) to herbicide exposure under future climate scenarios. Sci. Total Environ. 736, 140308. https://doi.org/10.1016/j.scitotenv.2020.140308 (2020).Article 
    CAS 

    Google Scholar 
    22.van Dam, J. W., Negri, A. P., Mueller, J. F. & Uthicke, S. Symbiont-specific responses in foraminifera to the herbicide diuron. Mar. Pollut. Bull. 65, 373–383. https://doi.org/10.1016/j.marpolbul.2011.08.008 (2012).Article 
    PubMed 
    CAS 

    Google Scholar 
    23.Thomas, M. C., Flores, F., Kaserzon, S., Fisher, R. & Negri, A. P. Toxicity of ten herbicides to the tropical marine microalgae Rhodomonas salina. Sci. Rep. 10, 1–16. https://doi.org/10.1038/s41598-020-64116-y (2020).Article 
    CAS 

    Google Scholar 
    24.Magnusson, M., Heimann, K. & Negri, A. P. Comparative effects of herbicides on photosynthesis and growth of tropical estuarine microalgae. Mar. Pollut. Bull. 56, 1545–1552. https://doi.org/10.1016/j.marpolbul.2008.05.023 (2008).Article 
    PubMed 
    CAS 

    Google Scholar 
    25.Muscatine, L. The role of symbiotic algae in carbon and energy flux in reef corals. Coral Reefs 25, 1–29 (1990).
    Google Scholar 
    26.Oettmeier, W. Herbicides of photosystems II. In Structure, Function and Molecular Biology (ed. Barber, J.) 349–408 (Elsevier, 1992).
    Google Scholar 
    27.Jones, R. J., Muller, J., Haynes, D. & Schreiber, U. Effects of herbicides diuron and atrazine on corals of the Great Barrier Reef, Australia. Mar. Ecol. Prog. Ser. 251, 153–167. https://doi.org/10.3354/meps251153 (2003).ADS 
    Article 
    CAS 

    Google Scholar 
    28.Jones, R. J. & Kerswell, A. P. Phytotoxicity of Photosystem II (PSII) herbicides to coral. Mar. Ecol. Prog. Ser. 261, 149–159. https://doi.org/10.3354/meps261149 (2003).ADS 
    Article 
    CAS 

    Google Scholar 
    29.Cantin, N. E., Negri, A. P. & Willis, B. L. Photoinhibition from chronic herbicide exposure reduces reproductive output of reef-building corals. Mar. Ecol. Prog. Ser. 344, 81–93. https://doi.org/10.3354/meps07059 (2007).ADS 
    Article 
    CAS 

    Google Scholar 
    30.Negri, A. et al. Effects of the herbicide diuron on the early life history stages of coral. Mar. Pollut. Bull. 51, 370–383. https://doi.org/10.1016/j.marpolbul.2004.10.053 (2005).Article 
    PubMed 
    CAS 

    Google Scholar 
    31.Decelle, J. et al. Worldwide occurrence and activity of the reef-building coral symbiont Symbiodinium in the open ocean. Curr. Biol. 28, 3625–3633. https://doi.org/10.1016/j.cub.2018.09.024 (2018).Article 
    PubMed 
    CAS 

    Google Scholar 
    32.Baker, A. C. Reef corals bleach to survive change. Nature 411, 765–766. https://doi.org/10.1038/35081151 (2001).ADS 
    Article 
    PubMed 
    CAS 

    Google Scholar 
    33.Muller-Parker, G., D’elia, C. F. & Cook, C. B. Coral Reefs in the Anthropocene 99–116 (Springer, 2015). https://pdfs.semanticscholar.org/191e119/119ba111eab744a4054c4068f4057a4003bb4058bd4001b9628.pdf.34.Chakravarti, L. J., Negri, A. P. & Oppen, M. J. Thermal and herbicide tolerances of chromerid algae and their ability to form a symbiosis with corals. Front. Microbiol. 10, 173. https://doi.org/10.3389/fmicb.2019.00173 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    35.van Dam, J., Uthicke, S., Beltran, V., Mueller, J. & Negri, A. Combined thermal and herbicide stress in functionally diverse coral symbionts. Environ. Pollut. 204, 271–279. https://doi.org/10.1016/j.envpol.2015.05.013 (2015).Article 
    PubMed 
    CAS 

    Google Scholar 
    36.Mercurio, P. et al. Contribution of transformation products towards the total herbicide toxicity to tropical marine organisms. Sci. Rep. 8, 1–12. https://doi.org/10.1038/s41598-018-23153-4 (2018).Article 
    CAS 

    Google Scholar 
    37.Magnusson, M., Heimann, K., Ridd, M. & Negri, A. P. Pesticide contamination and phytotoxicity of sediment interstitial water to tropical benthic microalgae. Water Res. 47, 5211–5221. https://doi.org/10.1016/j.watres.2013.06.003 (2013).Article 
    PubMed 
    CAS 

    Google Scholar 
    38.Thomas, M. C., Flores, F., Kaserzon, S., Reeks, T. & Negri, A. P. Toxicity of the herbicides diuron, propazine, tebuthiuron, and haloxyfop to the diatom Chaetoceros muelleri. Sci. Rep. 10, 19592. https://doi.org/10.1038/s41598-020-76363-0 (2020).ADS 
    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    39.Warne, M. St. J., King, O. & Smith, R. Ecotoxicity thresholds for ametryn, diuron, hexazinone and simazine in fresh and marine waters. Environ. Sci. Pollut. Res. 25, 3151–3169. https://doi.org/10.1007/s11356-017-1097-5 (2018).Article 
    CAS 

    Google Scholar 
    40.Traas, T. P. et al. In Species Sensitivity Distributions in Ecotoxicology (eds Posthuma, L. et al.) 315–344 (CRC Press, 2002).
    Google Scholar 
    41.ANZG. Australian and New Zealand Guidelines for Fresh and Marine Water Quality. 1–103 (Australian and New Zealand Governments and Australian State and Territory Governments, 2018). http://waterquality.gov.au/anz-guidelines.42.King, O., Smith, R., Mann, R. & Warne, M. St. J. Proposed Aquatic Ecosystem Protection Guideline Values for Pesticides Commonly Used in the Great Barrier Reef catchment Area: Part 2— Bromacil, Chlorothalonil, Fipronil, Fluometuron, Fluroxypyr, Haloxyfop, MCPA, Pendimethalin, Prometryn, Propazine, Propiconazole, Terbutryn, Triclopyr and Terbuthylazine. (Department of Environment and Science, 2017). https://www.publications.qld.gov.au/dataset/proposed-guideline-values-27-pesticides-used-in-the-gbr-catchment.43.King, O., Smith, R., Mann, R. & Warne, M. St. J. Proposed Aquatic Ecosystem Protection Guideline Values for Pesticides Commonly Used in the Great Barrier Reef Catchment Area: Part 1–2, 4-D, Ametryn, Diuron, Glyphosate, Hexazinone, Imazapic, Imidacloprid, Isoxaflutole, Metolachlor, Metribuzin, Metsulfuron-methyl, Simazine and Tebuthiuron 296 (Department of Environment and Science, 2017). https://www.publications.qld.gov.au/dataset/proposed-guideline-values-27-pesticides-used-in-the-gbr-catchment.44.Marie, D., Rigaut-Jalabert, F. & Vaulot, D. An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples. Cytom. Part A 85, 962–968. https://doi.org/10.1002/cyto.a.22517 (2014).Article 
    CAS 

    Google Scholar 
    45.Warne, M. St. J. et al. Revised Method for Deriving Australian and New Zealand Water Quality Guideline Values for Toxicants: Update of 2015 Version. Prepared for the Revision of the Australian and New Zealand Guidelines for Fresh and Marine Water Quality 48 (Australian and New Zealand Governments and Australian State and Territory Governments, 2018). https://www.waterquality.gov.au/sites/default/files/documents/warne-wqg-derivation2018.pdf.46.Vinyard, D. J., Ananyev, G. M. & Charles Dismukes, G. Photosystem II: The reaction center of oxygenic photosynthesis. Annu. Rev. Biochem. 82, 577–606. https://doi.org/10.1146/annurev-biochem-070511-100425 (2013).Article 
    PubMed 
    CAS 

    Google Scholar 
    47.Haworth, P. & Steinback, K. E. Interaction of herbicides and quinone with the qb-protein of the diuron-resistant Chlamydomonas reinhardtii mutant Dr2. Plant Physiol. 83, 1027–1031. https://doi.org/10.1104/pp.83.4.1027 (1987).Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    48.USEPA. ECOTOX User Guide: ECOTOXicology Database System. Version 5.0. (United States Environmental Protection Agency, 2019) http://cfpub.epa.gov/ecotox/.49.Magnusson, M. Effects of Priority Herbicides and Their Breakdown Products on Tropical, ESTUARINE Microalgae of the Great Barrier Reef Lagoon. PhD thesis, James Cook University (2009).50.MacBean, C. The Pesticide Manual: A World Compendium (British Crop Protection Council, 2012).
    Google Scholar 
    51.Haq, S., Bachvaroff, T. R. & Place, A. R. Characterization of acetyl-CoA carboxylases in the basal dinoflagellate Amphidinium carterae. Mar. Drugs 15, 149. https://doi.org/10.3390/md15060149 (2017).Article 
    PubMed Central 
    CAS 

    Google Scholar 
    52.Tang, C. Y., Huang, Z. & Allen, H. C. Interfacial water structure and effects of Mg2+ and Ca2+ binding to the COOH headgroup of a palmitic acid monolayer studied by sum frequency spectroscopy. J. Phys. Chem. B 115, 34–40. https://doi.org/10.1021/jp1062447 (2011).Article 
    PubMed 
    CAS 

    Google Scholar 
    53.Brzozowska, A., Duits, M. H. & Mugele, F. Stability of stearic acid monolayers on artificial sea water. Colloid Surf. A 407, 38–48 (2012).Article 
    CAS 

    Google Scholar 
    54.McCourt, J. & Duggleby, R. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 31, 173–210. https://doi.org/10.1007/s00726-005-0297-3 (2006).Article 
    PubMed 
    CAS 

    Google Scholar 
    55.Genty, B., Briantais, J.-M. & Baker, N. R. The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. BBA 990, 87–92. https://doi.org/10.1016/S0304-4165(89)80016-9 (1989).Article 
    CAS 

    Google Scholar 
    56.Jeong, H. J. et al. Heterotrophic feeding as a newly identified survival strategy of the dinoflagellate Symbiodinium. Proc. Natl. Acad. Sci. U.S.A. 109, 12604–12609. https://doi.org/10.1073/pnas.1204302109 (2012).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    57.Ralph, P., Smith, R., Macinnis-Ng, C. & Seery, C. Use of fluorescence-based ecotoxicological bioassays in monitoring toxicants and pollution in aquatic systems. Toxicol. Environ. Chem. 89, 589–607. https://doi.org/10.1080/02772240701561593 (2007).Article 
    CAS 

    Google Scholar 
    58.OECD. Test No. 201: Freshwater Alga and Cyanobacteria, Growth Inhibition Test, OECD Guidelines for the Testing of Chemicals, Section 2 (OECD Publishing, 2011).
    Google Scholar 
    59.Kamei, M., Takayama, K., Ishibashi, H. & Takeuchi, I. Effects of ecologically relevant concentrations of Irgarol 1051 in tropical to subtropical coastal seawater on hermatypic coral Acropora tenuis and its symbiotic dinoflagellates. Mar. Poll. Bull. 150, 110734. https://doi.org/10.1016/j.marpolbul.2019.110734 (2020).Article 
    CAS 

    Google Scholar 
    60.McKenzie, M. R., Templeman, M. A. & Kingsford, M. J. Detecting effects of herbicide runoff: The use of Cassiopea maremetens as a biomonitor to hexazinone. Aquat. Toxicol. 221, 105442. https://doi.org/10.1016/j.aquatox.2020.105442 (2020).Article 
    PubMed 
    CAS 

    Google Scholar 
    61.Howe, P. L., Reichelt-Brushett, A. J., Clark, M. W. & Seery, C. R. Toxicity estimates for diuron and atrazine for the tropical marine cnidarian Exaiptasia pallida and in-hospite Symbiodinium spp. using PAM chlorophyll-a fluorometry. J. Photochem. Photobiol. B 171, 125–132. https://doi.org/10.1016/j.jphotobiol.2017.05.006 (2017).Article 
    PubMed 
    CAS 

    Google Scholar 
    62.Takahashi, S., Whitney, S. M. & Badger, M. R. Different thermal sensitivity of the repair of photodamaged photosynthetic machinery in cultured Symbiodinium species. Proc. Natl. Acad. Sci. U.S.A. 106, 3237–3242. https://doi.org/10.1073/pnas.0808363106 (2009).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    63.Jones, R. The ecotoxicological effects of Photosystem II herbicides on corals. Mar. Pollut. Bull. 51, 495–506. https://doi.org/10.1016/j.marpolbul.2005.06.027 (2005).Article 
    PubMed 
    CAS 

    Google Scholar 
    64.Rowen, D. J., Templeman, M. A. & Kingsford, M. J. Herbicide effects on the growth and photosynthetic efficiency of Cassiopea maremetens. Chemosphere 182, 143–148. https://doi.org/10.1016/j.chemosphere.2017.05.001 (2017).ADS 
    Article 
    PubMed 
    CAS 

    Google Scholar 
    65.Cantin, N. E., van Oppen, M. J., Willis, B. L., Mieog, J. C. & Negri, A. P. Juvenile corals can acquire more carbon from high-performance algal symbionts. Coral Reefs 28, 405. https://doi.org/10.1007/s00338-009-0478-8 (2009).ADS 
    Article 

    Google Scholar 
    66.Fitt, W. & Trench, R. The relation of diel patterns of cell division to diel patterns of motility in the symbiotic dinoflagellate Symbiodinium microadria ticum Freudenthal in culture. New Phytol. 94, 421–432 (1983).Article 

    Google Scholar 
    67.Randall, C. J. et al. Sexual production of corals for reef restoration in the Anthropocene. Mar. Ecol. Prog. Ser. 635, 203–232. https://doi.org/10.3354/meps13206 (2020).ADS 
    Article 

    Google Scholar 
    68.Baird, A. H., Bhagooli, R., Ralph, P. J. & Takahashi, S. Coral bleaching: The role of the host. Trends Ecol. Evol. 24, 16–20. https://doi.org/10.1016/j.tree.2008.09.005 (2009).Article 
    PubMed 

    Google Scholar 
    69.Flores, F., Kaserzon, S., Elisei, G., Ricardo, G. & Negri, A. P. Toxicity thresholds of three insecticides and two fungicides to larvae of the coral Acropora tenuis. PeerJ 8, e9615. https://doi.org/10.7717/peerj.9615 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    70.LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580. https://doi.org/10.1016/j.cub.2018.07.008 (2018).Article 
    PubMed 
    CAS 

    Google Scholar 
    71.Trenfield, M. A. et al. Aluminium, gallium, and molybdenum toxicity to the tropical marine microalga Isochrysis galbana. Environ. Toxicol. Chem. 34, 1833–1840. https://doi.org/10.1002/etc.2996 (2015).Article 
    PubMed 
    CAS 

    Google Scholar 
    72.Hennige, S., Suggett, D., Warner, M., McDougall, K. & Smith, D. Photobiology of Symbiodinium revisited: Bio-physical and bio-optical signatures. Coral Reefs 28, 179–195. https://doi.org/10.1007/s00338-008-0444-x (2009).ADS 
    Article 

    Google Scholar 
    73.Klueter, A., Trapani, J., Archer, F. I., McIlroy, S. E. & Coffroth, M. A. Comparative growth rates of cultured marine dinoflagellates in the genus Symbiodinium and the effects of temperature and light. PLoS ONE 12, e0187707. https://doi.org/10.1371/journal.pone.0187707 (2017).Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    74.Rogers, J. E. & Davis, R. H. Application of a new micro-culturing technique to assess the effects of temperature and salinity on specific growth rates of six Symbiodinium isolates. Bull. Mar. Sci. 79, 113–126 (2006).
    Google Scholar 
    75.Sakami, T. Effects of temperature, irradiance, salinity and inorganic nitrogen concentration on coral zooxanthellae in culture. Fish. Res. 66, 1006–1013. https://doi.org/10.1046/j.1444-2906.2000.00162.x (2000).Article 
    CAS 

    Google Scholar 
    76.Schreiber, U., Müller, J. F., Haugg, A. & Gademann, R. New type of dual-channel PAM chlorophyll fluorometer for highly sensitive water toxicity biotests. Photosynth. Res. 74, 317–330. https://doi.org/10.1023/A:1021276003145 (2002).Article 
    PubMed 
    CAS 

    Google Scholar 
    77.Karim, W., Nakaema, S. & Hidaka, M. Temperature effects on the growth rates and photosynthetic activities of Symbiodinium cells. J. Mar. Sci. Eng. 3, 368–381. https://doi.org/10.3390/jmse3020368 (2015).Article 

    Google Scholar 
    78.Mercurio, P., Mueller, J. F., Eaglesham, G., Flores, F. & Negri, A. P. Herbicide persistence in seawater simulation experiments. PLoS ONE 10, e0136391. https://doi.org/10.1371/journal.pone.0136391 (2015).Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    79.Mercurio, P. Herbicide Persistence and Toxicity in the Tropical Marine Environment. PhD thesis, The University of Queensland (2016).80.Fisher, R., Ricardo, G. & Fox, D. jags NEC: A Bayesian No Effect Concentration (NEC) Package. https://github.com/AIMS/NEC-estimation. (2019).81.Fox, D. R. A Bayesian approach for determining the no effect concentration and hazardous concentration in ecotoxicology. Ecotoxicol. Environ. Saf. 73, 123–131. https://doi.org/10.1016/j.ecoenv.2009.09.012 (2010).Article 
    PubMed 
    CAS 

    Google Scholar  More

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    The hump-shaped effect of plant functional diversity on the biological control of a multi-species pest community

    Design of species assemblages with contrasting species and functional diversitiesWe designed eight assemblages of native and perennial plants differing in terms of species richness (three levels), functional diversity of the traits involved in plant–arthropod interactions (two levels) and species identity (two sets of species). We combined these first two factors to define four categories of plant assemblages for further study:

    Low functional diversity and medium species richness (14 species), LFMS;

    High functional diversity and low species richness (9 species), HFLS;

    High functional diversity and medium species richness (14 species), HFMS;

    High functional diversity and high species richness (29 species), HFHS.

    For each of these four categories, we designed two assemblages with different species identities, as described in the Supplementary information, resulting in eight plant assemblages in total. Functional characterization was based on a rough classification of plant species into functional groups (Supplementary Table S1), according to the mains traits involved in plant–species interactions easily accessible from databases: (1) flower resources, i.e. floral and extrafloral nectar or pollen, (2) accessibility of the resource, depending on flower shape, (3) availability of the resource, i.e. the flowering period and (4) flowering height.We generated the seed mixtures from commercial seeds, using ecotypes of local origin wherever possible (northern part of the Parisian basin, France). All applicable international, national, and institutional guidelines relevant for the use of plants were followed.Experimental designThe experiment was conducted between 2013 and 2017 in a 6.5-ha field at Grignon, France (N 48.837, E 1.956), on a deep loamy clay soil, in which soil depth decreased along a gradient from north to south. The field was divided in three blocks running from north to south to take this soil heterogeneity into account.Each assemblage was sown on a 6 × 44 m2 strip, with three replicates (Supplementary Fig. S2), with each assemblage represented once per block. A control treatment, sown with the same crop species as the rest of the field, was also included in the experimental design, resulting in nine experimental treatments in total. From the autumn of 2013 to the 2017 harvest, a winter barley–maize–faba bean–oilseed rape rotation was grown in the field. Crops were managed without insecticide treatment, but with a mean of 0.75 fungicide and 1.25 herbicide treatments per year. The observations were made in faba bean in 2016 and in oilseed rape in 2017.Botanical assessments and functional characterization of the plant communitiesBotanical assessments were conducted in April and June, in 2016 and 2017. In each treatment, the vegetation was assessed in 3 × 15 m2 plots at a position representative of the whole strip, generally in the center of the strip, to prevent edge effects. The percentage of the ground covered by each sown or spontaneously growing plant species was estimated by eye, by the same observer in each case. We noted the phenological development stage of each species in each treatment on an 11-point scale, to ensure an accurate assessment of flowering phenology. In the control plots (sown with the crop species only), we took into account the resources provided by weed species.The functional characterization of plant communities was based on the plant traits assumed to be involved in plant–parasitoid interactions6 (Supplementary Table S3). These traits were related to (1) the provision of trophic resources (presence of floral and extrafloral nectar, qualitative estimation of floral nectar), (2) the temporal availability of the resource (date of flowering onset and duration of flowering), (3) flower attractiveness (flower or inflorescence diameter, color, UV reflectance pattern), (4) nectar accessibility (flower opening diameter, corolla height, nectar depth and nectar tube diameter) and (5) the provision of physical habitats (leaf distribution, vegetative and flowering height). We measured most of these traits, particularly all those relating to flower morphology, phenology and nectar provision (see more detailed methods in the Supplementary information). Only a few were retrieved from previous publications and online databases: flower color and UV reflectance pattern, leaf distribution, vegetative and flower height.These traits were used (1) to determine the accessibility of nectar to each parasitoid (see below) and (2) to calculate the functional diversity of the plant assemblages. We calculated functional dispersion as the abundance-weighted mean distance of individual species from the centroid of all species in the trait space50 and Rao quadratic entropy51. Since these two parameters were highly correlated (Supplementary information), we considered only functional dispersion a measurement of functional diversity. The traits associated with the provision, availability and accessibility of nectar resources were measured for all the dicotyledonous species sown and for all spontaneous species occurring in the plant communities and flowering during parasitoid activity. Overall, considering the traits we measured and those retrieved from databases, the trait matrix was complete for more than 95% of the species, accounting for 99.6% of total plant cover.Assessment of the levels of parasitism on five herbivorous pests of faba bean and oilseed rapeIn the adjacent crop, 5 and 20 m from the wildflower strip, we measured the level of parasitism in one herbivorous pest of faba bean (2016) and four herbivorous pests of oilseed rape (2017). We chose a distance close to the strip (5 m) to prevent confounding effects with the other adjacent strips, knowing that their effect is the strongest in the first few meters from the strip52. A further distance was also chosen (20 m) to determine whether the strips promoted biological control at field level, while taking into account the spatial constraint of the distance between strips (50 m between opposing strips).All the protocols are detailed in the Supplementary information. Parasitism was assessed in Bruchus rufimanus larvae after the visual examination of faba bean seeds after harvest. For oilseed rape, we collected and reared Ceutorhynchus pallidactylus and Psylliodes chrysocephala larvae until the adult stage or parasitoid emergence. In Brassicogethes aeneus larvae, parasitism was assessed by observing the eggs of Tersilochus heterocerus in the host larvae in oilseed rape flowers. Finally, after oilseed rape harvest, we retrieved cocoons of Dasineura brassicae from the soil, which we dissected, recording the number of cocoons occupied by parasitoids.Measurement of parasitoid traitsWe carried out morphological measurements on parasitoids (Supplementary Table S4), to determine their degree of access to the nectar provided by plants, as a function of the size of their mouthparts and head, which limit corolla penetration, using an approach analogous to that of van Rijn and Wäckers16. Parasitoid individuals, preserved in 70% ethanol, were obtained (1) from our rearing experiments (for Bruchus rufimanus, Psylliodes chrysocephala and Ceutorhynchus pallidactylus), (2) from the dissection of cocoons for Dasineura brassicae or (3) by field sampling in the flower strips with a sweep net in April 2017 to collect Tersilochus heterocerus, parasitoids of Brassicogethes aeneus identified with53. For each parasitoid species or morphospecies, we measured, on at least 10 individuals, proboscis length, proboscis width (at mid-length)54 and the maximum dorsal head width, including the eyes. Observations were carried out under a binocular microscope (Leica M80, 60 ×) linked to a video camera (Moticam 10, Motic), and measurements were made with ImageJ v1.50i digital image analysis software (National Institute of Health, Bethesda, http://imagej.nih.gov/ij).Nectar resources for parasitoidsWe estimated the amount of nectar provided by the plants by summing, for each flower strip corresponding to a treatment, the percent cover of plants providing available and accessible nectar, as assessed in vegetation surveys. Separate estimates were obtained for each parasitoid species or morphospecies.Plant species producing floral or extrafloral nectar were first selected on the basis of the observations detailed in the botanical assessment section. Nectar was considered to be available when it was produced during the period of parasitoid activity (Supplementary Table S4), by selecting species at the flowering stage or producing extrafloral nectar based on the phenological observations carried out during the botanical assessments. Nectar accessibility depended on morphological matching between plants and insects. Extrafloral nectar, which is not enclosed in a perianth, but produced on bracts or stipules, was considered to be accessible. We determined the accessibility of floral nectar with a mechanistic trait-based approach (Supplementary Information), by adapting the geometric model proposed by van Rijn and Wäckers16. A decision tree was built (Fig. 2) to take into account the three constraints limiting nectar accessibility: (1) ability of the insect to penetrate the flower, which is dependent on head size and flower opening, (2) ability to reach the nectar, which depends on proboscis length, nectar depth and corolla height, and (3) proboscis width and nectar tube diameter in the presence of nectar.Statistical analysesWe investigated the effects of the different plant assemblages on the rates of parasitism for the five herbivorous species, at 5 and 20 m from the flower strip, considered separately as individual response variables. We first tested the effect of each assemblage (nine treatments as factors) on parasitism rates. We used generalized linear mixed models in the lme package55, with a binomial error distribution. The models included plot (n = 9 flower strips × 3 replicates = 27), strip (1–3) or block (1–3) as a random effect. All models were run three times with each random effect variable, and the model giving the lowest AIC was retained. Strips consistently yielded the lowest AIC. This factor was therefore introduced as a random effect variable for all statistical analyses. The significance of the fixed effects was evaluated by type II analyses of deviance with Wald chi-squared tests from the Anova function from the car package56. If a significant effect (p value  More

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    Inferring predator–prey interaction in the subterranean environment: a case study from Dinaric caves

    1.Sih, A., Crowley, P., McPeek, M., Petranka, J. & Strohmeier, K. Predation, competition, and prey communities: A review of field experiments. Annu. Rev. Ecol. Syst. 16, 269–311 (1985).Article 

    Google Scholar 
    2.Werner, E. E. & Peacor, S. D. A review of trait-mediated indirect interactions in ecological communities. Ecology 84, 1083–1100 (2003).Article 

    Google Scholar 
    3.Abrams, P. A. The evolution of predator–prey interactions: theory and evidence. Annu. Rev. Ecol. Syst. 31, 79–105 (2000).Article 

    Google Scholar 
    4.Lima, S. L. & Bednekoff, P. A. Temporal variation in danger drives antipredator behavior: The predation risk allocation hypothesis. Am. Nat. 153, 649–659 (1999).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    5.Peacor, S. D. & Werner, E. E. Nonconsumptive effects of predators and trait-mediated indirect effects. Encycl. Life Sci. https://doi.org/10.1002/9780470015902.a0021216 (2008).Article 

    Google Scholar 
    6.Schmitz, O. J., Krivan, V. & Ovadia, O. Trophic cascades: The primacy of trait-mediated indirect interactions. Ecol. Lett. 7, 153–163 (2004).Article 

    Google Scholar 
    7.Mittelbach, G. G. Fish foraging and habitat choice: a theoretical perspective. In Handbook of Fish Biology and Fisheries, Volume 1 Fish Biology (eds Hart, P. J. B. & Reynolds, J. D.) 251–266 (Blackwell, 2002).Chapter 

    Google Scholar 
    8.Mittelbach, G. G. & McGill, B. J. Community Ecology (Oxford University Press, 2019) https://doi.org/10.1017/CBO9781107415324.004.Book 

    Google Scholar 
    9.Lima, S. L. Nonlethal effects in the ecology of predator-prey interactions. Bioscience 48, 25–34 (1998).Article 

    Google Scholar 
    10.Jeschke, J. M., Laforsch, C. & Tollrian, R. Animal prey defenses. In Encyclopedia of Ecology 189–194 (2008).11.Harvell, C. D. The ecology and evolution of inducible defenses. Q. Rev. Biol. 65, 323–340 (1990).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Peckarsky, B. L. et al. Revisiting the classics: Considering nonconsumptive effects in textbook examples of predator prey interactions. Ecology 89, 2416–2425 (2008).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    13.Goricki, Š et al. Environmental DNA in subterranean biology: Range extension and taxonomic implications for Proteus. Sci. Rep. 7, 91–93 (2017).Article 
    CAS 

    Google Scholar 
    14.Sket, B. Distribution of Proteus (Amphibia: Urodela: Proteidae) and its possible explanation. J. Biogeogr. 24, 263–280 (1997).Article 

    Google Scholar 
    15.Jugovic, J., Prevorčnik, S., Aljančič, G. & Sketa, B. The atyid shrimp (Crustacea: Decapoda: Atyidae) rostrum: Phylogeny versus adaptation, taxonomy versus trophic ecology. J. Nat. Hist. 44, 2509–2533 (2010).Article 

    Google Scholar 
    16.Aljančič, M. Prehrana močerila. Proteus 23, 224–225 (1961).
    Google Scholar 
    17.Parzefall, J., Durand, J. P. & Sket, B. Prouteus anguinus Laurenti, 1768—Grottenolm. In Handbuch der Reptilien und Amphibien Europas (ed. Böhme, W.) 59–76 (Aula-Verlag, 1999).
    Google Scholar 
    18.Trontelj, P., Blejec, A. & Fišer, C. Ecomorphological convergence of cave communities. Evolution 66, 3852–3865 (2012).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Karaman, S. Podrod Orniphargus u Jugoslaviji I. & II. in O nekim amfipodima—izopodima Balkana i o njihovoj sistematici 119–159 (Srpska akademija nauka-Posebna izdanja CLXIII, 1950).20.Fišer, C., Trontelj, P. & Sket, B. Phylogenetic analysis of the Niphargus orcinus species-aggregate (Crustacea: Amphipoda: Niphargidae) with description of new taxa. J. Nat. Hist. 40, 2265–2315 (2006).Article 

    Google Scholar 
    21.Bollache, L. Ï., Kaldonski, N., Troussard, J. P., Lagrue, C. & Rigaud, T. Spines and behaviour as defences against fish predators in an invasive freshwater amphipod. Anim. Behav. 72, 627–633 (2006).Article 

    Google Scholar 
    22.Copilaş-Ciocianu, D., Borza, P. & Petrusek, A. Extensive variation in the morphological anti-predator defense mechanism of Gammarus roeselii Gervais, 1835 (Crustacea:Amphipoda). Freshw. Sci. 39, 47–55 (2020).Article 

    Google Scholar 
    23.Veech, J. A. A probabilistic model for analysing species co-occurrence. Glob. Ecol. Biogeogr. 22, 252–260 (2013).Article 

    Google Scholar 
    24.Borko, Š, Trontelj, P., Seehausen, O., Moškrič, A. & Fišer, C. A subterranean adaptive radiation of amphipods in Europe. Nat. Commun. 12, 1–12 (2021).Article 
    CAS 

    Google Scholar 
    25.SubBioDB. Subterranean Fauna Database. Research group for speleobiology, Biotechnical faculty, University of Ljubljana. https://db.subbio.net/ (2021).26.Culver, D. C., Fong, D. W. & Jernigan, R. W. Species interactions in cave stream communities: Experimental results and microdistribution effects. Am. Midl. Nat. 126, 364 (1991).Article 

    Google Scholar 
    27.Lavoie, K. H., Helf, K. L. & Poulson, T. L. The biology and ecology of North American cave crickets. J. Cave Karst Stud. 69, 114–134 (2007).
    Google Scholar 
    28.Ercoli, F. et al. Differing trophic niches of three French stygobionts and their implications for conservation of endemic stygofauna. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 2193–2203 (2019).Article 

    Google Scholar 
    29.Pacioglu, O. et al. Ecophysiological and life-history adaptations of Gammarus balcanicus (Schäferna, 1922) in a sinking-cave stream from Western Carpathians (Romania). Zoology 139, 125754 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Parimuchová, A., Dušátková, L. P., Kováč, Ľ & Macháčková, T. The food web in a subterranean ecosystem is driven by intraguild predation. Sci. Rep. https://doi.org/10.1038/s41598-021-84521-1 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    31.Premate, E. et al. Cave amphipods reveal co-variation between morphology and trophic niche in a low-productivity environment. Freshw. Biol. 66, 1876–1888 (2021).Article 

    Google Scholar 
    32.Sacco, M. et al. Elucidating stygofaunal trophic web interactions via isotopic ecology. PLoS ONE 14, 1–25 (2019).MathSciNet 
    Article 
    CAS 

    Google Scholar 
    33.Pohlman, J. W., Iliffe, T. M. & Cifuentes, L. A. A stable isotope study of organic cycling and the ecology of an anchialine cave ecosystem. Mar. Ecol. Prog. Ser. 155, 17–27 (1997).ADS 
    CAS 
    Article 

    Google Scholar 
    34.Graening, G. O. & Brown, A. V. Ecosystem dynamics and pollution effects in an Ozark cave stream. J. Am. Water Resour. Assoc. 39, 1497–1507 (2003).ADS 
    CAS 
    Article 

    Google Scholar 
    35.Manenti, R., Melotto, A., Guillaume, O., Ficetola, G. F. & Lunghi, E. Switching from mesopredator to apex predator: How do responses vary in amphibians adapted to cave living?. Behav. Ecol. Sociobiol. 74, 1–13 (2020).Article 

    Google Scholar 
    36.Uiblein, F. & Juberthie, C. Predation in caves: the effects of prey immobility and darkness on the foraging behaviour of two salamanders, Euproctus asper and Proteus anguinus. Behav. Process. 28, 33–40 (1992).CAS 
    Article 

    Google Scholar 
    37.Prevorčnik, S., Verovnik, R., Zagmajster, M. & Sket, B. Biogeography and phylogenetic relations within the Dinaric subgenus Monolistra (Microlistra) (Crustacea: Isopoda: Sphaeromatidae), with a description of two new species. Zool. J. Linn. Soc. 159, 1–21 (2010).Article 

    Google Scholar 
    38.Mammola, S. Finding answers in the dark: Caves as models in ecology fifty years after Poulson and White. Ecography 42, 1331–1351 (2019).Article 

    Google Scholar 
    39.Culver, D. C. & Pipan, T. The Biology of Caves and Other Subterranean Habitats (Oxford University Press, 2009).
    Google Scholar 
    40.Kellner, K. F. & Swihart, R. K. Accounting for imperfect detection in ecology: A quantitative review. PLoS ONE 9, e111436 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    41.Mackenzie, D. I., Bailey, L. L. & Nichols, J. D. Investigating species co-occurrence patterns when species are detected imperfectly. J. Anim. Ecol. 73, 546–555 (2004).Article 

    Google Scholar 
    42.Vörös, J., Márton, O., Schmidt, B. R., Tünde Gál, J. & Jelić, D. Surveying Europe’s only cave-dwelling chordate species (Proteus anguinus) using environmental DNA. PLoS ONE 12, e0170945 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    43.Niemiller, M. L. et al. Evaluation of eDNA for groundwater invertebrate detection and monitoring: A case study with endangered Stygobromus (Amphipoda: Crangonyctidae). Conserv. Genet. Resour. 10, 247–257 (2018).Article 

    Google Scholar 
    44.Yonezawa, S., Nakano, T., Nakahama, N., Tomikawa, K. & Isagi, Y. Environmental DNA reveals cryptic diversity within the subterranean amphipod genus Pseudocrangonyx Akatsuka & Komai, 1922 (Amphipoda: Crangonyctoidea: Pseudocrangonyctidae) from Central Japan. J. Crustac. Biol. 40, 479–483 (2020).Article 

    Google Scholar 
    45.Arntzen, J. W. et al. Proteus anguinus. IUCN Red List Threat. Species (2009).46.Communities, T. C. of E. Council Directive 92/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora. Official J. Eur. Communities 35, 8–51 (1992).
    Google Scholar 
    47.Vörös, J., Ursenbacher, S. & Jelić, D. Population genetic analyses using 10 new polymorphic microsatellite loci confirms genetic subdivision within the olm, Proteus anguinus. J. Hered. 110, 211–218 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Gorički, Š & Trontelj, P. Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus. Gene 378, 31–41 (2006).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    49.Gravel, D., Albouy, C. & Thuiller, W. The meaning of functional trait composition of food webs for ecosystem functioning. Philos. Trans. R. Soc. B Biol. Sci. 371, 20150268 (2016).Article 

    Google Scholar 
    50.Schmitz, O. Predator and prey functional traits: Understanding the adaptive machinery driving predator-prey interactions. F1000Research 6, 1767 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.R Development Core Team. A language and environment for statistical computing. (2020).52.R Studio Team. RStudio: Integrated Development for R. (2020).53.Wickham, H. & Bryan, J. readxl: Read Excel Files. R package version 1.3.1. (2019).54.Dragulescu, A. A. & Arendt, C. xlsx: Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files. R package version 0.6.1. (2018).55.Wickham, H., Francois, R., Henry, L. & Müller, K. dplyr: A Grammar of Data Manipulation. R package version 0.8.3. (2019).56.Wickham, H. ggplot2: Elegant Graphics for Data Analysis. (Springer-Verlag, 2016).57.Kong, D. Ipaper: Collection of personal practical R functions. (2021).58.Pebesma, E. Simple features for R: Standardized support for spatial vector data. R J. 10, 439–446 (2018).Article 

    Google Scholar 
    59.Hijmas, R. J. raster: Geographic Data Analysis and Modeling. (2020).60.Baddeley, A., Rubak, E. & Turner, R. Spatial Point Patterns: Methodology and Applications with R (Chapman and Hall/CRC Press, 2015).MATH 
    Book 

    Google Scholar 
    61.Kassambara, A. rstatix: Pipe-Friendly Framework for Basic Statistical Tests. R package version 0.5.0. (2020).62.Griffith, D. M., Veech, J. A. & Marsh, C. J. Cooccur: Probabilistic species co-occurrence analysis in R. J. Stat. Softw. 69, 1–17 (2016).Article 

    Google Scholar 
    63.Revell, L. J. phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).Article 

    Google Scholar 
    64.Meade, A. & Pagel, M. Bayes Traits V3. (2017).65.Griffin, R. H. btw: Run BayesTraitsV3 from R. (2018). More

  • in

    Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

    1.McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. USA 110, 3229–3236 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Bang, C. et al. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology 127, 1–9 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Mueller, U. G. & Sachs, J. L. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 23, 606–617 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    4.Theis, K. R., Whittaker, D. J. & Rojas, C. A. A hologenomic approach to animal behavior. In Evolution in Action: Past, Present and Future 247–263 (Springer, 2020).5.Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43–51 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Ziegler, M., Seneca, F. O., Yum, L. K., Palumbi, S. R. & Voolstra, C. R. Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat. Commun. 8, 1–8 (2017).Article 
    CAS 

    Google Scholar 
    7.Robbins, S. J. et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat. Microbiol. 4, 2090–2100 (2019).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    8.Berendsen, R. L., Pieterse, C. M. & Bakker, P. A. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    9.Voolstra, C. R. & Ziegler, M. Adapting with microbial help: Microbiome flexibility facilitates rapid responses to environmental change. BioEssays 2, 2000004 (2020).Article 

    Google Scholar 
    10.Cárdenas, C. A., Bell, J. J., Davy, S. K., Hoggard, M. & Taylor, M. W. Influence of environmental variation on symbiotic bacterial communities of two temperate sponges. FEMS Microbiol. Ecol. 88, 516–527 (2014).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    11.Pantos, O., Bongaerts, P., Dennis, P. G., Tyson, G. W. & Hoegh-Guldberg, O. Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. ISME J. 9, 1916–1927 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    12.Roder, C., Bayer, T., Aranda, M., Kruse, M. & Voolstra, C. R. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences. Mol. Ecol. 24, 3501–3511 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    13.Neave, M. J. et al. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME J. 11, 186–200 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    14.Carrier, T. J. & Reitzel, A. M. Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes. Nat. Commun. 9, 1–9 (2018).CAS 
    Article 

    Google Scholar 
    15.Pollock, F. J. et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat. Commun. 9, 1–13 (2018).CAS 
    Article 

    Google Scholar 
    16.Glasl, B., Smith, C. E., Bourne, D. G. & Webster, N. S. Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7, e6377 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    17.Macke, E., Callens, M., De Meester, L. & Decaestecker, E. Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. Nat. Commun. 8, 1–13 (2017).CAS 
    Article 

    Google Scholar 
    18.Casey, J. M., Connolly, S. R. & Ainsworth, T. D. Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens. Sci. Rep. 5, 11903 (2015).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Ziegler, M. et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat. Commun. 10, 1–11 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    20.Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Spor, A., Koren, O. & Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9, 279–290 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Jaspers, C. et al. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 113, 81–87 (2019).Article 

    Google Scholar 
    24.Blackall, L. L., Wilson, B. & van Oppen, M. J. H. Coral—the world’s most diverse symbiotic ecosystem. Mol. Ecol. 24, 5330–5347 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    25.Hernandez-Agreda, A., Gates, R. D. & Ainsworth, T. D. Defining the core microbiome in corals’ microbial soup. Trends Microbiol. 25, 125–140 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

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

    Google Scholar 
    28.Rosenberg, E., Koren, O., Reshef, L., Efrony, R. & Zilber-Rosenberg, I. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355–362 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Bourne, D. G., Morrow, K. M. & Webster, N. S. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu. Rev. Microbiol. 70, 317–340 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Muscatine, L., Porter, J. W. & Kaplan, I. R. Resource partitioning by reef corals as determined from stable isotope composition. Mar. Biol. 100, 185–193 (1989).Article 

    Google Scholar 
    31.Rädecker, N., Pogoreutz, C., Voolstra, C. R., Wiedenmann, J. & Wild, C. Nitrogen cycling in corals: the key to understanding holobiont functioning? Trends Microbiol. 23, 490–497 (2015).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    32.Wegley, L., Edwards, R., Rodriguez‐Brito, B., Liu, H. & Rohwer, F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9, 2707–2719 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    33.Raina, J. B., Tapiolas, D., Willis, B. L. & Bourne, D. G. Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl. Environ. Microbiol. 75, 3492–3501 (2009).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Lema, K. A., Willis, B. L. & Bourne, D. G. Corals form characteristic associations with symbiotic nitrogen-fixing bacteria. Appl. Environ. Microbiol. 78, 3136–3144 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Krediet, C. J., Ritchie, K. B., Paul, V. J. & Teplitski, M. Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases. Proc. R. Soc. B 280, 20122328 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Glasl, B., Herndl, G. J. & Frade, P. R. The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. ISME J. 10, 2280–2292 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.Boilard, A. et al. Defining coral bleaching as a microbial dysbiosis within the coral holobiont. Microorganisms 8, 1682 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    38.Apprill, A., Weber, L. G. & Santoro, A. E. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems 1, e00143–16 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Glasl, E.B., B. et al. Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 7, 1–13 (2019).Article 

    Google Scholar 
    40.Damjanovic, K., Blackall, L. L., Peplow, L. M. & van Oppen, M. J. H. Assessment of bacterial community composition within and among Acropora loripes colonies in the wild and in captivity. Coral Reefs 39, 1245–1255 (2020).Article 

    Google Scholar 
    41.Dubé, E. B. et al. Ecology, biology and genetics of Millepora hydrocorals on coral reefs. In Invertebrates – Ecophysiology and Management (eds. Ray, S., Diarte-Plata, G. &  Escamilla-Montes, R.), (IntechOpen, 2019).42.Rodríguez, L. et al. Genetic relationships of the hydrocoral Millepora alcicornis and its symbionts within and between locations across the Atlantic. Coral Reefs 38, 255–268 (2019).ADS 
    Article 

    Google Scholar 
    43.Lewis, J. B. Biology and ecology of the hydrocoral Millepora on coral reefs. Adv. Mar. Biol. 50, 1–55 (2006).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    44.Arrigoni, R. et al. An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea. Coral Reefs 37, 967–984 (2018).ADS 
    Article 

    Google Scholar 
    45.Boissin, E., Leung, J. K., Denis, V., Bourmaud, C. A. & Gravier-Bonnet, N. Morpho-molecular delineation of structurally important reef species, the fire corals, Millepora spp., at Réunion Island, Southwestern Indian Ocean. Hydrobiologia 847, 1237–1255 (2020).Article 

    Google Scholar 
    46.Dubé, C. E., Boissin, E., Maynard, J. A. & Planes, S. Fire coral clones demonstrate phenotypic plasticity among reef habitats. Mol. Ecol. 26, 3860–3869 (2017).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    47.Schwartzman, J. A. & Ruby, E. G. Stress as a normal cue in the symbiotic environment. Trends Microbiol. 24, 414–424 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    48.van Oppen, M. J. H. et al. Adaptation to reef habitats through selection on the coral animal and its associated microbiome. Mol. Ecol. 27, 2956–2971 (2018).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    49.Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 6237 (2015).Article 
    CAS 

    Google Scholar 
    50.Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.Hernandez-Agreda, A., Leggat, W., Bongaerts, P., Herrera, C. & Ainsworth, T. D. Rethinking the coral microbiome: simplicity exists within a diverse microbial biosphere. MBio 9, e00812–18 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    52.Bongaerts, P. et al. Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evol. Biol. 11, 303 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    53.Albright, R., Benthuysen, J., Cantin, N., Caldeira, K. & Anthony, K. Coral reef metabolism and carbon chemistry dynamics of a coral reef flat. Geophys. Res. Lett. 42, 3980–3988 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    54.Pootakham, W. et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event. MicrobiologyOpen 7, e00604 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    55.Neave, M. J., Apprill, A., Ferrier-Pagès, C. & Voolstra, C. R. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl. Microbiol. Biotechnol. 100, 8315–8324 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    56.Meyer, J. L., Paul, V. J. & Teplitski, M. Community shifts in the surface microbiomes of the coral Porites astreoides with unusual lesions. PLoS ONE 9, e100316 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    57.Bayer, T. et al. The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria. Appl. Environ. Microbiol. 79, 4759–4762 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    58.Jessen, C. et al. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the Red Sea coral Acropora hemprichii. PLoS ONE 8, e62091 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Morrow, K. M. et al. Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges. ISME J. 9, 894–908 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    60.Dubé, C. E., Ky, C. L. & Planes, S. Microbiome of the black-lipped pearl oyster Pinctada margaritifera, a multi-tissue description with functional profiling. Front. Microbiol. 10, 1548 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    61.Neave, M. J., Michell, C. T., Apprill, A. & Voolstra, C. R. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci. Rep. 7, 40579 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    62.Tandon, K. et al. Comparative genomics: dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). ISME J. 14, 1290–1303 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    63.Ngugi, D. K., Ziegler, M., Duarte, C. M. & Voolstra, C. R. Genomic blueprint of glycine betaine metabolism in coral metaorganisms and their contribution to reef nitrogen budgets. iScience 23, 101120 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    64.González, J. M., Kiene, R. P. & Moran, M. A. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65, 3810–3819 (1999).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.Curson, A. R. J., Rogers, R., Todd, J. D., Brearley, C. A. & Johnston, A. W. B. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine α-proteobacteria and Rhodobacter spharoides. Environ. Microbiol. 10, 757–767 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    66.Reisch, C. R., Moran, M. A. & Whitman, W. B. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Front. Microbiol. 2, 172 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Thompson, J. R., Rivera, H. E., Closek, C. J. & Medina, M. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions. Front. Cell. Infect. Microbiol. 4, 176 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Durante, M. K., Baums, I. B., Williams, D. E., Vohsen, S. & Kemp, D. W. What drives phenotypic divergence among coral clonemates of Acropora palmata? Mol. Ecol. 28, 3208–3224 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    69.Wagner, M. R. et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7, 1–5 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    70.Fuerst, J. & Sagulenko, E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat. Rev. Microbiol. 9, 403–413 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    71.Forquin-Gomez, M. P. et al. The family Brevibacteriaceae. In Prokaryotes Actinobacteria. 4th edn., (eds. Rosenberg E. et al.), 141–153 (Springer, 2014).72.Baker, B. J., Lazar, C. S., Teske, A. P. & Dick, G. J. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome 3, 14 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    73.Tian, R. M. et al. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur‐oxidizing bacterium in sponge. Environ. Microbiol. 16, 3548–3561 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    74.Gauthier, M. E., Watson, J. R. & Degnan, S. M. Draft genomes shed light on the dual bacterial symbiosis that dominates the microbiome of the coral reef sponge Amphimedon queenslandica. Front. Mar. Sci. 3, 196 (2016).Article 

    Google Scholar 
    75.Dyksma, S. et al. Ubiquitous Gammaproteo-bacteria dominate dark carbon fixation in coastal sediments. ISME J. 8, 1939–1953 (2016).Article 
    CAS 

    Google Scholar 
    76.Raina, J. B., Dinsdale, E. A., Willis, B. L. & Bourne, D. G. Do the organic sulfur compounds DMSP and DMS drive coral microbial associations? Trends Microbiol. 18, 101–108 (2010).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    77.Morrow, K. M., Moss, A. G., Chadwick, N. E. & Liles, M. R. Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl. Environ. Microbiol. 78, 6438–6449 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Sabdono, A. & Radjasa, O. K. Phylogenetic diversity of organophosphorous pesticide-degrading coral bacteria from mid-west coast of Indonesia. Biotechnology 7, 694–701 (2008).CAS 
    Article 

    Google Scholar 
    79.Kannapiran, E. & Ravindran, J. Dynamics and diversity of phosphate mineralizing bacteria in the coral reefs of Gulf of Mannar. J. Basic Microbiol. 52, 91–98 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    80.Mahmoud, H. M. & Kalendar, A. A. Coral-associated actinobacteria: diversity, abundance, and biotechnological potentials. Front. Microbiol. 7, 204 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    81.Probandt, D. et al. Permeability shapes bacterial communities in sublittoral surface sediments. Environ. Microbiol. 19, 1584–1599 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    82.Doolittle, W. F. & Booth, A. It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol. Philos. 32, 5–24 (2017).Article 

    Google Scholar 
    83.Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    84.Kelly, L. W. et al. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proc. Natl Acad. Sci. USA 111, 10227–10232 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    85.Peixoto, R. S., Rosado, P. M., Leite, D. C. D. A., Rosado, A. S. & Bourne, D. G. Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience. Front. Microbiol. 8, 341 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Peixoto, R. S. et al. Coral probiotics: premise, promise, prospects. Annu. Rev. Anim. Biosci. 9, 265–288 (2021).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    87.Voolstra, C. R. et al. Extending the natural adaptive capacity of coral holobionts. Nat Rev Earth Environ. 1–16 (2021). https://doi.org/10.1038/s43017-021-00214-3.88.Santoro, E. P. et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv. 7 (2021). https://doi.org/10.1126/sciadv.abg3088.89.Adam, T. C. et al. Landscape‐scale patterns of nutrient enrichment in a coral reef ecosystem: implications for coral to algae phase shifts. Ecol. Appl. 31, e2227 (2021).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    90.Buckling, A., Kassen, R., Bell, G. & Rainey, P. B. Disturbance and diversity in experimental microcosms. Nature 408, 961–964 (2000).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    91.Berga, M., Szekely, A. J. & Langenheder, S. Effects of disturbance intensity and frequency on bacterial community composition and function. PLoS ONE 7, e36959 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    92.Neulinger, S. C., Järnegren, J., Ludvigsen, M., Lochte, K. & Dullo, W. C. Phenotype-specific bacterial communities in the cold-water coral Lophelia pertusa (Scleractinia) and their implications for the coral’s nutrition, health, and distribution. Appl. Environ. Microbiol. 74, 7272–7285 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    93.Kanukollu, S. et al. Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea. FEMS Microbiol. Ecol. 92, 1 (2016).Article 
    CAS 

    Google Scholar 
    94.Santos, H. F. et al. Climate change affects key nitrogen-fixing bacterial populations on coral reefs. ISME J. 8, 2272–2279 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    95.Sorokin, D. Y., Tourova, T. P. & Muyzer, G. Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea. Syst. Appl. Microbiol. 28, 679–687 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    96.Chen, Y. J. et al. Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem. bioRxiv (2020). Preprint at https://doi.org/10.1101/2020.02.12.94522097.Spring, S., Scheuner, C., Göker, M. & Klenk, H. P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front. Microbiol. 9, 281 (2015).
    Google Scholar 
    98.Preston, G. M. Metropolitan microbes: type III secretion in multi-host symbionts. Cell Host Microbe 2, 291–294 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    99.Lutz, A., Raina, J.-B., Motti, C. A., Miller, D. J. & van Oppen, M. J. H. Host coenzyme Q redox state is an early biomarker of thermal stress in the coral Acropora millepora. PLoS ONE 10, e0139290 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    100.Smith, D. J., Suggett, D. J. & Baker, N. R. Is photoinhibition of zooxanthellae photosynthesis the primary cause of thermal bleaching in corals? Glob. Chang. Biol. 11, 1–11 (2005).ADS 
    Article 

    Google Scholar 
    101.Gardner, S. G. et al. A multi-trait systems approach reveals a response cascade to bleaching in corals. BMC Biol. 15, 1–14 (2017).Article 
    CAS 

    Google Scholar 
    102.Lema, K. A., Bourne, D. G. & Willis, B. L. Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora. Mol. Ecol. 23, 4682–4695 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    103.Pogoreutz, C. et al. Nitrogen fixation aligns with nifH abundance and expression in two coral trophic functional groups. Front. Microbiol. 8, 1187 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    104.Marangoni, L. F. et al. Peroxynitrite generation and increased heterotrophic capacity are linked to the disruption of the coral–dinoflagellate symbiosis in a scleractinian and hydrocoral species. Microorganisms 7, 426 (2019).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    105.Quigley, K. M., Alvarez Roa, C., Torda, G., Bourne, D. G. & Willis, B. L. Co‐dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. MicrobiologyOpen 9, e959 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    106.Dubé, C. E., Mercière, A., Vermeij, M. J. A. & Planes, S. Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia. PLoS ONE 12, e0173513 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    107.Agostini, S. et al. Biological and chemical characteristics of the coral gastric cavity. Coral Reefs 31, 147–156 (2012).ADS 
    Article 

    Google Scholar 
    108.Williams, A. D., Brown, B. E., Putchim, L. & Sweet, M. J. Age-related shifts in bacterial diversity in a reef coral. PLoS ONE 10, e0144902 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    109.Sweet, M. J., Brown, B. E., Dunne, R. P., Singleton, I. & Bulling, M. Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera. Coral Reefs 36, 815–828 (2017).ADS 
    Article 

    Google Scholar 
    110.Dubé, C. E., Boissin, E., Mercière, A. & Planes, S. Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free‐spawning marine invertebrate. Mol. Ecol. 29, 1508–1522 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    111.Abràmoff, M. D., Magalhães, P. J. & Ram, S. J. Image processing with ImageJ. Biophotonics Int. 11, 36–42 (2004).
    Google Scholar 
    112.Dubé, C. E., Planes, S., Zhou, Y., Berteaux-Lecellier, V. & Boissin, E. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci. PeerJ 5, e2936 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    113.Arnaud-Haond, S. & Belkhir, K. GENCLONE: A computer pro- gram to analyze genotypic data, test for clonality and describe spatial clonal organization. Mol. Ecol. Notes 7, 15–17 (2007).CAS 
    Article 

    Google Scholar 
    114.Peakall, R. & Smouse, P. E. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295 (2006).Article 

    Google Scholar 
    115.Wickham, H. ggplot2: Elegant Graphics for Data Analysis. (Springer, 2016).116.R Development Core Team. R: A language and environment for statistical computing (ISBN 3-900051-07-0, http://www.R-project.org/ (R Foundation for Statistical Computing, 2020).117.Andersson, A. F. et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS ONE 3, e2836 (2008).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    118.Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    119.Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    120.Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. 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 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    121.Pedregosa, F. et al. Scikit-learn: Machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).MathSciNet 
    MATH 

    Google Scholar 
    122.Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 1–17 (2018).Article 

    Google Scholar 
    123.Yilmaz, P. et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucl. Acids Res. 42, D643–D648 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    124.Oksanen, J. et al. vegan: Community Ecology Package (2018).125.Weerdt, W. H. Transplantation experiments with Caribbean Millepora species (Hydrozoa, Coelenterata), including some ecological observations on growth forms. Bijdr. Dierkd. 51, 1–19 (1981).Article 

    Google Scholar 
    126.Cáceres, M. D. & Legendre, P. Associations between species and groups of sites: indices and statistical inference. Ecology 90, 3566–3574 (2009).PubMed 
    Article 
    PubMed Central 

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

    Google Scholar 
    128.Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Extreme climate event promotes phenological mismatch between sexes in hibernating ground squirrels

    1.Parmesan, C. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 37, 637–669 (2006).Article 

    Google Scholar 
    2.IPCC. Climate change 2014: Synthesis report. Contribution of working groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change. (2014).3.Inouye, D. W., Barr, B., Armitage, K. B. & Inouye, B. D. Climate change is affecting altitudinal migrants and hibernating species. Proc. Natl. Acad. Sci. 97, 1630–1633 (2000).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    4.Adamík, P. & Král, M. Climate- and resource-driven long-term changes in dormice populations negatively affect hole-nesting songbirds. J. Zool. 275, 209–215 (2008).Article 

    Google Scholar 
    5.Ozgul, A. et al. Coupled dynamics of body mass and population growth in response to environmental change. Nature 466, 482–485 (2010).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Moyes, K. et al. Advancing breeding phenology in response to environmental change in a wild red deer population. Glob. Chang. Biol. 17, 2455–2469 (2011).ADS 
    Article 

    Google Scholar 
    7.Both, C., Van Asch, M., Bijlsma, R. G., Van Den Burg, A. B. & Visser, M. E. Climate change and unequal phenological changes across four trophic levels: Constraints or adaptations?. J. Anim. Ecol. 78, 73–83 (2009).PubMed 
    Article 

    Google Scholar 
    8.Visser, M. E., Van Noordwijk, A. J., Tinbergen, J. M. & Lessells, C. M. Warmer springs lead to mistimed reproduction in great tits (Parus major). Proc. R. Soc. B Biol. Sci. 265, 1867–1870 (1998).Article 

    Google Scholar 
    9.Thackeray, S. J. et al. Trophic level asynchrony in rates of phenological change for marine, freshwater and terrestrial environments. Glob. Chang. Biol. 16, 3304–3313 (2010).ADS 
    Article 

    Google Scholar 
    10.Spooner, F. E. B., Pearson, R. G. & Freeman, R. Rapid warming is associated with population decline among terrestrial birds and mammals globally. Glob. Chang. Biol. 24, 4521–4531 (2018).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Sheriff, M. J., Boonstra, R., Palme, R., Loren Buck, C. & Barnes, B. M. Coping with differences in snow cover: The impact on the condition, physiology and fitness of an arctic hibernator. Conserv. Physiol. 5, 1–12 (2017).Article 

    Google Scholar 
    12.Easterling, D. R. et al. Climate extremes: Observations, modeling, and impacts. Science 289, 2068–2075 (2000).ADS 
    CAS 
    Article 

    Google Scholar 
    13.IPCC. Managing the risks of extreme events and disasters to advance climate change adaptation: Special report of the Intergovernmental Panel on Climate Change. (2012).14.Krause, J. S. et al. The effect of extreme spring weather on body condition and stress physiology in Lapland longspurs and white-crowned sparrows breeding in the Arctic. Gen. Comp. Endocrinol. 237, 10–18 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    15.Latimer, C. E. & Zuckerberg, B. How extreme is extreme? Demographic approaches inform the occurrence and ecological relevance of extreme events. Ecol. Monogr. 89, 1–15 (2019).Article 

    Google Scholar 
    16.Gutschick, V. P. & BassiriRad, H. Extreme events as shaping physiology, ecology, and evolution of plants: Toward a unified definition and evaluation of their consequences. New Phytol. 160, 21–42 (2003).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    17.Bailey, L. D. & van de Pol, M. Tackling extremes: Challenges for ecological and evolutionary research on extreme climatic events. J. Anim. Ecol. 85, 85–96 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.Welbergen, J. A., Klose, S. M., Markus, N. & Eby, P. Climate change and the effects of temperature extremes on Australian flying-foxes. Proc. R. Soc. B Biol. Sci. 275, 419–425 (2008).Article 

    Google Scholar 
    19.Boucek, R. E. & Rehage, J. S. Climate extremes drive changes in functional community structure. Glob. Chang. Biol. 20, 1821–1831 (2014).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    20.Hale, S. et al. Fire and climatic extremes shape mammal distributions in a fire-prone landscape. Divers. Distrib. 22, 1127–1138 (2016).Article 

    Google Scholar 
    21.Frederiksen, M., Daunt, F., Harris, M. P. & Wanless, S. The demographic impact of extreme events: Stochastic weather drives survival and population dynamics in a long-lived seabird. J. Anim. Ecol. 77, 1020–1029 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Wingfield, J. C., Kelley, J. P. & Angelier, F. What are extreme environmental conditions and how do organisms cope with them?. Curr. Zool. 57, 363–374 (2011).Article 

    Google Scholar 
    23.Helm, B. et al. Annual rhythms that underlie phenology: Biological time-keeping meets environmental change. Proc. R. Soc. B Biol. Sci. 280, 1–10 (2013).
    Google Scholar 
    24.Sheriff, M. J., Richter, M. M., Buck, C. L. & Barnes, B. M. Changing seasonality and phenological responses of free-living male Arctic ground squirrels: The importance of sex. Philos. Trans. R. Soc. B Biol. Sci. 368, (2013).25.Michener, G. R. & Locklear, L. Differential costs of reproductive effort for male and female Richardson’s ground squirrels. Ecology 71, 855–868 (1990).Article 

    Google Scholar 
    26.Williams, C. T., Barnes, B. M., Kenagy, G. J. & Buck, C. L. Phenology of hibernation and reproduction in ground squirrels: Integration of environmental cues with endogenous programming. J. Zool. 292, 112–124 (2014).Article 

    Google Scholar 
    27.Michener, G. R. Age, sex, and species differences in the annual cycles of ground-dwelling sciurids: Implications for sociality. in The biology of ground-dwelling squirrels: annual cycles, behavioral ecology, and sociality (eds. Murie, J. O. & Michener, G. R.) 81–107 (University of Nebraska Press, Lincoln, 1984).28.Kenagy, G. J., Sharbaugh, S. M. & Nagy, K. A. Annual cycle of energy and time expenditure in a golden-mantled ground squirrel population. Oecologia 78, 269–282 (1989).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Michener, G. R. Sexual Differences in over-winter torpor patterns of Richardson’s ground squirrels in natural hibernacula. Oecologia 89, 397–406 (1992).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Michener, G. R. Effect of climatic conditions on the annual activity and hibernation cycle of Richardson’s ground squirrels and Columbian ground squirrels. Can. J. Zool. 55, 693–703 (1977).Article 

    Google Scholar 
    31.Michener, G. R. The circannual cycle of Richardson’s ground squirrels in southern Alberta. J. Mammal. 60, 760–768 (1979).Article 

    Google Scholar 
    32.Sheriff, M. J., Buck, C. L. & Barnes, B. M. Autumn conditions as a driver of spring phenology in a free-living arctic mammal. Clim. Chang. Responses 2, 1–7 (2015).Article 

    Google Scholar 
    33.Edic, M. N., Martin, J. G. A. & Blumstein, D. T. Heritable variation in the timing of emergence from hibernation. Evol. Ecol. 34, 763–776 (2020).Article 

    Google Scholar 
    34.Lane, J. E., Kruuk, L. E. B., Charmantier, A., Murie, J. O. & Dobson, F. S. Delayed phenology and reduced fitness associated with climate change in a wild hibernator. Nature 489, 554–557 (2012).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    35.Dobson, F. S., Lane, J. E., Low, M. & Murie, J. O. Fitness implications of seasonal climate variation in Columbian ground squirrels. Ecol. Evol. 6, 5614–5622 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Armitage, K. B. Climate change and the conservation of marmots. Nat. Sci. 05, 36–43 (2013).
    Google Scholar 
    37.Neuhaus, P., Bennett, R. & Hubbs, A. Effects of a late snowstorm and rain on survival and reproductive success in Columbian ground squirrels (Spermophilus columbianus). Can. J. Zool. 77, 879–884 (1999).Article 

    Google Scholar 
    38.Williams, C. T. et al. Sex-dependent phenological plasticity in an arctic hibernator. Am. Nat. 190, 854–859 (2017).PubMed 
    Article 

    Google Scholar 
    39.Barnes, B. M. Relationship between hibernation and reproduction in male ground squirrels. in Adaptations to the Cold: Tenth International Hibernation Symposium (eds. Geiser, F., Hulbert, A. J. & Nicol, S. C.) 71–80 (University of New England Press, 1996).40.Lee, T. M., Pelz, K., Licht, P. & Zucker, I. Testosterone influences hibernation in golden-mantled ground squirrels. Am. J. Physiol. Regul. Integr. Comput. Physiol. 259, 760–767 (1990).Article 

    Google Scholar 
    41.Richter, M. M., Barnes, B. M., Reilly, K. M. O., Fenn, A. M. & Buck, C. L. The influence of androgens on hibernation phenology of free-livingmale arctic ground squirrels. Horm. Behav. 89, 92–97 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.Michener, G. R. Spring emergence schedules and vernal behavior of Richardson’s ground squirrels: Why do males emerge from hibernation before females?. Behav. Ecol. Sociobiol. 14, 29–38 (1983).Article 

    Google Scholar 
    43.Wells, L. J. Seasonal sexual Rhythm and its experimental modification in the male of the thirteen-lined ground squirrel (Citellus tridecemlineatus). Anat. Rec. 62, 409–447 (1935).Article 

    Google Scholar 
    44.Michener, G. R. & Locklear, L. Over-winter weight loss by Richardson’s ground squirrels in relation to sexual differences in mating effort. J. Mammal. 71, 489–499 (1990).Article 

    Google Scholar 
    45.Poiani, A. Complexity of seminal fluid: A review. Behav. Ecol. Sociobiol. 60, 289–310 (2006).Article 

    Google Scholar 
    46.Michener, G. R. Estrous and gestation periods in Richardson’s ground squirrels. J. Mammal. 61, 531–534 (1980).Article 

    Google Scholar 
    47.Michener, G. R. Chronology of reproductive events for female Richardson’s ground aquirrels. J. Mammal. 66, 280–288 (1985).Article 

    Google Scholar 
    48.Michener, G. R. & McLean, I. G. Reproductive behaviour and operational sex ratio in Richardson’s ground squirrels. Anim. Behav. 52, 743–758 (1996).Article 

    Google Scholar 
    49.Hare, J. F., Todd, G. & Untereiner, W. A. Multiple mating results in multiple paternity in Richardson’s Ground Squirrels Spermophilus richardsonii. Can. Field Nat. 118, 90–94 (2004).Article 

    Google Scholar 
    50.Grumm, R., Arnott, J. & Halblaub, J. The epic eastern North American warm episode of March 2012. J. Oper. Meteorol. 2, 36–50 (2014).Article 

    Google Scholar 
    51.Environment and Climate Change Canada (ECCC). Top ten weather stories for 2012: story four—March’s meteorological mildness. (2017). Available at: https://www.ec.gc.ca/meteo-weather/default.asp?lang=En&n=70B4A3E9-1. (Accessed: 20th May 2020)52.Wilson, D. F. & Hare, J. F. Ground squirrel uses ultrasonic alarms. Nature 430, 523 (2004).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.Waterman, J. M., Macklin, G. F. & Enright, C. Sex-biased parasitism in Richardson’s ground squirrels (Urocitellus richardsonii) depends on the parasite examined. Can. J. Zool. 92, 73–79 (2014).Article 

    Google Scholar 
    54.Murie, J. O. & Harris, M. A. Annual variation of spring emergence and breeding in Columbian ground squirrels (Spermophilus columbianus). J. Mammal. 63, 431–439 (1982).Article 

    Google Scholar 
    55.Sikes, R. S. & Gannon, W. L. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. J. Mammal. 92, 235–253 (2011).Article 

    Google Scholar 
    56.Gannon, W. L. & Sikes, R. S. Guidelines of the American society of mammalogists for the use of wild mammals in research. J. Mammal. 88, 809–823 (2007).Article 

    Google Scholar 
    57.Zucker, I. & Boshes, M. Circannual body weight rhythms of ground squirrels: Role of gonadal hormones. Am. J. Physiol. Regul. Int. Comput. Physiol. 12, 546–551 (1982).Article 

    Google Scholar 
    58.Boonstra, R., Hubbs, A. H., Lacey, E. A. & McColl, C. J. Seasonal changes in glucocorticoid and testosterone concentrations in free-living arctic ground squirrels from the boreal forest of the Yukon. Can. J. Zool. 79, 49–58 (2001).Article 

    Google Scholar 
    59.Bottini Luzardo, M., Centurion Castro, F., Alfaro Gamboa, M., Lopez, A. & Ake Lopez, A. Osmolarity of coconut water (Cocos nucifera) based diluents and their effect over viability of frozen boar semen. Am. J. Anim. Vet. Sci. 5, 187–191 (2010).Article 

    Google Scholar 
    60.Mollineau, W. M., Adogwa, A. O. & Garcia, G. W. Liquid and frozen storage of agouti (Dasyprocta leporina) semen extended with UHT milk, unpasteurized coconut water, and pasteurized coconut water. Vet. Med. Int. 2011, 1–5 (2011).Article 

    Google Scholar 
    61.Schulte-Hostedde, A. I., Millar, J. S. & Hickling, G. J. Evaluating body condition in small mammals. Can. J. Zool. 79, 1021–1029 (2001).Article 

    Google Scholar 
    62.Møller, A. P. & Birkhead, T. R. Copulation behaviour in mammals: Evidence that sperm competition is widespread. Biol. J. Linn. Soc. 38, 119–131 (1989).Article 

    Google Scholar 
    63.Sugg, D. W. & Chesser, R. K. Effective population sizes with multiple paternity. Genetics 137, 1147–1155 (1994).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    64.Murie, J. O. & Harris, M. A. Territoriality and dominance in male Columbian ground squirrels (Spermophilus columbianus). Can. J. Zool. 56, 2402–2412 (1978).Article 

    Google Scholar 
    65.Morton, M. L. & Gallup, J. S. Reproductive cycle of the Belding ground squirrel (Spermophilus beldingi beldingi): Seasonal and age differences. Gt. Basin Nat. 35, 427–433 (1975).
    Google Scholar 
    66.Barnes, B. M., Kretzmann, M., Licht, P. & Zucker, I. The influence of hibernation on testis growth and spermatogenesis in the golden-mantled ground squirrel Spermophilus lateralis. Biol. Reprod. 35, 1289–1297 (1986).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar  More

  • in

    The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes

    1.Eckstein, F. Phosphorothioation of DNA in bacteria. Nat. Chem. Biol. 3, 689–690 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    2.Wang, L. et al. Phosphorothioation of DNA in bacteria by dnd genes. Nat. Chem. Biol. 3, 709–710 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    3.Zhou, X. et al. A novel DNA modification by sulphur. Mol. Microbiol. 57, 1428–1438 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    4.Chen, S., Wang, L. & Deng, Z. Twenty years hunting for sulfur in DNA. Protein cell 1, 14–21 (2010).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    5.Xu, T. et al. DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. BMC Microbiol. 9, 41 (2009).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    6.You, D., Wang, L., Yao, F., Zhou, X. & Deng, Z. A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces liVidans. Biochemistry 46, 6126–6133 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    7.Chen, F. et al. Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation. PLoS ONE 7, e36635 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    8.An, X. et al. A novel target of IscS in Escherichia coli: participating in DNA phosphorothioation. PLoS ONE 7, e51265 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Wang, L., Jiang, S., Deng, Z., Dedon, P. C. & Chen, S. DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. FEMS Microbiol. Rev. 43, 109–122 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    10.Yao, F., Xu, T., Zhou, X., Deng, Z. & You, D. Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. FEBS Lett. 583, 729–733 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Hu, W. et al. Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification. Cell Res. 22, 1203–1206 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    12.Cheng, Q. et al. Regulation of DNA phosphorothioate modifications by the transcriptional regulator DptB in Salmonella. Mol. Microbiol. 97, 1186–1194 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    13.Xiong, W., Zhao, G., Yu, H. & He, X. Interactions of Dnd proteins involved in bacterial DNA phosphorothioate modification. Front. Microbiol. 6, 1139 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    14.Dai, D. et al. DNA phosphorothioate modification plays a role in peroxides resistance in Streptomyces lividans. Front. Microbiol. 7, 1380 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    15.Xie, X. et al. Phosphorothioate DNA as an antioxidant in bacteria. Nucleic Acids Res. 40, 9115–9124 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    16.Yang, Y. et al. DNA backbone sulfur-modification expands microbial growth range under multiple stresses by its anti-oxidation function. Sci. Rep. 7 (2017).17.Xu, T., Yao, F., Zhou, X., Deng, Z. & You, D. A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res. 38, 7133–7141 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Liu, G. et al. Cleavage of phosphorothioated DNA and methylated DNA by the Type IV restriction endonuclease ScoMcrA. PLoS Genet. 6, e1001253 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Tong, T. et al. Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria. Proc. Natl Acad. Sci. USA 115, E2988–E2996 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Xiong, L. et al. A new type of DNA phosphorothioation-based antiviral system in archaea. Nat. Commun. 10 (2019).21.Xiong, X. et al. SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat. Microbiol. 5, 917–928 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Dai, D., Pu, T., Liang, J., Wang, Z. & Tang, A. Regulation of dndB gene expression in Streptomyces lividans. Front. Microbiol. 9, 2387 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Zhou, X., Deng, Z., Firmin, J. L., Hopwood, D. A. & Kieser, T. Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res. 16, 4341–4352 (1988).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    24.Sun, Y. et al. DNA phosphorothioate modifications are widely distributed in the human microbiome. Biomolecules 10, 1175 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    25.Khan, H. et al. DNA phosphorothioate modification facilitates the dissemination of mcr-1 and blaNDM-1 in drinking water supply systems. Environ. Pollut. 268, 115799 (2021).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.Wang, L. et al. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Natl Acad. Sci. USA 108, 2963–2968 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    27.Blow, M. J. et al. The epigenomic landscape of prokaryotes. PLoS Genet. 12, e1005854 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    28.Yang, X., Jian, H. & Wang, F. pSW2, a novel low-temperature-inducible gene expression vector based on a filamentous phage of the deep-sea bacterium Shewanella piezotolerans WP3. Appl. Environ. Microbiol. 81, 5519–5526 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Cao, B. et al. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat. Commun. 5, 3951 (2014).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Jian, H. et al. Multiple mechanisms are involved in repression of filamentous phage SW1 transcription by the DNA-binding protein FpsR. J. Mol. Biol. 431, 1113–1126 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    31.Lai, C. et al. In vivo mutational characterization of DndE involved in DNA phosphorothioate modification. PLoS ONE 9, e107981 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    32.Schoemaker, J. M., Gayda, R. C. & Markovitz, A. Regulation of cell division in Escherichia coli: SOS induction and cellular location of the SulA protein, a key to lon-associated filamentation and death. J. Bacteriol. 158, 551–561 (1984).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Jian, H., Xiong, L., Xu, G., Xiao, X. & Wang, F. Long 5′ untranslated regions regulate the RNA stability of the deep-sea filamentous phage SW1. Sci. Rep. 6, 21908 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Chen, C. et al. Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes. Proc. Natl Acad. Sci. USA 114, 4501–4506 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Maleki, F., Khosravi, A., Nasser, A., Taghinejad, H. & Azizian, M. Bacterial heat shock protein activity. J. Clin. Diagnostic Res. 10, BE01–BE03 (2016).CAS 

    Google Scholar 
    36.Knoll, A. H. Paleobiological perspectives on early microbial evolution. Cold Spring Harb. Perspect. Biol. 7, a018093 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.Schirrmeister, B. E., Gugger, M. & Donoghue, P. C. Cyanobacteria and the great oxidation event: evidence from genes and fossils. Palaeontology 58, 769–785 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    38.Luo, G. et al. Rapid oxygenation of Earth’s atmosphere 2.33 billion years ago. Sci. Adv. 2, e1600134 (2016).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    39.Wacey, D., Kilburn, M. R., Saunders, M., Cliff, J. & Brasier, M. D. Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia. Nat. Geosci. 4, 698–702 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    40.Bontognali, T. R. R. et al. Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism. Proc. Natl Acad. Sci. USA 109, 15146–15151 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    41.Schirrmeister, B. E., Vos, J. M. D., Antonelli, A. & Bagheri, H. C. Evolution of multicellularity coincided with increased diversification of cyanobacteria and the great oxidation event. Proc. Natl Acad. Sci. USA 110, 1791–1796 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Pang, K. et al. Nitrogen-fixing heterocystous Cyanobacteria in the tonian period. Curr. Biol. 28, 616–622 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    43.Demoulin, C. F. et al. Cyanobacteria evolution: Insight from the fossil record. Free Radic. Biol. Med. in press (2021).44.Soo, R. M., Hemp, J., Parks, D. H., Fischer, W. W. & Hugenholtz, P. On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science 355, 1436–1440 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    45.Ou, H.-Y. et al. dndDB: a database focused on phosphorothioation of the DNA backbone. PLoS ONE 4, e5132 (2009).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    46.Janda, J. M. & Abbott, S. L. The genus Shewanella: from the briny depths below to human pathogen. Crit. Rev. Microbiol. 40, 293–312 (2014).PubMed 
    Article 

    Google Scholar 
    47.Fredrickson, J. K. et al. Towards environmental systems biology of Shewanella. Nat. Rev. Microbiol. 6, 592–603 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    48.Hau, H. H. & Gralnick, J. A. Ecology and biotechnology of the genus Shewanella. Annu. Rev. Microbiol. 61, 237–258 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    49.Nealson, K. H. & Scott, J. Ecophysiology of the Genus Shewanella. Prokaryotes 6, 1133–1151 (2006).Article 

    Google Scholar 
    50.Roux, S. et al. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat. Microbiol. 4, 1895–1906 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.Hay, I. D. & Lithgow, T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep. 20, e47427 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    52.Mai-Prochnow, A. et al. ‘Big things in small packages: the genetics of filamentous phage and effects on fitness of their host’. FEMS Microbiol. Rev. 39, 465–487 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.Middelboe, M., Glud, R. N. & Finster, K. Distribution of viruses and bacteria in relation to diagenetic activity in an estuarine sediment. Limnol. Oceanogr. 48, 1447–1456 (2003).ADS 
    Article 

    Google Scholar 
    54.Engelhardt, T., Orsi, W. D. & Jørgensen, B. B. Viral activities and life cycles in deep subseafloor sediments. Environ. Microbiol. Rep. 7, 868–873 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Dell’Anno, A., Corinaldesi, C. & Danovaro, R. Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning. Proc. Natl Acad. Sci. USA 112, E2014–E2019 (2015).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    56.Rakonjac, J. Filamentous Bacteriophages: Biology and Applications. eLS (2012).57.Güemes, A. G. C. et al. Viruses as winners in the game of life. Annu. Rev. Virol. 3, 197–214 (2016).Article 
    CAS 

    Google Scholar 
    58.Breitbart, M. Marine viruses: truth or dare. Annu. Rev. Mar. Sci. 4, 425–448 (2012).ADS 
    Article 

    Google Scholar 
    59.Danovaro, R. et al. Marine viruses and global climate change. FEMS Microbiol. Rev. 35, 993–1034 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    60.Rohwer, F. & Thurber, R. V. Viruses manipulate the marine environment. Nature 459, 207–212 (2009).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    61.Touchon, M., Bernheim, A. & Rocha, E. P. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 10, 2744–2754 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    62.Harrison, E. & Brockhurst, M. A. Ecological and evolutionary benefits of temperate phage: what does or doesn’t kill you makes you stronger. Bioessays 39, 201700112 (2017).Article 

    Google Scholar 
    63.Paul, J. H. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2, 579–589 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Wu, X. et al. Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. PNAS 117, 14322–14330 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    65.Willbanks, A. et al. The evolution of epigenetics: from prokaryotes to humans and its biological consequences. Genet. Epigenet. 8, 25–36 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Razin, A. & Cedar, H. DNA methylation and gene expression. Microbiol. Rev. 55, 451–458 (1991).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Casadesús, J. & Low, D. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70, 830–856 (2006).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    68.Iyer, L. M., Abhiman, S. & Aravind, L. Natural history of eukaryotic DNA methylation systems. Prog. Mol. Biol. Transl. Sci. 101, 25–104 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    69.Weiss, M. C. et al. The physiology and habitat of the last universal common ancestor. Nat. Microbiol. 1, 16116 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    70.Gan, R. et al. DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks. Sci. Rep. 4, 6642 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    71.Chen, L. et al. Theoretical study on the relationship between Rp-phosphorothioation and base-step in S-DNA: based on energetic and structural analysis. J. Phys. Chem. B 119, 474–481 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    72.Kellner, S. et al. Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability. Nat. Chem. Biol. 13, 888–894 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    73.Ślesak, I., Kula, M., Ślesak, H., Miszalski, Z. & Strzałka, K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free Radic. Biol. Med. 140, 61–73 (2019).PubMed 
    Article 
    CAS 

    Google Scholar 
    74.Brioukhanov, A. L., Thauer, R. K. & Netrusov, A. I. Catalase and superoxide dismutase in the cells of strictly anaerobic microorganisms. Microbiol. (Russ. Acad. Sci.) 71, 330–335 (2002).
    Google Scholar 
    75.Sebaihia, M. et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat. Genet. 38, 779–786 (2006).PubMed 
    Article 
    CAS 

    Google Scholar 
    76.Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    77.Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    78.Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 90 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    79.Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109–1123 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    80.Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    81.Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    82.Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    83.Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36, 1925–1927 (2020).CAS 

    Google Scholar 
    84.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood treesfor large alignments. PLoS ONE 5, e9490 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    85.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    87.Kwak, S. G. & Kim, J. H. Central limit theorem: the cornerstone of modern statistics. Korean J. Anesthesiol. 70, 144–156 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    88.Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    89.R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2013).90.Chok, N. S. Pearson’s versus Spearman’s and Kendall’s correlation coefficients for continuous data Master of Science thesis, University of Pittsburgh, (2010).91.Jian, H., Xu, G., Gai, Y., Xu, J. & Xiao, X. The histone-like nucleoid structuring protein (H-NS) is a negative regulator of the lateral flagellar system in the deep-sea bacterium Shewanella piezotolerans WP3. Appl. Environ. Microbiol. 82, 2388–2398 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    92.Wang, F. et al. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS ONE 3, e1937 (2008).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    93.Jian, H., Xu, J., Xiao, X. & Wang, F. Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature. PLoS ONE 7, e41578 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    94.Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2016).Article 
    CAS 

    Google Scholar 
    95.Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    96.Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    97.Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).CAS 
    Article 

    Google Scholar 
    98.Wang, L., Feng, Z., Wang, X., Wang, X. & Zhang, X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136–138 (2010).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    99.Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    100.Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    101.Gao, H. et al. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. ISME J. 3, 966–976 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    102.Lenski, R. E., Rose, M. R., Simpson, S. C. & Tadler, S. C. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2000 generations. Am. Naturalist 138, 1315–1341 (1991).Article 

    Google Scholar  More

  • in

    Antibiotic resistance in the environment

    1.D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011). This study shows that different ARGs are present in 30,000-year-old permafrost.
    Google Scholar 
    2.Bhullar, K. et al. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS ONE 7, e34953 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    3.Lugli, G. A. et al. Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age. Microbiome 5, 5 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    4.Perry, J., Waglechner, N. & Wright, G. The prehistory of antibiotic resistance. Cold Spring Harb. Perspect. Med. 6, a025197 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    5.Davies, J. & Davies, D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433 (2010). This authoritative and educational review discusses in an insightful way the evolution of resistance, including its origins and future implications.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    6.Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).CAS 
    PubMed 

    Google Scholar 
    7.Martinez, J. L. The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc. R. Soc. B Biol. Sci. 276, 2521–2530 (2009).
    Google Scholar 
    8.Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz935 (2019).Article 
    PubMed Central 

    Google Scholar 
    9.Mackenzie, J. S. & Jeggo, M. The one health approach — why is it so important? Trop. Med. Infect. Dis. 4, 88 (2019).PubMed Central 

    Google Scholar 
    10.Buschhardt, T. et al. A one health glossary to support communication and information exchange between the human health, animal health and food safety sectors. One Health 13, 100263 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    11.Berendonk, T. U. et al. Tackling antibiotic resistance: the environmental framework. Nat. Rev. Microbiol. 13, 310–317 (2015).CAS 
    PubMed 

    Google Scholar 
    12.Wellington, E. M. et al. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect. Dis. 13, 155–165 (2013).CAS 
    PubMed 

    Google Scholar 
    13.Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol. Rev. https://doi.org/10.1093/femsre/fux053 (2017).Article 
    PubMed Central 

    Google Scholar 
    14.Chow, L. K. M., Ghaly, T. M. & Gillings, M. R. A survey of sub-inhibitory concentrations of antibiotics in the environment. J. Environ. Sci. 99, 21–27 (2021).
    Google Scholar 
    15.Andersson, D. I. et al. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol. Rev. 44, 171–188 (2020).CAS 
    PubMed 

    Google Scholar 
    16.Singer, A. C., Shaw, H., Rhodes, V. & Hart, A. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.01728 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    17.United Nations Environment Programme. Frontiers 2017: emerging issues of environmental concern, https://www.unenvironment.org/resources/frontiers-2017-emerging-issues-environmental-concern (2017).18.Access to Medicines Foundation. 2020 antimicrobial resistance benchmark, https://accesstomedicinefoundation.org/publications/2020-antimicrobial-resistance-benchmark (2020).19.Review on Antimicrobial Resistance. Antimicrobials in agriculture and the environment: reducing unnecessary waste, https://amr-review.org/Publications.html (2015).20.European Parliament. Strategic approach to pharmaceuticals in the environment, https://www.europarl.europa.eu/doceo/document/TA-9-2020-0226_EN.pdf (2020).21.WHO. Technical brief on water, sanitation, hygiene (WASH) and wastewater management to prevent infections and reduce the spread of antimicrobial resistance (AMR)., https://www.who.int/water_sanitation_health/publications/wash-wastewater-management-to-prevent-infections-and-reduce-amr/en/ (2020).22.Graham, D. W. et al. Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems. Ann. N. Y. Acad. Sci. 1441, 17–30 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    23.Smalla, K., Cook, K., Djordjevic, S. P., Klümper, U. & Gillings, M. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiy195 (2018).Article 
    PubMed 

    Google Scholar 
    24.Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).CAS 
    PubMed 

    Google Scholar 
    25.Schulz, F. et al. Towards a balanced view of the bacterial tree of life. Microbiome https://doi.org/10.1186/s40168-017-0360-9 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    26.Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012). This study demonstrates numerous identical resistance gene loci between multiresistant soil bacteria and diverse human pathogens, providing evidence for recent gene exchange across species and environments.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    27.Berglund, F. et al. Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data. Microbiome 5, 134 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    28.Dantas, G., Sommer, M. O. A., Oluwasegun, R. D. & Church, G. M. Bacteria subsisting on antibiotics. Science 320, 100–103 (2008).CAS 
    PubMed 

    Google Scholar 
    29.Berglund, F. et al. Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. Microb. Genomics https://doi.org/10.1099/mgen.0.000455 (2020).Article 

    Google Scholar 
    30.Pawlowski, A. C. et al. A diverse intrinsic antibiotic resistome from a cave bacterium. Nat. Commun. 7, 13803 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    31.Morar, M. & Wright, G. D. The genomic enzymology of antibiotic resistance. Annu. Rev. Genet. 44, 25–51 (2010).CAS 
    PubMed 

    Google Scholar 
    32.Andersson, D. I., Jerlström-Hultqvist, J. & Näsvall, J. Evolution of new functions de novo and from preexisting genes. Cold Spring Harb. Perspect. Biol. 7, a017996 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    33.Razavi, M., Kristiansson, E., Flach, C.-F. & Larsson, D. G. J. The association between insertion sequences and antibiotic resistance genes. mSphere https://doi.org/10.1128/msphere.00418-20 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    34.Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. https://doi.org/10.1128/cmr.00088-17 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    35.Gillings, M. et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190, 5095–5100 (2008).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Razavi, M. et al. Discovery of the fourth mobile sulfonamide resistance gene. Microbiome https://doi.org/10.1186/s40168-017-0379-y (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    37.Flach, C.-F. et al. Does antifouling paint select for antibiotic resistance? Sci. Total Environ. 590–591, 461–468 (2017).PubMed 

    Google Scholar 
    38.Shintani, M. et al. Plant species-dependent increased abundance and diversity of IncP-1 plasmids in the rhizosphere: new insights into their role and ecology. Front. Microbiol. 11, 590776 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    39.Baquero, F., Coque, T. M., Martínez, J.-L., Aracil-Gisbert, S. & Lanza, V. F. Gene transmission in the one health microbiosphere and the channels of antimicrobial resistance. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.02892 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    40.Vandecraen, J., Chandler, M., Aertsen, A. & Van Houdt, R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43, 709–730 (2017).CAS 
    PubMed 

    Google Scholar 
    41.Depardieu, F., Podglajen, I., Leclercq, R., Collatz, E. & Courvalin, P. Modes and modulations of antibiotic resistance gene expression. Clin. Microbiol. Rev. 20, 79–114 (2007).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Jutkina, J., Marathe, N. P., Flach, C. F. & Larsson, D. G. J. Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations. Sci. Total Environ. 616-617, 172–178 (2018).CAS 
    PubMed 

    Google Scholar 
    43.Scornec, H., Bellanger, X., Guilloteau, H., Groshenry, G. & Merlin, C. Inducibility of Tn916 conjugative transfer in Enterococcus faecalis by subinhibitory concentrations of ribosome-targeting antibiotics. J. Antimicrob. Chemother. 72, 2722–2728 (2017).CAS 
    PubMed 

    Google Scholar 
    44.Aminov, R. I. Horizontal gene exchange in environmental microbiota. Front. Microbiol. https://doi.org/10.3389/fmicb.2011.00158 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    45.Knöppel, A., Näsvall, J. & Andersson, D. I. Evolution of antibiotic resistance without antibiotic exposure. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.01495-17 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    46.Kimura, M. & Ohta, T. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763–771 (1969).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    47.Letten, A. D., Hall, A. R. & Levine, J. M. Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nat. Ecol. Evol. 5, 431–441 (2021).PubMed 

    Google Scholar 
    48.Waglechner, N. & Wright, G. D. Antibiotic resistance: it’s bad, but why isn’t it worse? BMC Biol. https://doi.org/10.1186/s12915-017-0423-1 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    49.Ebmeyer, S., Erik, K. & Larsson, D. G. J. A framework for identifying the recent origins of mobile antibiotic resistance genes. Commun. Biol. https://doi.org/10.1038/s42003-020-01545-5 (2021). This study amends, summarizes and scrutinizes current evidence for proposed recent origin species for mobile ARGs.Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    50.Andersson, D. I. & Hughes, D. Persistence of antibiotic resistance in bacterial populations. FEMS Microbiol. Rev. 35, 901–911 (2011).CAS 
    PubMed 

    Google Scholar 
    51.Wang, J., Chu, L., Wojnárovits, L. & Takács, E. Occurrence and fate of antibiotics, antibiotic resistant genes (ARGs) and antibiotic resistant bacteria (ARB) in municipal wastewater treatment plant: an overview. Sci. Total. Environ. 744, 140997 (2020).CAS 
    PubMed 

    Google Scholar 
    52.Tran, N. H., Reinhard, M. & Gin, K. Y.-H. Occurrence and fate of emerging contaminants in municipal wastewater treatment plants from different geographical regions-a review. Water Res. 133, 182–207 (2018).CAS 
    PubMed 

    Google Scholar 
    53.Szymańska, U. et al. Presence of antibiotics in the aquatic environment in Europe and their analytical monitoring: recent trends and perspectives. Microchem. J. 147, 729–740 (2019).
    Google Scholar 
    54.Anwar, M., Iqbal, Q. & Saleem, F. Improper disposal of unused antibiotics: an often overlooked driver of antimicrobial resistance. Expert Rev. Antiinfect Ther. https://doi.org/10.1080/14787210.2020.1754797 (2020).Article 

    Google Scholar 
    55.Cabello, F. C. et al. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environ. Microbiol. 15, 1917–1942 (2013).PubMed 

    Google Scholar 
    56.Cabello, F. C., Godfrey, H. P., Buschmann, A. H. & Dölz, H. J. Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance. Lancet Infect. Dis. 16, e127–e133 (2016).PubMed 

    Google Scholar 
    57.Taylor, P. & Reeder, R. Antibiotic use on crops in low and middle-income countries based on recommendations made by agricultural advisors. CABI Agric. Biosci. https://doi.org/10.1186/s43170-020-00001-y (2020).Article 

    Google Scholar 
    58.Larsson, D. G. J. Pollution from drug manufacturing: review and perspectives. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130571 (2014).
    Google Scholar 
    59.Larsson, D. G. J., De Pedro, C. & Paxeus, N. Effluent from drug manufactures contains extremely high levels of pharmaceuticals. J. Hazard. Mater. 148, 751–755 (2007).CAS 
    PubMed 

    Google Scholar 
    60.Milaković, M. et al. Pollution from azithromycin-manufacturing promotes macrolide-resistance gene propagation and induces spatial and seasonal bacterial community shifts in receiving river sediments. Environ. Int. 123, 501–511 (2019).PubMed 

    Google Scholar 
    61.Bielen, A. et al. Negative environmental impacts of antibiotic-contaminated effluents from pharmaceutical industries. Water Res. 126, 79–87 (2017).CAS 
    PubMed 

    Google Scholar 
    62.Fick, J. et al. Contamination of surface, ground, and drinking water from pharmaceutical production. Environ. Toxicol. Chem. 28, 2522–2527 (2009).CAS 
    PubMed 

    Google Scholar 
    63.Bengtsson-Palme, J. & Larsson, D. G. J. Concentrations of antibiotics predicted to select for resistant bacteria: proposed limits for environmental regulation. Environ. Int. 86, 140–149 (2016). This study uses a simplified approach based on available MIC data for many species to predict concentrations of 111 antibiotics that are not likely to select for resistance.CAS 
    PubMed 

    Google Scholar 
    64.Gullberg, E. et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 7, e1002158 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    65.Karkman, A., Pärnänen, K. & Larsson, D. G. J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat. Commun. https://doi.org/10.1038/s41467-018-07992-3 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    66.Yang, Y., Li, B., Zou, S., Fang, H. H. P. & Zhang, T. Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach. Water Res. 62, 97–106 (2014).CAS 
    PubMed 

    Google Scholar 
    67.Bengtsson-Palme, J. et al. Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci. Total Environ. 572, 697–712 (2016).CAS 
    PubMed 

    Google Scholar 
    68.Manaia, C. M. et al. Antibiotic resistance in wastewater treatment plants: tackling the black box. Environ. Int. 115, 312–324 (2018).CAS 
    PubMed 

    Google Scholar 
    69.Flach, C. F., Genheden, M., Fick, J. & Joakim Larsson, D. G. A comprehensive screening of Escherichia coli isolates from Scandinavia’s largest sewage treatment plant indicates no selection for antibiotic resistance. Environ. Sci. Technol. 52, 11419–11428 (2018).CAS 
    PubMed 

    Google Scholar 
    70.Kraupner, N. et al. Evidence for selection of multi-resistant E. coli by hospital effluent. Environ. Int. 150, 106436 (2021).CAS 
    PubMed 

    Google Scholar 
    71.Flach, C. F. et al. Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake. J. Antimicrob. Chemother. 70, 2709–2717 (2015).CAS 
    PubMed 

    Google Scholar 
    72.Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E. & Larsson, D. G. J. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front. Microbiol. https://doi.org/10.3389/fmicb.2014.00648 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    73.Marathe, N. P. et al. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. Environ. Int. 112, 279–286 (2018).CAS 
    PubMed 

    Google Scholar 
    74.Thiele-Bruhn, S. Pharmaceutical antibiotic compounds in soils–a review. J. Plant Nutr. Soil Sci. 166, 145–167 (2003).CAS 

    Google Scholar 
    75.Li, W., Shi, Y., Gao, L., Liu, J. & Cai, Y. Occurrence, distribution and potential affecting factors of antibiotics in sewage sludge of wastewater treatment plants in China. Sci. Total. Environ. 445–446, 306–313 (2013).PubMed 

    Google Scholar 
    76.Reinthaler, F. F. et al. Resistance patterns of Escherichia coli isolated from sewage sludge in comparison with those isolated from human patients in 2000 and 2009. J. Water Health 11, 13–20 (2013).PubMed 

    Google Scholar 
    77.Rutgersson, C. et al. Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome. Environ. Int. 137, 105339 (2020).CAS 
    PubMed 

    Google Scholar 
    78.Jechalke, S., Heuer, H., Siemens, J., Amelung, W. & Smalla, K. Fate and effects of veterinary antibiotics in soil. Trends Microbiol. 22, 536–545 (2014).CAS 
    PubMed 

    Google Scholar 
    79.Boxall, A. B. et al. Pharmaceuticals and personal care products in the environment: what are the big questions? Environ. Health Perspect. 120, 1221–1229 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    80.Song, J., Rensing, C., Holm, P. E., Virta, M. & Brandt, K. K. Comparison of metals and tetracycline as selective agents for development of tetracycline resistant bacterial communities in agricultural soil. Environ. Sci. Technol. 51, 3040–3047 (2017).CAS 
    PubMed 

    Google Scholar 
    81.Jechalke, S. et al. Plasmid-mediated fitness advantage of Acinetobacter baylyi in sulfadiazine-polluted soil. FEMS Microbiol. Lett. 348, 127–132 (2013). This study shows that a commonly used antibiotic in pig farming has the potential to select for a resistant Acinetobacter strain in manure-amended soils.CAS 
    PubMed 

    Google Scholar 
    82.Pal, C. et al. Metal resistance and its association with antibiotic resistance. Adv. Microb. Physiol. 70, 261–313 (2017).CAS 
    PubMed 

    Google Scholar 
    83.Wales, A. & Davies, R. Co-selection of resistance to antibiotics, biocides and heavy metals, and its relevance to foodborne pathogens. Antibiotics 4, 567–604 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    84.Pal, C., Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics https://doi.org/10.1186/s12864-015-2153-5 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    85.Klümper, U. et al. Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner. ISME J. 11, 152–165 (2017).PubMed 

    Google Scholar 
    86.Jutkina, J., Rutgersson, C., Flach, C. F. & Joakim Larsson, D. G. An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance. Sci. Total. Environ. 548–549, 131–138 (2016).PubMed 

    Google Scholar 
    87.Wang, Y. et al. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. ISME J. 14, 2179–2196 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    88.Klumper, U. et al. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community. ISME J. 9, 934–945 (2015). This study shows that plasmids that are common in pathogens can easily be taken up by diverse environmental bacteria, thereby providing pathways for the exchange of resistance genes.CAS 
    PubMed 

    Google Scholar 
    89.Gillings, M. R., Paulsen, I. T. & Tetu, S. G. Genomics and the evolution of antibiotic resistance. Ann. N. Y. Acad. Sci. 1388, 92–107 (2017).PubMed 

    Google Scholar 
    90.Heuer, H. & Smalla, K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 36, 1083–1104 (2012).CAS 
    PubMed 

    Google Scholar 
    91.Bengtsson-Palme, J. & Larsson, D. G. Antibiotic resistance genes in the environment: prioritizing risks. Nat. Rev. Microbiol. 13, 396 (2015).CAS 
    PubMed 

    Google Scholar 
    92.Leonard, A. F. C. et al. Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey). Environ. Int. 114, 326–333 (2018). This is one of few studies showing that people more likely to ingest surface waters are also more prone to be carriers of resistant bacteria compared with matched controls.PubMed 

    Google Scholar 
    93.Manaia, C. M. Assessing the risk of antibiotic resistance transmission from the environment to humans: non-direct proportionality between abundance and risk. Trends Microbiol. 25, 173–181 (2017).CAS 
    PubMed 

    Google Scholar 
    94.Schijven, J. F., Blaak, H., Schets, F. M. & De Roda Husman, A. M. Fate of extended-spectrum β-lactamase-producing Escherichia coli from faecal sources in surface water and probability of human exposure through swimming. Environ. Sci. Technol. 49, 11825–11833 (2015).CAS 
    PubMed 

    Google Scholar 
    95.Collignon, P., Beggs, J. J., Walsh, T. R., Gandra, S. & Laxminarayan, R. Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis. Lancet Planet. Health 2, e398–e405 (2018).PubMed 

    Google Scholar 
    96.Dancer, S. J. Controlling hospital-acquired infection: focus on the role of the environment and new technologies for decontamination. Clin. Microbiol. Rev. 27, 665–690 (2014).PubMed 
    PubMed Central 

    Google Scholar 
    97.Weber, D. J., Anderson, D. & Rutala, W. A. The role of the surface environment in healthcare-associated infections. Curr. Opin. Infect. Dis. 26, 338–344 (2013).PubMed 

    Google Scholar 
    98.Søraas, A., Sundsfjord, A., Sandven, I., Brunborg, C. & Jenum, P. A. Risk factors for community-acquired urinary tract infections caused by ESBL-producing Enterobacteriaceae –a case–control study in a low prevalence country. PLoS ONE 8, e69581 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    99.Zhou, S.-Y.-D. et al. Prevalence of antibiotic resistome in ready-to-eat salad. Front. Public Health https://doi.org/10.3389/fpubh.2020.00092 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    100.Uyttendaele, M. et al. Microbial hazards in irrigation water: standards, norms, and testing to manage use of water in fresh produce primary production. Compr. Rev. Food Sci. Food Saf. 14, 336–356 (2015).
    Google Scholar 
    101.Reid, C. J., Blau, K., Jechalke, S., Smalla, K. & Djordjevic, S. P. Whole genome sequencing of Escherichia coli from store-bought produce. Front. Microbiol. 10, 3050 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    102.Blau, K. et al. The transferable resistome of produce. mBio 9, e01300-18 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    103.Zhu, Y.-G. et al. Soil biota, antimicrobial resistance and planetary health. Environ. Int. 131, 105059 (2019).PubMed 

    Google Scholar 
    104.Pal, C., Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. The structure and diversity of human, animal and environmental resistomes. Microbiome 4, 54 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    105.Kozajda, A., Jeżak, K. & Kapsa, A. Airborne Staphylococcus aureus in different environments — a review. Environ. Sci. Pollut. Res. 26, 34741–34753 (2019).CAS 

    Google Scholar 
    106.Ashbolt, N. J. et al. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ. Health Perspect. 121, 993–1001 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    107.Franz, E., Schijven, J., De Roda Husman, A. M. & Blaak, H. Meta-regression analysis of commensal and pathogenic Escherichia coli survival in soil and water. Environ. Sci. Technol. 48, 6763–6771 (2014).CAS 
    PubMed 

    Google Scholar 
    108.Lewis, K. Platforms for antibiotic discovery. Nat. Rev. Drug. Discov. 12, 371–387 (2013).CAS 
    PubMed 

    Google Scholar 
    109.Linton, K. B., Richmond, M. H., Bevan, R. & Gillespie, W. A. Antibiotic resistance and R factors in coliform bacilli isolated from hospital and domestic sewage. J. Med. Microbiol. 7, 91–103 (1974).CAS 
    PubMed 

    Google Scholar 
    110.Huijbers, P., Joakim Larsson, D. G. & Flach, C. F. Surveillance of antibiotic resistant Escherichia coli in human populations through urban wastewater in ten European countries. Environ. Pollut. 261, 114200 (2020).CAS 
    PubMed 

    Google Scholar 
    111.Hutinel, M. et al. Population-level surveillance of antibiotic resistance in Escherichia coli through sewage analysis. Euro Surveill. https://doi.org/10.2807/1560-7917.es.2019.24.37.1800497 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    112.Aarestrup, F. M. & Woolhouse, M. E. J. Using sewage for surveillance of antimicrobial resistance. Science 367, 630–632 (2020).CAS 
    PubMed 

    Google Scholar 
    113.Kwak, Y. K. et al. Surveillance of antimicrobial resistance among Escherichia coli in wastewater in Stockholm during 1 year: does it reflect the resistance trends in the society? Int. J. Antimicrob. Agents 45, 25–32 (2015).CAS 
    PubMed 

    Google Scholar 
    114.Parnanen, K. M. M. et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Sci. Adv. 5, eaau9124 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    115.Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019). This is the most comprehensive survey of ARGs in sewage across the world to date, showing distinct differences between regions.PubMed 
    PubMed Central 

    Google Scholar 
    116.Huijbers, P. M. C., Flach, C. F. & Larsson, D. G. J. A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance. Environ. Int. 130, 104880 (2019).CAS 
    PubMed 

    Google Scholar 
    117.Böhm, M.-E., Razavi, M., Marathe, N. P., Flach, C.-F. & Larsson, D. G. J. Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. Microbiome https://doi.org/10.1186/s40168-020-00814-z (2020). Using a functional assay targeting mobile genes, this study explores environment communities and finds a completely novel resistance gene that had escaped discovery in clinics despite its presence in pathogens on different continents.Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    118.Flach, C.-F., Hutinel, M., Razavi, M., Åhrén, C. & Larsson, D. G. J. Monitoring of hospital sewage shows both promise and limitations as an early-warning system for carbapenemase-producing Enterobacterales in a low-prevalence setting. Water Res. 200, 117261 (2021).CAS 
    PubMed 

    Google Scholar 
    119.Karkman, A., Berglund, F., Flach, C.-F., Kristiansson, E. & Larsson, D. G. J. Predicting clinical resistance prevalence using sewage metagenomic data. Commun. Biol. https://doi.org/10.1038/s42003-020-01439-6 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    120.European Centre for Disease Prevention and Control. Surveillance of antimicrobial resistance in Europe 2017 (Stockholm, Sweden, 2018).121.Hovi, T. et al. Role of environmental poliovirus surveillance in global polio eradication and beyond. Epidemiol. Infect. 140, 1–13 (2012).CAS 
    PubMed 

    Google Scholar 
    122.Agrawal, S., Orschler, L. & Lackner, S. Long-term monitoring of SARS-CoV-2 RNA in wastewater of the Frankfurt metropolitan area in southern Germany. Sci. Rep. https://doi.org/10.1038/s41598-021-84914-2 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    123.Medema, G., Heijnen, L., Elsinga, G., Italiaander, R. & Brouwer, A. Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands. Environ. Sci. Technol. Lett. 7, 511–516 (2020).CAS 

    Google Scholar 
    124.Lundstrom, S. V. et al. Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Sci. Total Environ. 553, 587–595 (2016).PubMed 

    Google Scholar 
    125.McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125, 497–504 (2019).CAS 
    PubMed 

    Google Scholar 
    126.Pruden, A., Arabi, M. & Storteboom, H. N. Correlation between upstream human activities and riverine antibiotic resistance genes. Environ. Sci. Technol. 46, 11541–11549 (2012).CAS 
    PubMed 

    Google Scholar 
    127.Zhu, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).CAS 
    PubMed 

    Google Scholar 
    128.Zhu, Y.-G. et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl Acad. Sci. USA 110, 3435–3440 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    129.Knapp, C. W., Dolfing, J., Ehlert, P. A. I. & Graham, D. W. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ. Sci. Technol. 44, 580–587 (2010).CAS 
    PubMed 

    Google Scholar 
    130.Nesme, J. & Simonet, P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. 17, 913–930 (2015).PubMed 

    Google Scholar 
    131.Finley, R. L. et al. The scourge of antibiotic resistance: the important role of the environment. Clin. Infect. Dis. 57, 704–710 (2013).PubMed 

    Google Scholar 
    132.Sjölund, M. et al. Dissemination of multidrug-resistant bacteria into the Arctic. Emerg. Infect. Dis. 14, 70–72 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    133.Zhu, G. et al. Air pollution could drive global dissemination of antibiotic resistance genes. ISME J. https://doi.org/10.1038/s41396-020-00780-2 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    134.Nichols, D. et al. Use of Ichip for high-throughput in situ cultivation of “Uncultivable” microbial species. Appl. Environ. Microbiol. 76, 2445–2450 (2010).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    135.Ashton, P. M. et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol. 33, 296–300 (2015).CAS 
    PubMed 

    Google Scholar 
    136.Spencer, S. J. et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 10, 427–436 (2016).CAS 
    PubMed 

    Google Scholar 
    137.Rice, E. W., Wang, P., Smith, A. L. & Stadler, L. B. Determining hosts of antibiotic resistance genes: a review of methodological advances. Environ. Sci. Technol. Lett. 7, 282–291 (2020).CAS 

    Google Scholar 
    138.Sivalingam, P., Poté, J. & Prabakar, K. Extracellular DNA (eDNA): neglected and potential sources of antibiotic resistant genes (ARGs) in the aquatic environments. Pathogens 9, 874 (2020).CAS 
    PubMed Central 

    Google Scholar 
    139.Bengtsson-Palme, J., Larsson, D. G. J. & Kristiansson, E. Using metagenomics to investigate human and environmental resistomes. J. Antimicrob. Chemother. 72, 2690–2703 (2017).CAS 
    PubMed 

    Google Scholar 
    140.Karkman, A. et al. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 92, https://doi.org/10.1093/femsec/fiw014 (2016).141.Gillings, M. R. et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9, 1269–1279 (2015).CAS 
    PubMed 

    Google Scholar 
    142.Gaze, W. H., Abdouslam, N., Hawkey, P. M. & Wellington, E. M. H. Incidence of Class 1 integrons in a quaternary ammonium compound-polluted environment. Antimicrob. Agents Chemother. 49, 1802–1807 (2005).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    143.Sommer, M. O. A., Munck, C., Toft-Kehler, R. V. & Andersson, D. I. Prediction of antibiotic resistance: time for a new preclinical paradigm? Nat. Rev. Microbiol. 15, 689–696 (2017). This article highlights the needs to consider the environmental gene reservoir and other factors influencing resistance evolution in the development process for new antibiotics.CAS 
    PubMed 

    Google Scholar 
    144.Pehrsson, E. C., Forsberg, K. J., Gibson, M. K., Ahmadi, S. & Dantas, G. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs. Front. Microbiol. https://doi.org/10.3389/fmicb.2013.00145 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    145.Kim, C., Ryu, H.-D., Chung, E. G., Kim, Y. & Lee, J.-K. A review of analytical procedures for the simultaneous determination of medically important veterinary antibiotics in environmental water: sample preparation, liquid chromatography, and mass spectrometry. J. Environ. Manag. 217, 629–645 (2018).CAS 

    Google Scholar 
    146.Fahrenfeld, N. & Bisceglia, K. J. Emerging investigators series: sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology. Environ. Sci. Water Res. Technol. 2, 788–799 (2016).CAS 

    Google Scholar 
    147.Anliker, S. et al. Assessing emissions from pharmaceutical manufacturing based on temporal high-resolution mass spectrometry data. Environ. Sci. Technol. 54, 4110–4120 (2020). This recent study elegantly uses the erratic emission profiles of drugs from manufacturing plants to attribute a large portion of the pharmaceutical residues found in a Swiss river to industrial emissions, further showing that curbing such pollution is an ongoing, worldwide challenge.CAS 
    PubMed 

    Google Scholar 
    148.Klümper, U. et al. Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. ISME J. 13, 2927–2937 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    149.Kraupner, N. et al. Selective concentrations for trimethoprim resistance in aquatic environments. Environ. Int. 144, 106083 (2020).CAS 
    PubMed 

    Google Scholar 
    150.Murray, A. K. et al. Novel insights into selection for antibiotic resistance in complex microbial communities. mBio https://doi.org/10.1128/mbio.00969-18 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    151.Government of India. Environment (Protection) Amendment Rules, 2020 – Inviting comments/suggestions on Environmental Standards for Bulk Drug and Formulation (Pharmaceutical) Industry, http://moef.gov.in/g-s-r-44-e-date-23-01-2020-environment-protection-amendment-rules-2020-inviting-commentssuggestions-on-environmental-standards-for-bulk-drug-and-formulation-pharmaceutical-indu/ (2020).152.Tell, J. et al. Science-based targets for antibiotics in receiving waters from pharmaceutical manufacturing operations. Integr. Environ. Assess. Manag. 15, 312–319 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    153.Greenfield, B. K. et al. Modeling the emergence of antibiotic resistance in the environment: an analytical solution for the minimum selection concentration. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.01686-17 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    154.Murray, A. K. et al. The ‘Selection end points in Communities of bacTeria’ (SELECT) method: a novel experimental assay to facilitate risk assessment of selection for antimicrobial resistance in the environment. Environ. Health Perspect. 128, 107007 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    155.Andersson, D. I. & Hughes, D. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat. Rev. Microbiol. 8, 260–271 (2010).CAS 
    PubMed 

    Google Scholar 
    156.Stanton, I. C., Murray, A. K., Zhang, L., Snape, J. & Gaze, W. H. Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration. Commun. Biol. https://doi.org/10.1038/s42003-020-01176-w (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    157.Nijsingh, N., Munthe, C. & Larsson, D. G. J. Managing pollution from antibiotics manufacturing: charting actors, incentives and disincentives. Environ. Health 18, 95 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    158.Sundin, G. W. & Wang, N. Antibiotic resistance in plant-pathogenic bacteria. Annu. Rev. Phytopathol. 56, 161–180 (2018).CAS 
    PubMed 

    Google Scholar 
    159.Government of Sweden. Uppdrag angående försöksverksamhet för en miljöpremie i läkemedelsförmånssystemet, https://www.regeringen.se/499677/contentassets/36dcec65be904fd58e5e6b01c2f99709/uppdrag-angaende-forsoksverksamhet-for-en-miljopremie-i-lakemedelsformanssystemet-tlv.pdf (2021).160.Norwegian Hospital Procurement Trust. New environmental criteria for the procurement of pharmaceuticals, https://sykehusinnkjop.no/nyheter/new-environmental-criteria-for-the-procurement-of-pharmaceuticals (2019).161.Swedish Procurement Agency. Pharmaceuticals, https://www.upphandlingsmyndigheten.se/kriterier/sjukvard-och-omsorg/lakemedel/ (2021).162.G7. G7 Health Ministers’ Declaration, Oxford, 4 June 2021, https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/992268/G7-health_ministers-communique-oxford-4-june-2021_5.pdf (2021).163.Årdal, C. et al. Supply chain transparency and the availability of essential medicines. Bull. World Health Organ. 99, 319–320 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    164.Graham, D., Giesen, M. & Bunce, J. Strategic approach for prioritising local and regional sanitation interventions for reducing global antibiotic resistance. Water 11, 27 (2018).
    Google Scholar 
    165.Margot, J. et al. Treatment of micropollutants in municipal wastewater: ozone or powdered activated carbon? Sci. Total. Environ. 461–462, 480–498 (2013).PubMed 

    Google Scholar 
    166.Larsson, D. G. J. et al. Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environ. Int. 117, 132–138 (2018).PubMed 

    Google Scholar 
    167.Laxminarayan, R. et al. The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later. Lancet Infect. Dis. 20, e51–e60 (2020).PubMed 

    Google Scholar 
    168.Ahammad, Z. S., Sreekrishnan, T. R., Hands, C. L., Knapp, C. W. & Graham, D. W. Increased waterborne blaNDM-1 resistance gene abundances associated with seasonal human pilgrimages to the upper Ganges River. Environ. Sci. Technol. 48, 3014–3020 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    169.Kookana, R. S. et al. Potential ecological footprints of active pharmaceutical ingredients: an examination of risk factors in low-, middle- and high-income countries. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130586 (2014).
    Google Scholar  More