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    Microplastic contamination of the drilling bivalve Hiatella arctica in Arctic rhodolith beds

    1.PlasticsEurope. Plastics the—Facts 2019: An Analysis of European Plastics Production, Demand and Waste Data (PlasticsEurope, 2019).
    Google Scholar 
    2.Eriksen, M. et al. Plastic pollution in the world’s oceans: More than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLoS ONE 9, e111913. https://doi.org/10.1371/journal.pone.0111913 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    3.Borrelle, S. B. et al. Predicted growth in plastic waste exceeds efforts to mitigate plastic pollution. Science 369, 1515–1518. https://doi.org/10.1126/science.aba3656 (2020).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    4.Bergmann, M., Tekman, M. B. & Gutow, L. Sea change for plastic pollution. Nature 544, 297. https://doi.org/10.1038/544297a (2017).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    5.Imhof, H. K. et al. Spatial and temporal variation of macro-, meso- and microplastic abundance on a remote coral island of the Maldives, Indian Ocean. Mar. Pollut. Bull. 116, 340–347. https://doi.org/10.1016/j.marpolbul.2017.01.010 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    6.Obbard, R. W. Microplastics in polar regions: The role of long range transport. Curr. Opin. Environ. Sci. Health 1, 24–29. https://doi.org/10.1016/j.coesh.2017.10.004 (2018).Article 

    Google Scholar 
    7.Wessel, C. C., Lockridge, G. R., Battiste, D. & Cebrian, J. Abundance and characteristics of microplastics in beach sediments: Insights into microplastic accumulation in northern Gulf of Mexico estuaries. Mar. Pollut. Bull. 109, 178–183. https://doi.org/10.1016/j.marpolbul.2016.06.002 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    8.Woodall, L. C. et al. The deep sea is a major sink for microplastic debris. Royal Soc. Open Sci. https://doi.org/10.1098/rsos.140317 (2014).Article 

    Google Scholar 
    9.Barnes, D. K. A., Galgani, F., Thompson, R. C. & Barlaz, M. Accumulation and fragmentation of plastic debris in global environments. Philos. Trans. Royal Soc. Lond. Ser. B, Biol. Sci. 364, 1985–1998. https://doi.org/10.1098/rstb.2008.0205 (2009).CAS 
    Article 

    Google Scholar 
    10.Arthur, C., Baker, J. E. & Bamford, H. A. Proceedings of the International Research Workshop on the Occurrence, Effects, and Fate of Microplastic Marine Debris, September 9–11, 2008 (University of Washington Tacoma, 2009).
    Google Scholar 
    11.Hartmann, N. B. et al. Are we speaking the same language? Recommendations for a definition and categorization framework for plastic Debris. Environ. Sci. Technol. 53, 1039–1047. https://doi.org/10.1021/acs.est.8b05297 (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    12.Lusher, A. in Marine Anthropogenic Litter (eds Bergmann, M., Gutow, L. & Klages, M.) 245–307 (Springer International Publishing, 2015).13.Cole, M., Lindeque, P., Halsband, C. & Galloway, T. S. Microplastics as contaminants in the marine environment: A review. Mar. Pollut. Bull. 62, 2588–2597. https://doi.org/10.1016/j.marpolbul.2011.09.025 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    14.Wright, S. L., Thompson, R. C. & Galloway, T. S. The physical impacts of microplastics on marine organisms: A review. Environ. Pollut. 178, 483–492. https://doi.org/10.1016/j.envpol.2013.02.031 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    15.de Sá, L. C., Oliveira, M., Ribeiro, F., Rocha, T. L. & Futter, M. N. Studies of the effects of microplastics on aquatic organisms: What do we know and where should we focus our efforts in the future?. Sci. Total Environ. 645, 1029–1039. https://doi.org/10.1016/j.scitotenv.2018.07.207 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    16.Bråte, I. L. N. et al. Mytilus spp. as sentinels for monitoring microplastic pollution in Norwegian coastal waters: A qualitative and quantitative study. Environ. Pollut. 243, 383–393. https://doi.org/10.1016/j.envpol.2018.08.077 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    17.Lusher, A. L., Tirelli, V., O’Connor, I. & Officer, R. Microplastics in Arctic polar waters: The first reported values of particles in surface and sub-surface samples. Sci. Rep. 5, 14947. https://doi.org/10.1038/srep14947 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    18.Cózar, A. et al. The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the thermohaline circulation. Sci. Adv. 3, e1600582. https://doi.org/10.1126/sciadv.1600582 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Kanhai, L. D. K. et al. Microplastics in sub-surface waters of the Arctic Central Basin. Mar. Pollut. Bull. 130, 8–18. https://doi.org/10.1016/j.marpolbul.2018.03.011 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    20.Tekman, M. B. et al. Tying up loose ends of microplastic pollution in the Arctic: Distribution from the sea surface through the water column to deep-sea sediments at the HAUSGARTEN observatory. Environ. Sci. Technol. 54, 4079–4090. https://doi.org/10.1021/acs.est.9b06981 (2020).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    21.Obbard, R. W. et al. Global warming releases microplastic legacy frozen in Arctic Sea ice. Earth’s Future 2, 315–320. https://doi.org/10.1002/2014EF000240 (2014).ADS 
    Article 

    Google Scholar 
    22.Peeken, I. et al. Arctic sea ice is an important temporal sink and means of transport for microplastic. Nat. Commun. 9, 1505. https://doi.org/10.1038/s41467-018-03825-5 (2018).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Kanhai, L. D. K., Gardfeldt, K., Krumpen, T., Thompson, R. C. & O’Connor, I. Microplastics in sea ice and seawater beneath ice floes from the Arctic Ocean. Sci. Rep. 10, 5004. https://doi.org/10.1038/s41598-020-61948-6 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    24.Bergmann, M. et al. White and wonderful? Microplastics prevail in snow from the Alps to the Arctic. J. Sci. Adv. 5, eaax1157. https://doi.org/10.1126/sciadv.aax1157 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    25.Amélineau, F. et al. Microplastic pollution in the Greenland Sea: Background levels and selective contamination of planktivorous diving seabirds. Environ. Pollut. 219, 1131–1139. https://doi.org/10.1016/j.envpol.2016.09.017 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    26.Kühn, S. et al. Plastic ingestion by juvenile polar cod (Boreogadus saida) in the Arctic Ocean. Polar Biol. 41, 1269–1278. https://doi.org/10.1007/s00300-018-2283-8 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    27.Fang, C. et al. Microplastic contamination in benthic organisms from the Arctic and sub-Arctic regions. Chemosphere 209, 298–306. https://doi.org/10.1016/j.chemosphere.2018.06.101 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    28.Bråte, I. L. N. et al. Microplastics in Marine Bivalves from the Nordic Environment Vol. 504 (Nordic Council of Ministers, 2020).Book 

    Google Scholar 
    29.Misund, O. A. et al. Norwegian fisheries in the Svalbard zone since 1980. Regulations, profitability and warming waters affect landings. Polar Sci. 10, 312–322. https://doi.org/10.1016/j.polar.2016.02.001 (2016).ADS 
    Article 

    Google Scholar 
    30.Jones, C. G., Lawton, J. H. & Shachak, M. Organisms as ecosystem engineers. Oikos 69, 373–386. https://doi.org/10.2307/3545850 (1994).Article 

    Google Scholar 
    31.Foster, M. S. Rhodoliths: Between rocks and soft places. J. Phycol. 37, 659–667 (2001).Article 

    Google Scholar 
    32.Fredericq, S. et al. The critical importance of rhodoliths in the life cycle completion of both macro- and microalgae, and as holobionts for the establishment and maintenance of marine biodiversity. Front. Mar. Sci. https://doi.org/10.3389/fmars.2018.00502 (2019).Article 

    Google Scholar 
    33.Krayesky-Self, S. et al. Eukaryotic life inhabits rhodolith-forming coralline algae (Hapalidiales, Rhodophyta), remarkable marine benthic microhabitats. Sci. Rep. 7, 45850. https://doi.org/10.1038/srep45850 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    34.Kamenos, N. A., Moore, P. G., Hall-Spencer, J. & Donnan, D. Maerl: Its value as a habitat for commercial species. Shellfish News 18, 8–9 (2004).
    Google Scholar 
    35.Kamenos, N. A., Moore, P. G. & Hall-Spencer, J. M. Nursery-area function of maerl grounds for juvenile queen scallops Aequipecten opercularis and other invertebrates. Mar. Ecol. Prog. Ser. 274, 183–189. https://doi.org/10.3354/meps274183 (2004).ADS 
    Article 

    Google Scholar 
    36.Gagnon, P., Matheson, K. & Stapleton, M. Variation in rhodolith morphology and biogenic potential of newly discovered rhodolith beds in Newfoundland and Labrador (Canada). Bot. Mar. 55, 85–99 (2012).Article 

    Google Scholar 
    37.Teichert, S. et al. Rhodolith beds (Corallinales, Rhodophyta) and their physical and biological environment at 80°31’N in Nordkappbukta (Nordaustlandet, Svalbard Archipelago, Norway). Phycologia 51, 371–390 (2012).Article 

    Google Scholar 
    38.Teichert, S. et al. Arctic rhodolith beds and their environmental controls. Facies 60, 15–37. https://doi.org/10.1007/s10347-013-0372-2 (2014).Article 

    Google Scholar 
    39.Teichert, S. Hollow rhodoliths increase Svalbard’s shelf biodiversity. Sci. Rep. 4, 6972. https://doi.org/10.1038/srep06972 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    40.Denisenko, S. G., Denisenko, N. V., Lehtonen, K. K., Andersin, A. B. & Laine, A. O. Macrozoobenthos of the Pechora Sea (SE Barents Sea): Community structure and spatial distribution in relation to environmental conditions. Mar. Ecol. Prog. Ser. 258, 109–123 (2003).ADS 
    Article 

    Google Scholar 
    41.Rees, H. L. & Dare, P. J. Sources of Mortality and Associated Life-Cycle Traits of Selected Benthic Species: A Review Vol. 33, 36 (CEFAS Directorate of Fisheries Research, 1993).
    Google Scholar 
    42.Sejr, M. K. et al. Growth and production of Hiatella arctica (Bivalvia) in a high-Arctic fjord (Young Sound, Northeast Greenland). Mar. Ecol. Prog. Ser. 244, 163–169. https://doi.org/10.3354/meps244163 (2002).ADS 
    Article 

    Google Scholar 
    43.Witman, J. D. & Sebens, K. P. Regional variation in fish predation intensity: A historical perspective in the Gulf of Maine. Oecologia 90, 305–315. https://doi.org/10.1007/bf00317686 (1992).ADS 
    Article 
    PubMed 

    Google Scholar 
    44.Kamenos, N. A., Moore, P. G. & Hall-Spencer, J. M. Small-scale distribution of juvenile gadoids in shallow inshore waters; what role does maerl play?. ICES J. Mar. Sci. 61, 422–429 (2004).Article 

    Google Scholar 
    45.Teichert, S., Voigt, N. & Wisshak, M. Do skeletal Mg/Ca ratios of Arctic rhodoliths reflect atmospheric CO2 concentrations?. Polar Biol. 43, 2059–2069. https://doi.org/10.1007/s00300-020-02767-3 (2020).Article 

    Google Scholar 
    46.Ragazzola, F. et al. Phenotypic plasticity of coralline algae in a High CO2 world. Ecol. Evol. 3, 3436–3446. https://doi.org/10.1002/ece3.723 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    47.Teichert, S. & Freiwald, A. Polar coralline algal CaCO3-production rates correspond to intensity and duration of the solar radiation. Biogeosciences 11, 833–842. https://doi.org/10.5194/bg-11-833-2014 (2014).ADS 
    Article 

    Google Scholar 
    48.Büdenbender, J., Riebesell, U. & Form, A. Calcification of the Arctic coralline red algae Lithothamnion glaciale in response to elevated CO2. Mar. Ecol. Prog. Ser. 441, 79–87 (2011).ADS 
    Article 

    Google Scholar 
    49.Wisshak, M. et al. Habitat Characteristics and Carbonate Cycling of Macrophyte-Supported Polar Carbonate Factories (Svalbard)—Cruise No. MSM55—June 11–June 29, 2016—Reykjavik (Iceland)—Longyearbyen (Norway) 58 (Bremen, 2017).50.Löder, M. G. J. et al. Enzymatic purification of microplastics in environmental samples. Environ. Sci. Technol. 51, 14283–14292. https://doi.org/10.1021/acs.est.7b03055 (2017).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    51.Hufnagl, B. et al. A methodology for the fast identification and monitoring of microplastics in environmental samples using random decision forest classifiers. Anal. Methods 11, 2277–2285. https://doi.org/10.1039/C9AY00252A (2019).CAS 
    Article 

    Google Scholar 
    52.Yanfang, L., Hua, Z. & Cheng, T. A review of possible pathways of marine microplastics transport in the ocean. Anthr. Coasts 3, 6–13. https://doi.org/10.1139/anc-2018-0030 (2020).Article 

    Google Scholar 
    53.Erni-Cassola, G., Zadjelovic, V., Gibson, M. I. & Christie-Oleza, J. A. Distribution of plastic polymer types in the marine environment; A meta-analysis. J. Hazard. Mater. 369, 691–698. https://doi.org/10.1016/j.jhazmat.2019.02.067 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    54.Choy, C. A. et al. The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column. Sci. Rep. 9, 7843. https://doi.org/10.1038/s41598-019-44117-2 (2019).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    55.Kooi, M. et al. The effect of particle properties on the depth profile of buoyant plastics in the ocean. Sci. Rep. 6, 33882. https://doi.org/10.1038/srep33882 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    56.Vinay Kumar, B. N., Löschel, L. A., Imhof, H. K., Löder, M. G. J. & Laforsch, C. Analysis of microplastics of a broad size range in commercially important mussels by combining FTIR and Raman spectroscopy approaches. Environ. Pollut. https://doi.org/10.1016/j.envpol.2020.116147 (2020).Article 
    PubMed 

    Google Scholar 
    57.Löder, M. G. J. & Gerdts, G. in Marine Anthropogenic Litter (eds Bergmann, M., Gutow, L. & Klages, M.) 201–227 (Springer International Publishing, 2015).58.Wisshak, M. et al. Epibenthos dynamics and environmental fluctuations in two contrasting Polar carbonate factories (Mosselbukta and Bjørnøy-Banken, Svalbard). Front. Mar. Sci. 6, 667. https://doi.org/10.3389/fmars.2019.00667 (2019).Article 

    Google Scholar 
    59.Frias, J. P. G. L., Lyashevska, O., Joyce, H., Pagter, E. & Nash, R. Floating microplastics in a coastal embayment: A multifaceted issue. Mar. Pollut. Bull. 158, 111361. https://doi.org/10.1016/j.marpolbul.2020.111361 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    60.Rochman, C. M. et al. Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption. Sci. Rep. 5, 14340. https://doi.org/10.1038/srep14340 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    61.Digka, N., Tsangaris, C., Torre, M., Anastasopoulou, A. & Zeri, C. Microplastics in mussels and fish from the Northern Ionian Sea. Mar. Pollut. Bull. 135, 30–40. https://doi.org/10.1016/j.marpolbul.2018.06.063 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    62.Santana, M. F. M., Ascer, L. G., Custódio, M. R., Moreira, F. T. & Turra, A. Microplastic contamination in natural mussel beds from a Brazilian urbanized coastal region: Rapid evaluation through bioassessment. Mar. Pollut. Bull. 106, 183–189. https://doi.org/10.1016/j.marpolbul.2016.02.074 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    63.Gomiero, A., Strafella, P., Øysæd, K. B. & Fabi, G. First occurrence and composition assessment of microplastics in native mussels collected from coastal and offshore areas of the northern and central Adriatic Sea. Environ. Sci. Pollut. Res. Int. 26, 24407–24416. https://doi.org/10.1007/s11356-019-05693-y (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    64.Mathalon, A. & Hill, P. Microplastic fibers in the intertidal ecosystem surrounding Halifax Harbor, Nova Scotia. Mar. Pollut. Bull. 81, 69–79. https://doi.org/10.1016/j.marpolbul.2014.02.018 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    65.Van Cauwenberghe, L., Claessens, M., Vandegehuchte, M. B. & Janssen, C. R. Microplastics are taken up by mussels (Mytilus edulis) and lugworms (Arenicola marina) living in natural habitats. Environ. Pollut. 199, 10–17. https://doi.org/10.1016/j.envpol.2015.01.008 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    66.Li, J. et al. Using mussel as a global bioindicator of coastal microplastic pollution. Environ. Pollut. 244, 522–533. https://doi.org/10.1016/j.envpol.2018.10.032 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    67.Woodall, L. C. et al. Using a forensic science approach to minimize environmental contamination and to identify microfibres in marine sediments. Mar. Pollut. Bull. 95, 40–46. https://doi.org/10.1016/j.marpolbul.2015.04.044 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    68.Kowalski, N., Reichardt, A. M. & Waniek, J. J. Sinking rates of microplastics and potential implications of their alteration by physical, biological, and chemical factors. Mar. Pollut. Bull. 109, 310–319. https://doi.org/10.1016/j.marpolbul.2016.05.064 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    69.Kooi, M., Nes, E. H. V., Scheffer, M. & Koelmans, A. A. Ups and downs in the ocean: Effects of biofouling on vertical transport of microplastics. Environ. Sci. Technol. 51, 7963–7971. https://doi.org/10.1021/acs.est.6b04702 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    70.Barrows, A. P. W., Cathey, S. E. & Petersen, C. W. Marine environment microfiber contamination: Global patterns and the diversity of microparticle origins. Environ. Pollut. 237, 275–284. https://doi.org/10.1016/j.envpol.2018.02.062 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    71.Halsband, C. & Herzke, D. Plastic litter in the European Arctic: What do we know?. Emerg. Contam. 5, 308–318. https://doi.org/10.1016/j.emcon.2019.11.001 (2019).Article 

    Google Scholar 
    72.Bergmann, M., Lutz, B., Tekman, M. B. & Gutow, L. Citizen scientists reveal: Marine litter pollutes Arctic beaches and affects wild life. Mar. Pollut. Bull. 125, 535–540. https://doi.org/10.1016/j.marpolbul.2017.09.055 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    73.von Moos, N., Burkhardt-Holm, P. & Köhler, A. Uptake and effects of microplastics on cells and tissue of the blue mussel Mytilus edulis L. after an experimental exposure. Environ. Sci. Technol. 46, 11327–11335. https://doi.org/10.1021/es302332w (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    74.Kolandhasamy, P. et al. Adherence of microplastics to soft tissue of mussels: A novel way to uptake microplastics beyond ingestion. Sci. Total Environ. 610–611, 635–640. https://doi.org/10.1016/j.scitotenv.2017.08.053 (2018).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    75.Löder, M. G. J., Kuczera, M., Mintenig, S., Lorenz, C. & Gerdts, G. Focal plane array detector-based micro-Fourier-transform infrared imaging for the analysis of microplastics in environmental samples. J. Environ. Chem. 12, 563–581. https://doi.org/10.1071/EN14205 (2015).CAS 
    Article 

    Google Scholar 
    76.Hammer, Ø., Harper, D. A. T. & Ryan, P. D. PAST: Paleontological statistics software package for education and data analysis. Palaeontol. Electron. 4, 9 (2001).
    Google Scholar 
    77.R Foundation for Statistical Computing. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).
    Google Scholar 
    78.Venables, W. N. & Ripley, B. D. Modern Applied Statistics with S 4th edn, 498 (Springer, 2002).Book 

    Google Scholar 
    79.Vegan: Community Ecology Package (2020). More

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    A global dataset of inland fisheries expert knowledge

    Freshwater fish are important contributors to human livelihoods, food and nutrition, recreation, ecosystem services, and biological diversity. Yet, they inhabit some of the most threatened ecosystems globally1, face higher declines relative to marine and terrestrial species2, and are disproportionally understudied3,4. Inland fisheries are subjected to a suite of anthropogenic stressors across aquatic-terrestrial landscapes5, including flow alterations, dams, invasive species, sedimentation, drought, and pollution6,7,8. Evaluating stressors and their impacts on global inland fisheries is essential for effective management, monitoring, and conservation6, but unlike marine fisheries, there is no standardized method to assess inland fisheries9.Data inputs for a fisheries threat assessment typically include baseline information, such as species-specific landings or in situ population data (volume and composition), size (population and landings), and biomass. In addition, multi-stressor interactions (e.g., synergistic, additive) across complex habitats often warrant cross-ecosystem and cross-sector evaluations at multiple scales10,11. However, in the case of inland fisheries, these data inputs are severely deficient and often disparate in many regions12,13, which challenges the development of a global assessment. Thus, evaluating stressors and their impacts on inland fisheries necessitates the use of additional data sources (e.g., expert knowledge) beyond those typically derived directly from fish or fish habitats12,14. Local and subject-matter expertise can provide contextualized insights where spatial data are limited or unattainable (e.g., emerging threats15) and where empirical evidence is incomplete (e.g., multi-stressor interactions).Expert elicitation (i.e., expert opinion synthesis, where opinion is the preliminary state of knowledge of an individual) is increasingly used to inform ecological evaluations and guide water infrastructure, development, food security, and conservation decision-making and assessments, especially in data-poor scenarios14,16. While spatial data can be integrated as a suite of individual stressors (i.e., input variables) within ranking systems for the development of vulnerability or habitat assessments for conservation purposes14,17, the utilization of spatial variables is limited by the method for determining relative impacts (i.e., value judgment)18. Cumulate impact scores and systematic weighted ranking of threats are often based on geographically biased, small sized, or non-representative subsets of experts’ opinions (e.g., global weight determination from eight experts5). Thus, data collection for this study was motivated by the development of a global assessment of threats to major inland fisheries, and the overarching need for tractable freshwater indicators. The data generated contribute essential relative influence scores for the assessment and provide a timely snapshot of inland fisheries as perceived by fisheries professionals. Threat composition and influence have broader potential applications to inform vulnerability and adaptation components of freshwater conservation and management targets (e.g., United Nations (UN) Sustainable Development Goals, UN International Decade “Water for Sustainable Development,” Convention on Biological Diversity, Ramsar Convention on Wetlands).This paper introduces a dataset that can help address a knowledge gap in understanding natural and human influences on inland fisheries with local, contextualized fishery evaluations. Derived from an electronic survey, data comprise perceptions from fisheries professionals (n = 536) on the relative influence and spatial associations of fishery threats, recent successes, and adaptive capacity measures within the respondent’s fishery of expertise.In the context of the survey, we use the term “threat” as a proximate human activity or process (“direct threat”) causing degradation or impairment (“stress”; e.g., reduced population size, fragmented riparian habitat) to ecological targets (e.g., species, communities, ecosystems; in this case, fishery)19. We considered only the threats most proximate and direct to the target (fishery) and excluded stresses (i.e., symptoms, degraded key attributes) and contributing factors (i.e., root causes, underlying factors). For example, we considered pollutants (direct threat) rather than the pollution source (contributing factor) or the resulting contaminated water (stress, effect). We addressed the ambiguity of the term ‘fishery’20 by allowing respondents to indicate a geographic location (specific point) within their fishery area. This allows for spatial attribution with an inclusive use of ‘fishery’ as it pertains to threats (e.g., threats to a fish population of fishery-targeted species, catch characteristics, or the habitat in which the fishery operates).We structured survey questions about the occurrence and relative influence of threats to the production and health of inland fisheries using 29 specified individual threats derived from well-studied pressures to inland fisheries in addition to pressures emerging as threats to fisheries (e.g., climate change, plastics15). We categorized individual threats into five well-established categories: habitat degradation, pollution, overexploitation, species invasion, and climate change1,7 for organizational context in the survey. We also designed survey questions specifically to understand the social adaptive capacity of fishers using five major community-level domains: fisher access to assets (e.g., financial, technological, service), fisher and institutional flexibility to adapt to changing conditions (e.g., livelihood alternatives, adaptive management), social capital and organization to enable cooperation and collective action (e.g., co-management), learning and problem-solving for responding to threats, and fishers’ sense of agency to influence and shape actions and outcomes21.This dataset can be useful as an overview assessment, on which future assessments may expand for specific temporal or spatial interests. Some data in this dataset (e.g., microplastics, invasive species disturbances) are otherwise unattainable at relevant scales from geospatial information and therefore provide novel information. Potential uses include demographic influences on threat perceptions, spatial distribution of adaptive capacity measures paired with climate change or other threats, external factors driving multi-stressor interactions, and paired geospatial and expert-derived threat analysis. These data can provide insights on fisheries as a coupled human-natural system and inform regional and global freshwater assessments. More

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    Wood-inhabiting fungal responses to forest naturalness vary among morpho-groups

    1.Keenan, R. J. et al. Forest ecology and management dynamics of global forest area: Results from the FAO Global Forest Resources Assessment 2015. For. Ecol. Manag. 352, 9–20 (2015).Article 

    Google Scholar 
    2.Siitonen, J. Forest management, coarse woody debris and saproxylic organisms: Fennoscandian boreal forests as an example. Ecol. Bull. 49, 11–41 (2001).
    Google Scholar 
    3.Stokland, J. N., Siitonen, J. & Jonsson, B. G. Biodiversity in Dead Wood (Cambridge University Press, 2012).Book 

    Google Scholar 
    4.Nordén, J., Penttilä, R., Siitonen, J., Tomppo, E. & Ovaskainen, O. Specialist species of wood-inhabiting fungi struggle while generalists thrive in fragmented boreal forests. J. Ecol. 101, 701–712 (2013).Article 

    Google Scholar 
    5.Tikkanen, O.-P., Martikainen, P., Hyvärinen, E., Junninen, K. & Kouki, J. Red-listed boreal forest species of Finland: Associations with forst structure, tree species, and decaying wood. Ann. Zool. Fennici 43, 373–383 (2006).
    Google Scholar 
    6.Sippola, A.-L., Lehesvirta, T. & Renvall, P. Effect of selective logging on coarse woody debris and diversity of wood-decaying polypores in eastern Finland. Ecol. Bull. 49, 243–254 (2001).
    Google Scholar 
    7.Axelsson, A. L., Östlund, L. & Hellberg, E. Changes in mixed deciduous forests of boreal Sweden 1866–1999 based on interpretation of historical records. Landsc. Ecol. 17, 403–418 (2002).Article 

    Google Scholar 
    8.Eriksson, S., Skånes, H., Hammer, M. & Lönn, M. Current distribution of older and deciduous forests as legacies from historical use patterns in a Swedish boreal landscape (1725–2007). For. Ecol. Manag. 260, 1095–1103 (2010).Article 

    Google Scholar 
    9.Wallenius, T. H., Lilja, S. & Kuuluvainen, T. Fire history and tree species composition in managed Picea abies stands in southern Finland: Implications for restoration. For. Ecol. Manag. 250, 89–95 (2007).Article 

    Google Scholar 
    10.Stokland, J. N. Host-tree associattions. In Biodiversity in Dead Wood (eds Stokland, J. N. et al.) 82–109 (Cambridge University Press, 2012).Chapter 

    Google Scholar 
    11.Kouki, J., Arnold, K. & Martikainen, P. Long-term persistence of aspen – A key host for many threatened species—Is endangered in old-growth conservation areas in Finland. J. Nat. Conserv. 12, 41–52 (2004).Article 

    Google Scholar 
    12.Komonen, A., Tuominen, L., Purhonen, J. & Halme, P. Landscape structure influences browsing on a keystone tree species in conservation areas. For. Ecol. Manag. 457, 117724 (2020).Article 

    Google Scholar 
    13.Purhonen, J. et al. Morphological traits predict host-tree specialization in wood-inhabiting fungal communities. Fungal Ecol. 46, 100863 (2020).Article 

    Google Scholar 
    14.Dowding, P. Nutrient uptake and allocation during substrate exploitation by fungi. In The Fungal Community. Its Organization and Role in the Ecosystems (eds Wicklow, D. T. & Carroll, G. C.) 612–636 (Marcel Dekker Inc, 1981).
    Google Scholar 
    15.Boddy, L., Frankland, J. & van West, P. Ecology of Saprotrophic Basidiomycetes (Elsevier Ltd, 2008).
    Google Scholar 
    16.Kahl, T. et al. Wood decay rates of 13 temperate tree species in relation to wood properties, enzyme activities and organismic diversities. For. Ecol. Manag. 391, 86–95 (2017).Article 

    Google Scholar 
    17.Abrego, N. & Salcedo, I. Variety of woody debris as the factor influencing wood-inhabiting fungal richness and assemblages: Is it a question of quantity or quality?. For. Ecol. Manag. 291, 377–385 (2013).Article 

    Google Scholar 
    18.Lindblad, I. Wood-inhabiting fungi on fallen logs of Norway spruce: Relations to forest management and substrate quality. Nord. J. Bot. 18, 243–255 (1998).Article 

    Google Scholar 
    19.Tomao, A., Antonio Bonet, J., Castaño, C. & de-Miguel, S. How does forest management affect fungal diversity and community composition? Current knowledge and future perspectives for the conservation of forest fungi. For. Ecol. Manag. 457, 1176 (2020).Article 

    Google Scholar 
    20.Bader, P., Jansson, S. & Jonsson, B. G. Wood-inhabiting fungi and substratum decline in selectively logged boreal spruce forests. Biol. Conserv. 72, 355–362 (1995).Article 

    Google Scholar 
    21.Heilmann-Clausen, J. & Christensen, M. Does size matter?. For. Ecol. Manag. 201, 105–117 (2004).Article 

    Google Scholar 
    22.Nordén, B., Götmark, F., Tönnberg, M. & Ryberg, M. Dead wood in semi-natural temperate broadleaved woodland: Contribution of coarse and fine dead wood, attached dead wood and stumps. For. Ecol. Manag. 194, 235–248 (2004).Article 

    Google Scholar 
    23.Ottosson, E. et al. Diverse ecological roles within fungal communities in decomposing logs of Picea abies. FEMS Microbiol. Ecol. 91, 1–13 (2015).Article 
    CAS 

    Google Scholar 
    24.Juutilainen, K., Mönkkönen, M., Kotiranta, H. & Halme, P. The effects of forest management on wood-inhabiting fungi occupying dead wood of different diameter fractions. For. Ecol. Manag. 313, 283–291 (2014).Article 

    Google Scholar 
    25.Jönsson, M., Ruete, A., Kellner, O., Gunnarsson, U. & Snäll, T. Will forest conservation areas protect functionally important diversity of fungi and lichens over time?. Biodivers. Conserv. https://doi.org/10.1007/s10531-015-1035-0 (2016).Article 

    Google Scholar 
    26.Abrego, N., Norberg, A. & Ovaskainen, O. Measuring and predicting the influence of traits on the assembly processes of wood-inhabiting fungi. J. Ecol. https://doi.org/10.1111/1365-2745.12722 (2017).Article 

    Google Scholar 
    27.Bässler, C. et al. Functional response of lignicolous fungal guilds to bark beetle deforestation. Ecol. Indic. 65, 149–160 (2016).Article 

    Google Scholar 
    28.Bässler, C., Heilmann-Clausen, J., Karasch, P., Brandl, R. & Halbwachs, H. Ectomycorrhizal fungi have larger fruit bodies than saprotrophic fungi. Fungal Ecol. 17, 205–212 (2015).Article 

    Google Scholar 
    29.Sherwood, M. A. Convergent evolution in discomycetes from bark and wood. Bot. J. Linn. Soc. 82, 15–34 (1981).Article 

    Google Scholar 
    30.Unterseher, M., Otto, P. & Morawetz, W. Species richness and substrate specificity of lignicolous fungi in the canopy of a temperate, mixed deciduous forest. Mycol. Prog. 4, 117–132 (2005).Article 

    Google Scholar 
    31.Dawson, S. K. & Jönsson, M. Just how big is intraspecific trait variation in basidiomycete wood fungal fruit bodies?. Fungal Ecol. 46, 100865 (2020).Article 

    Google Scholar 
    32.Dawson, S. K. et al. Handbook for the measurement of macrofungal functional traits: A start with basidiomycete wood fungi. Funct. Ecol. 33, 372–387 (2019).Article 

    Google Scholar 
    33.Zanne, A. E. et al. Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi. Biol. Rev. 95, 409–433 (2020).PubMed 
    Article 

    Google Scholar 
    34.Nordén, B., Ryberg, M., Götmark, F. & Olausson, B. Relative importance of coarse and fine woody debris for the diversity of wood-inhabiting fungi in temperate broadleaf forests. Biol. Conserv. 117, 1–10 (2004).Article 

    Google Scholar 
    35.Stokland, J. N. & Larsson, K. Forest ecology and management legacies from natural forest dynamics : Different effects of forest management on wood-inhabiting fungi in pine and spruce forests. For. Ecol. Manag. 261, 1707–1721 (2011).Article 

    Google Scholar 
    36.Cajander, A. K. Forest types and their significance. Acta For. Fenn. 56, 1–69 (1949).
    Google Scholar 
    37.Ahti, T., Hämet-Ahti, L. & Jalas, J. Vegetation zones and their sections in northwestern Europe. Ann. Bot. Fenn. 5, 169–211 (1968).
    Google Scholar 
    38.Renaud, V., Innes, J. L., Dobbertin, M. & Rebetez, M. Comparison between open-site and below-canopy climatic conditions in Switzerland for different types of forests over 10 years (1998–2007). Theor. Appl. Climatol. 105, 119–127 (2011).ADS 
    Article 

    Google Scholar 
    39.Renvall, P. Community structure and dynamics of wood-rotting Basidiomycetes on decomposing conifer trunks in northern Finland. Karstenia 35, 1–51 (1995).Article 

    Google Scholar 
    40.Abrego, N., Halme, P., Purhonen, J. & Ovaskainen, O. Fruit body based inventories in wood-inhabiting fungi: Should we replicate in space or time?. Fungal Ecol. 20, 225–232 (2016).Article 

    Google Scholar 
    41.Halme, P. & Kotiaho, J. S. The importance of timing and number of surveys in fungal biodiversity research. Biodivers. Conserv. 21, 205–219 (2012).Article 

    Google Scholar 
    42.Purhonen, J., Huhtinen, S., Kotiranta, H. & Kotiaho, J. S. Detailed information on fruiting phenology provides new insights on wood-inhabiting fungal detection. Fungal Ecol. 27, 175–177 (2017).Article 

    Google Scholar 
    43.Royal Botanic Gardens Kew, Landcare Research-NZ & Chinese Academy of Science. Index Fungorum. www.indexfungorum.org 01.03.2017 (2017).44.Barton, K. MuMIn: Multi-Model Inference. R Package Version 1.43.6. https://CRAN.R-project.org/package=MuMIn 15.11.2020 (2019).45.R Core Team. R: A Language and Environment for Statistical Computing. Available at: https://www.r-project.org/ (2017).46.Magnusson, A. et al. glmmTMB: Generalized Linear Mixed Models Using Template Model Builder. https://cran.r-project.org/web/packages/glmmTMB/glmmTMB.pdf 30.08.2018 (2018).47.Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.4-4. https://cran.r-project.org/web/packages/vegan/index.html 30.12.2017 (2017).48.Abrego, N., Bässler, C., Christensen, M. & Heilmann-Clausen, J. Implications of reserve size and forest connectivity for the conservation of wood-inhabiting fungi in Europe. Biol. Conserv. 191, 469–477 (2015).Article 

    Google Scholar 
    49.Halme, P. et al. The effects of habitat degradation on metacommunity structure of wood-inhabiting fungi in European beech forests. Biol. Conserv. 168, 24–30 (2013).Article 

    Google Scholar 
    50.Edman, M., Kruys, N. & Jonsson, B. G. Local dispersal sources strongly affect colonization patterns of wood-decaying fungi on spruce logs. Ecol. Appl. 14, 893–901 (2004).Article 

    Google Scholar 
    51.Komonen, A. & Müller, J. Dispersal ecology of deadwood organisms and connectivity conservation. Conserv. Biol. 32, 535–545 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    52.Abrego, N. & Salcedo, I. How does fungal diversity change based on woody debris type? A case study in Northern Spain. Ekologija 57, 109–119 (2011).Article 

    Google Scholar 
    53.Juutilainen, K., Halme, P., Kotiranta, H. & Mönkkönen, M. Size matters in studies of dead wood and wood-inhabiting fungi. Fungal Ecol. 4, 342–349 (2011).Article 

    Google Scholar 
    54.Heilmann-Clausen, J. & Christensen, M. Wood-inhabiting macrofungi in Danish beech-forests ? conflicting diversity patterns and their implications in a conservation perspective. Biol. Conserv. 122, 633–642 (2005).Article 

    Google Scholar 
    55.Moore, D., Gange, A. C., Gange, E. G. & Boddy, L. Fruit bodies: Their production and develpoment in relation to environment. In Ecology of Saprotrophic Basidiomycetes (eds Boddy, L. et al.) (Elsevier, 2008).
    Google Scholar 
    56.Junninen, K., Similä, M., Kouki, J. & Kotiranta, H. Assemblages of wood-inhabiting fungi along the gradients of succession and naturalness in boreal pine-dominated forests in Fennoscandia. Ecography (Cop.) 29, 75–83 (2006).Article 

    Google Scholar 
    57.Agren, J. & Zackrisson, O. Age and size structure of Pinus sylvestris populations on mires in Central and Northern Sweden. J. Ecol. 78, 1049–1062 (1990).Article 

    Google Scholar 
    58.Niemelä, T., Wallenius, T. & Kotiranta, H. The kelo tree, a vanishing substrate of specified wood-inhabiting fungi. Polish Bot. J. 47, 91–101 (2002).
    Google Scholar 
    59.Venugopal, P., Julkunen-Tiitto, R., Junninen, K. & Kouki, J. Phenolic compounds in Scots pine heartwood: Are kelo trees a unique woody substrate?. Can. J. For. Res. 46, 225–233 (2016).CAS 
    Article 

    Google Scholar 
    60.Jonsson, B. G. et al. Dead wood availability in managed Swedish forests – Policy outcomes and implications for biodiversity. For. Ecol. Manag. 376, 174–182 (2016).Article 

    Google Scholar 
    61.Runnel, K. & Lõhmus, A. Deadwood-rich managed forests provide insights into the old-forest association of wood-inhabiting fungi. Fungal Ecol. 27, 155–167 (2017).Article 

    Google Scholar 
    62.Junninen, K. & Komonen, A. Conservation ecology of boreal polypores: A review. Biol. Conserv. 144, 11–20 (2011).Article 

    Google Scholar 
    63.Krah, F. S. et al. Independent effects of host and environment on the diversity of wood-inhabiting fungi. J. Ecol. 106, 1428–1442. https://doi.org/10.1111/1365-2745.12939 (2018).Article 

    Google Scholar 
    64.Hoppe, B. et al. Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests. Fungal Divers. 77, 367–379 (2016).Article 

    Google Scholar 
    65.Kubartová, A., Ottosson, E., Dahlberg, A. & Stenlid, J. Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing. Mol. Ecol. 21, 4514–4532 (2012).PubMed 
    Article 

    Google Scholar 
    66.Kazartsev, I., Shorohova, E., Kapitsa, E. & Kushnevskaya, H. Decaying Picea abies log bark hosts diverse fungal communities. Fungal Ecol. 33, 1–12 (2018).Article 

    Google Scholar 
    67.von Bonsdorff, T. et al. New national and regional biological records for Finland 8. Contributions to agaricoid, gastroid and ascomycetoid taxa of fungi 5. Memo. Soc. pro Fauna Flora Fenn. 92, 120–128 (2016).
    Google Scholar 
    68.von Bonsdorff, T. et al. New national and regional biological records for Finland 5. Contributions to agaricoid and ascomycetoid taxa of fungi 4. Memo. Soc. pro Fauna Flora Fenn. 91, 56–66 (2015).
    Google Scholar 
    69.Frøslev, T. G. et al. Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?. Biol. Conserv. 233, 201–212 (2019).Article 

    Google Scholar 
    70.Esri. ArcMap, version 10.5.1. http://desktop.arcgis.com/en/arcmap/ 04.09.2017 (2017). Available at: http://desktop.arcgis.com/en/arcmap/. More

  • in

    Long term relationship between farming damselfish, predators, competitors and benthic habitat on coral reefs of Moorea Island

    1.Spalding, M. D., Ravilious, C. & Green, E. P. World atlas of coral reefs, University of California Press, Berkeley, CA, USA (2001).2.Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).ADS 
    CAS 
    Article 

    Google Scholar 
    3.Hughes, T. P. et al. Phase shifts, herbivory, and the resilience of coral reefs to climate change. Curr. Biol. 17, 360–365 (2007).CAS 
    Article 

    Google Scholar 
    4.Moritz, C., Vii, J., Lee Long, W., Tamelander, J., Thomassin, A. & Planes, S. Status and Trends of Coral Reefs of the Pacific. Global Coral Reef Monitoring Network, 114 pp (2018).5.Morrison, T. H., Hughes, T. P., Adger, W. N. & Brown, K. Save reefs to rescue all ecosystems. Nature 573, 334–336 (2019).ADS 
    Article 

    Google Scholar 
    6.Bellwood, D. R., Hughes, T. P. & Hoey, A. S. Sleeping functional group drives coral-reef recovery. Curr. Biol. 16, 2434–2439 (2006).CAS 
    Article 

    Google Scholar 
    7.Graham, N. A. et al. Managing resilience to reverse phase shifts in coral reefs. Front. Ecol. Environ. 11, 541–548 (2013).Article 

    Google Scholar 
    8.Cavender-Bares, J., Keen, A. & Miles, B. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87, 109–122 (2006).Article 

    Google Scholar 
    9.Gajdzik, L. et al. Similar levels of trophic and functional diversity within damselfish assemblages across Indo- Pacific coral reefs. Function. Ecol. 32, 1358–1369 (2018).Article 

    Google Scholar 
    10.Holling, C. S. Resilience and stability of ecological systems. Ann. Rev. Ecol. Syst. 4, 1–23 (1973).Article 

    Google Scholar 
    11.Viviani, J. et al. Synchrony patterns reveal different degrees of trophic guild vulnerability after disturbances in a coral reef fish community. Divers. Distrib. 5, 1–12 (2019).
    Google Scholar 
    12.Paine, R. T. A note on trophic complexity and community stability. Am. Nat. 103, 91–93 (1969).Article 

    Google Scholar 
    13.Mills, L. C., Soule, M. E. & Doak, D. F. The keystone-species concept in ecology and conservation. Bioscience 4, 219–224 (1993).Article 

    Google Scholar 
    14.Bouchon, C. et al. Status of the coral reefs of the Lesser Antilles after 2005 coral bleaching event in Status of Caribbean coral reefs after bleaching and hurricanes in 2005 (eds. Wilkinson C et al.) 85–104 (Global Coral Reef Monitoring Network and Reef and Rainforest Research Center, Townsville, 2008).15.Jackson, J. B. C., Donovan, M. K., Cramer, K. L., Lam, V. V. Status and Trends of Caribbean Coral Reefs: 1970–2012. Global Coral Reef Monitoring Network, IUCN, Gland, Switzerland (2014)16.Cernohorsky, N. H., McClanahan, T. R., Babu, I. & Horsa, M. Small herbivores suppress algal accumulation on Agatti atoll, Indian Ocean. Coral Reefs 34, 1023–1035 (2015).ADS 
    Article 

    Google Scholar 
    17.Altman-Kurosaki, N. T., Priest, M. A., Golbuu, Y., Mumby, P. J. & Marshell, J. Microherbivores are significant grazers on Palau’s forereefs. Mar. Biol. 165, 74–86 (2018).Article 

    Google Scholar 
    18.Ceccarelli, D. M., Jones, G. P. & McCook, L. J. Territorial damselfishes as determinants of the structure of benthic communities on coral reefs. Oceanog. Mar. Biol. Annu. Rev. 39, 355–389 (2001).
    Google Scholar 
    19.Hata, H. & Ceccarelli, D. M. Farming behaviour of territorial Damselfishes in Biology of Damselfishes (eds. Parmentier, E. & Frederich B.) 122–152 (CRC Press, 2016).20.Brooker, R. M. et al. Niche construction and the natural selection of domestication. Nat. Commun. 11, 6253 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    21.Hata, H. & Kato, M. Monoculture and mixed-species algal farms on a coral reef are maintained through intensive and extensive management by damselfishes. J. Exp. Mar. Biol. Ecol. 313, 285–296 (2004).Article 

    Google Scholar 
    22.Ceccarelli, D. M. Modification of benthic communities by territorial damselfish: a multi-species comparison. Coral Reefs 26, 853–866 (2007).ADS 
    Article 

    Google Scholar 
    23.Emslie, M. J. et al. Regional-scale variation in the distribution and abundance of farming damselfishes on Australia’s Great Barrier Reef. Mar. Biol. 159, 1293–1304 (2012).Article 

    Google Scholar 
    24.Precht, W. F., Aronson, R. B. & Moody, R. M. Changing patterns of microhabitat utilization by the threespot damselfish, Stegastes planifrons, on Caribbean reefs. PloS ONE 5, e10835 (2010).25.Casey, J. M., Ainsworth, T. D., Choat, J. H. & Connolly, S. R. Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease. Proc. R. Soc. B. 281, 20141032 (2014).Article 

    Google Scholar 
    26.Randazzo-Eisemann, Á., Montero Muñoz, J. L., McField, M., Myton, J. & Arias-González, J. E. The effect of Algal-gardening damselfish on the resilience of the mesoamerican Reef. Front. Mar. Sci. 6, 414–421 (2019).27.Sandin, S. A. et al. Baselines and degradation of coral reefs in the Northern Line Islands. PLoS ONE 3, e1548 (2008).28.Naim, O. et al. Fringing reefs of Reunion Island and eutrophication effects: long term monitoring of primary producers. Atoll Res. Bull. 597, 1–14 (2013).ADS 
    Article 

    Google Scholar 
    29.Figueira, W. F., Lyman, S. J., Crowder, L. B. & Rilov, G. Small-scale demographic variability of the biocolor damselfish, Stegastes partitus, in the Florida Keys USA. Environ. Biol. Fish 81, 297–311 (2008).Article 

    Google Scholar 
    30.Carpenter, R. C. Partitioning herbivory and its effects on coral reef algal communities. Ecol. Monogr. 56, 345 (1986).Article 

    Google Scholar 
    31.Bellwood, D. R. & Fulton, C. J. Sediment-mediated suppression of herbivory on coral reefs: decreasing resilience to rising sea-levels and climate change?. Limnol. Oceanogr. 53(6), 2695–2701 (2008).ADS 
    Article 

    Google Scholar 
    32.Galzin, R. Biomasse ichtyologique dans les écosystèmes récifaux. Etude préliminaire de la dynamique d’une population de Stegastes nigricans dans le lagon de Moorea (Société, Polynésie française). Rev. Trav. Inst. Pêches Marit. 40, 575–578 (1977).33.Lison de Loma, T., Galzin, R. & Planes, S. A framework for assessing impacts of marine protected areas in Moorea (French Polynesia). Pacif. Sci. 62, 431–441(2008).34.Glaser, M. et al. Breaking resilience for a sustainable future: thoughts for the anthropocene. Front. Mar. Sci. 5, 34–40 (2018).Article 

    Google Scholar 
    35.Siu, G. et al. Shore fishes of French Polynesia. Cybium 41, 245–278 (2017).
    Google Scholar 
    36.Tebbett, S. B., Chase, T. J. & Bellwood, D. R. Farming damselfishes shape algal turf sediment dynamics on coral reefs. Mar. Envirron. Res. 160, 104988 (2020).37.Wilkes, A. A. et al. A comparison of damselfish densities on live staghorn coral (Acropora cervicornis) and coral rubble in Dry Tortugas National Park. Southeast. Nat. 7, 483–492 (2008).Article 

    Google Scholar 
    38.Blanchette, A. et al. Damselfish Stegastes nigricans increase algal growth within their territories on shallow coral reefs via enhanced nutrient supplies. J. Exp. Mar. Biol. Ecol. 513, 21–26 (2019).Article 

    Google Scholar 
    39.Galzin, R. Structure of fish communities of French Polynesian coral reefs. I. Spatial scales. Mar. Ecol. Prog. Ser. 41, 129–136 (1987a).40.Galzin, R. Structure of fish communities of French Polynesian coral reefs. II. Temporal scales. Mar. Ecol. Prog. Ser. 41, 137–145 (1987b).41.Lecchini, D. & Galzin, R. Spatial repartition and ontogenetic shifts in habitat use by coral reef fishes (Moorea, French Polynesia). Mar. Biol. 147, 47–58 (2005).Article 

    Google Scholar 
    42.Galzin, R., Marfin, J. P. & Salvat, B. Long term coral reef monitoring program: heterogeneity of the Tiahura barrier reef (Moorea, French Polynesia). Galaxea 11, 73–91 (1993).
    Google Scholar 
    43.Galzin, R., Lecchini, D., Lison de Loma, T., Moritz, C. & Siu, G. Long term monitoring of coral and fish assemblages (1983–2014) in Tiahura reefs, Moorea, French Polynesia. Cybium 40, 31–41 (2016).44.Froese, R. & Pauly, D. Eds. FishBase. World Wide Web electronic publication. www.fishbase.org (2018).45.Hamed, K. H. & Rao, A. R. A modified Mann-Kendall trend test for autocorrelated data. J. Hydrol. 204, 182–196 (1998).ADS 
    Article 

    Google Scholar 
    46.Patakamuri, S.K. & O’Brien, N. Modifiedmk: Modified versions of Mann Kendall and Spearman’s Rho trend tests. R package version 1.5.0 (2020).47.R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna (2017).48.RStudio Team. R Studio: Integrated Development for R. RStudio, PBC, Boston, MA (2020). More

  • in

    Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

    1.McInerney, J. O., McNally, A. & O’Connell, M. J. Why prokaryotes have pangenomes. Nat. Microbiol. 2, 17040 (2017).2.Tettelin, H., Riley, D., Cattuto, C. & Medini, D. Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol. 11, 472–477 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Bentley, S. Sequencing the species pan-genome. Nat. Rev. Microbiol. 7, 258–259 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    4.Bromham, L. & Penny, D. The modern molecular clock. Nat. Rev. Genet. 4, 216–224 (2003).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    5.Otto, S. P. & Whitlock, M. C. The probability of fixation in populations of changing size. Genetics 146, 723–733 (1997).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Moura, A. et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2, 16185 (2016).7.Linke, K. et al. Reservoirs of Listeria species in three environmental ecosystems. Appl. Environ. Microbiol. 80, 5583–5592 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    8.Liao, J., Wiedmann, M. & Kovac, J. Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference. Appl. Environ. Microbiol. 83, e00306–e00317 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    9.Duché, O., Trémoulet, F., Glaser, P. & Labadie, J. Salt stress proteins induced in Listeria monocytogenes. Appl. Environ. Microbiol. 68, 1491–1498 (2002).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    10.Mcclure, P. J., Roberts, T. A. & Oguru, P. O. Comparison of the effects of sodium chloride, pH and temperature on the growth of Listeria monocytogenes on gradient plates and in liquid medium. Lett. Appl. Microbiol. 9, 95–99 (1989).CAS 
    Article 

    Google Scholar 
    11.Schwarz, G., Mendel, R. R. & Ribbe, M. W. Molybdenum cofactors, enzymes and pathways. Nature 460, 839–847 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Cordero, O. X. & Polz, M. F. Explaining microbial genomic diversity in light of evolutionary ecology. Nat. Rev. Microbiol. 12, 263–273 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    13.Iranzo, J., Wolf, Y. I., Koonin, E. V. & Sela, I. Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat. Commun. 10, 5376 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    14.Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Smith, J. M., Feil, E. J. & Smith, N. H. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22, 1115–1122 (2000).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    16.Crits-Christoph, A., Olm, M. R., Diamond, S., Bouma-Gregson, K. & Banfield, J. F. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. 14, 1834–1846 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    17.Murrell, B. et al. Gene-wide identification of episodic selection. Mol. Biol. Evol. 32, 1365–1371 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Angelastro, A. Chemoenzymatic synthesis of isotopically labelled folates. J. Am. Chem. Soc. 139, 13047–13054 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    19.Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Choudoir, M. J., Doroghazi, J. R. & Buckley, D. H. Latitude delineates patterns of biogeography in terrestrial Streptomyces. Environ. Microbiol. 18, 4931–4945 (2016).PubMed 
    Article 

    Google Scholar 
    21.Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    24.Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    25.Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    26.Black, C. A., Evans, D. D., Ensminger, L. E., White, J. L. & Clark, F. E. Methods of Soil Analysis Part 1: Physical and Mineralogical Properties, Including Statistics of Measurement and Sampling 128–151 (American Society of Agronomy, 1965).27.Weller, D., Belias, A., Green, H., Roof, S. & Wiedmann, M. Landscape, water quality, and weather factors associated with an increased likelihood of foodborne pathogen contamination of New York streams used to source water for produce production. Food Sustain. Food Syst. 3, 124 (2020).Article 

    Google Scholar 
    28.Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
    Google Scholar 
    29.Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, 309–314 (2018).Article 
    CAS 

    Google Scholar 
    31.Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    32.Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.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 
    35.Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G. & Toth, I. K. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal. Methods 8, 12–24 (2016).Article 

    Google Scholar 
    36.Carlin, C. R. et al. Listeria cossartiae sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov. isolated from agricultural water and natural environments. Int J. Syst. Evol. Microbiol. 71, 004795 (2021).CAS 

    Google Scholar 
    37.Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. & Polz, M. F. A reverse ecology approach based on a biological definition of microbial populations. Cell 178, 820–834 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    38.Méric, G. et al. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter. PLoS ONE 9, e92798 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    39.Gardner, S. N., Slezak, T. & Hall, B. G. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31, 2877–2878 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    40.Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    41.Kelly, J. K. A test of neutrality based on interlocus associations. Genetics 146, 1197–1206 (1997).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    43.Martin, D. P., Murrell, B., Golden, M., Khoosal, A. & Muhire, B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1, vev003 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Liao, J. et al. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol. Biol. 19, 132 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    45.Pond, S. L. K., Posada, D., Gravenor, M. B., Woelk, C. H. & Frost, S. D. W. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23, 1891–1901 (2006).CAS 
    Article 

    Google Scholar  More

  • in

    Climate change may induce connectivity loss and mountaintop extinction in Central American forests

    1.Allen, C. D. et al. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For. Ecol. Manag. 259, 660–684 (2010).Article 

    Google Scholar 
    2.Chen, I.-C., Hill, J. K., Ohlemuller, R., Roy, D. B. & Thomas, C. D. Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Wiens, J. J. Climate-related local extinctions are already widespread among plant and animal species. PLOS Biol. 14, e2001104 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    4.Anadón, J. D., Sala, O. E. & Maestre, F. T. Climate change will increase savannas at the expense of forests and treeless vegetation in tropical and subtropical Americas. J. Ecol. 102, 1363–1373 (2014).Article 

    Google Scholar 
    5.ECLAC et al. Climate Change in Central America: Potential Impacts and Public Policy Options (United Nations, 2015).6.Khatun, K., Imbach, P. & Zamora, J. An assessment of climate change impacts on the tropical forests of Central America using the Holdridge Life Zone (HLZ) land classification system. iForest—Biogeosciences Forestry 6, 183 (2013).Article 

    Google Scholar 
    7.TEEB. The Economics of Ecosystems and Biodiversity: Mainstreaming the Economics of Nature: A synthesis of the approach, conclusions and recommendations of TEEB (Progress Press, 2010).8.Diffenbaugh, N. S. & Giorgi, F. Climate change hotspots in the CMIP5 global climate model ensemble. Climatic Change 114, 813–822 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Myers, N. Biodiversity hotspots revisited. BioScience 53, 916–917 (2003).Article 

    Google Scholar 
    10.Corrales, L., Bouroncle, C. & Zamora, J. C. In Climate Change Impacts on Tropical Forests in Central America (ed. Chiabai, A.) 17–38 (Routledge, 2015).11.Gunter, U., Ceddia, M. G. & Tröster, B. International ecotourism and economic development in Central America and the Caribbean. J. Sustain. Tour. 25, 43–60 (2017).Article 

    Google Scholar 
    12.Hernández-Blanco, M., Costanza, R., Anderson, S., Kubiszewski, I. & Sutton, P. Future scenarios for the value of ecosystem services in Latin America and the Caribbean to 2050. Curr. Res. Environ. Sustainability 2, 100008 (2020).Article 

    Google Scholar 
    13.Hecht, S. B. Forests lost and found in tropical Latin America: the woodland ‘green revolution’. J. Peasant Stud. 41, 877–909 (2014).Article 

    Google Scholar 
    14.Colwell, R. K., Brehm, G., Cardelús, C. L., Gilman, A. C. & Longino, J. T. Global warming, elevational range shifts, and lowland biotic attrition in the wet tropics. Science 322, 258–261 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Imbach, P. et al. Modeling potential equilibrium states of vegetation and terrestrial water cycle of Mesoamerica under climate change scenarios. J. Hydrometeor 13, 665–680 (2012).Article 

    Google Scholar 
    16.Newbold, T., Oppenheimer, P., Etard, A. & Williams, J. J. Tropical and Mediterranean biodiversity is disproportionately sensitive to land-use and climate change. Nat. Ecol. Evol. 1–9. https://doi.org/10.1038/s41559-020-01303-0 (2020).17.Freeman, B. G., Lee-Yaw, J. A., Sunday, J. M. & Hargreaves, A. L. Expanding, shifting and shrinking: the impact of global warming on species’ elevational distributions. Glob. Ecol. Biogeogr. 27, 1268–1276 (2018).Article 

    Google Scholar 
    18.Booth, T. H. Species distribution modelling tools and databases to assist managing forests under climate change. For. Ecol. Manag. 430, 196–203 (2018).Article 

    Google Scholar 
    19.Urbina-Cardona, N. et al. Species distribution modeling in Latin America: a 25-year retrospective review. Trop. Conserv. Sci. 12, 1940082919854058 (2019).Article 

    Google Scholar 
    20.Araújo, M. B. et al. Standards for distribution models in biodiversity assessments. Sci. Adv. 5, eaat4858 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.BIOMARCC-SINAC-GIZ. Estimación de los posibles cambios en la distribución de especies de flora arbórea en el Pacífico Norte y Sur de Costa Rica en respuesta a los efectos del Cambio Climático (2013).22.de Sousa, K. et al. Suitability of Key Central American Agroforestry Species Under Future Climates: an Atlas (World Agroforestry Centre, 2017).23.Calabrese, J. M., Certain, G., Kraan, C. & Dormann, C. F. Stacking species distribution models and adjusting bias by linking them to macroecological models. Glob. Ecol. Biogeogr. 23, 99–112 (2014).Article 

    Google Scholar 
    24.Biber, M. F., Voskamp, A., Niamir, A., Hickler, T. & Hof, C. A comparison of macroecological and stacked species distribution models to predict future global terrestrial vertebrate richness. J. Biogeogr. 47, 114–129 (2020).Article 

    Google Scholar 
    25.Zakharova, L., Meyer, K. M. & Seifan, M. Trait-based modelling in ecology: a review of two decades of research. Ecol. Model. 407, 108703 (2019).Article 

    Google Scholar 
    26.Lyra, A. et al. Projections of climate change impacts on central America tropical rainforest. Climatic Change 141, 93–105 (2017).CAS 
    Article 

    Google Scholar 
    27.Boukili, V. K. & Chazdon, R. L. Environmental filtering, local site factors and landscape context drive changes in functional trait composition during tropical forest succession. Perspect. Plant Ecol. Evol. Syst. 24, 37–47 (2017).Article 

    Google Scholar 
    28.Imbach, P. A., Locatelli, B., Molina, L. G., Ciais, P. & Leadley, P. W. Climate change and plant dispersal along corridors in fragmented landscapes of Mesoamerica. Ecol. Evol. 3, 2917–2932 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Meyer, N. F. V., Moreno, R., Reyna-Hurtado, R., Signer, J. & Balkenhol, N. Towards the restoration of the Mesoamerican Biological Corridor for large mammals in Panama: comparing multi-species occupancy to movement models. Mov. Ecol. 8, 3 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    30.Cabrera-Guzmán, E. & Reynoso, V. H. Amphibian and reptile communities of rainforest fragments: minimum patch size to support high richness and abundance. Biodivers. Conserv 21, 3243–3265 (2012).Article 

    Google Scholar 
    31.Crespin, S. J. & García-Villalta, J. E. Integration of land-sharing and land-sparing conservation strategies through regional networking: The Mesoamerican Biological Corridor as a Lifeline for Carnivores in El Salvador. AMBIO 43, 820–824 (2014).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    32.Rehm, E. & Feeley, K. J. Many species risk mountain top extinction long before they reach the top. Front. Biogeogr. 8, (2016).33.Fung, E. et al. Mapping conservation priorities and connectivity pathways under climate change for tropical ecosystems. Climatic Change 141, 77–92 (2017).Article 

    Google Scholar 
    34.Ojea, E., Zamora, J. C., Martin-Ortega, J. & Imbach, P. In Climate Change Impacts on Tropical Forests in Central America: an Ecosystem Service Perspective (ed. Chiabai, A.) 113–151 (Routledge, 2015).35.Bernal, B., Murray, L. T. & Pearson, T. R. H. Global carbon dioxide removal rates from forest landscape restoration activities. Carbon Balance Manag. 13, 22 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Toledo, M. et al. Climate is a stronger driver of tree and forest growth rates than soil and disturbance. J. Ecol. 99, 254–264 (2011).Article 

    Google Scholar 
    37.Rojas, M. R., Locatelli, B. & Billings, R. Climate change and outbreaks of Southern Pine Beetle in Honduras. For. Syst. 19, 70–76 (2010).
    Google Scholar 
    38.Estrada‐Villegas, S., Hall, J. S., Breugel, Mvan & Schnitzer, S. A. Lianas reduce biomass accumulation in early successional tropical forests. Ecology 101, e02989 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Balslev, H. et al. Species diversity and growth forms in Tropical American Palm Communities. Bot. Rev. 77, 381–425 (2011).Article 

    Google Scholar 
    40.Ratajczak, Z., D’Odorico, P. & Yu, K. The Enemy of My Enemy Hypothesis: Why Coexisting with Grasses May Be an Adaptive Strategy for Savanna Trees. Ecosystems 20, 1278–1295 (2017).Article 

    Google Scholar 
    41.Heijden, G. M. F., van der, Powers, J. S. & Schnitzer, S. A. Lianas reduce carbon accumulation and storage in tropical forests. PNAS 112, 13267–13271 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    42.da Cunha Vargas, B., Grombone-Guaratini, M. T. & Morellato, L. P. C. Lianas research in the Neotropics: overview, interaction with trees, and future perspectives. Trees https://doi.org/10.1007/s00468-020-02056-w. (2020).43.Nanni, A. S. et al. The neotropical reforestation hotspots: a biophysical and socioeconomic typology of contemporary forest expansion. Glob. Environ. Change 54, 148–159 (2019).Article 

    Google Scholar 
    44.Stan, K. et al. Climate change scenarios and projected impacts for forest productivity in Guanacaste Province (Costa Rica): lessons for tropical forest regions. Reg. Environ. Change 20, 14 (2020).Article 

    Google Scholar 
    45.Olson, D. M. et al. Terrestrial ecoregions of the World: a New Map of Life on Earth: a new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. BioScience 51, 933–938 (2001).Article 

    Google Scholar 
    46.Poorter, L. et al. Wet and dry tropical forests show opposite successional pathways in wood density but converge over time. Nat. Ecol. Evol. 3, 928–934 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    47.Condit, R., Pérez, R. & Daguerre, N. Trees of Panama and Costa Rica (Princeton University Press, 2010).48.CATIE. Árboles de Centroamérica: un Manual Para Extensionistas (CATIE, 2003).49.Flores-Vindas, E. & Obando-Vargas, G. Árboles del Trópico Húmedo: Importancia Socioeconómica (Editorial Tecnológica de Costa Rica, 2014).50.Hammel, B. E., Grayum, M. H., Herrera, C. & Zamora Villalobos, N. Manual de plantas de Costa Rica vols 1–6 (Missouri Botanical Garden, 2003).51.Boukili, V. Functional trait data for La Selva, database (2014).52.Burns, R. M., Mosquera, M. S. & Whitmore, J. L. Useful Trees of the Tropical Region of North America (North American Forestry Commission, 1998).53.CATIE. Rasgos funcionales, base de datos del Programa Producción y Conservación en Bosques del CATIE (colleción de resultados de tesis). (2019).54.Delgado, D. et al. Análisis de la Vulnerabilidad al Cambio Climático de Bosques de Montaña en Latinoamérica (Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), 2016).55.FAO. Crop Ecological Requirements Database (ECOCROP). http://www.fao.org/land-water/land/land-governance/land-resources-planning-toolbox/category/details/en/c/1027491/ (2020).56.Finegan, B., Camacho, M. & Zamora, N. Diameter increment patterns among 106 tree species in a logged and silviculturally treated Costa Rican rain forest. For. Ecol. Manag. 121, 159–176 (1999).Article 

    Google Scholar 
    57.Hall, J. S. & Ashton, M. S. Guide to Early Growth and Survival in Plantations of 64 Tree Species Native to Panama and the Neotropics. (Smithsonian Tropical Research Institute, 2016).58.MARENA/INAFOR. Guía de Especies Forestales (Editora de Arte, S.A, 2002).59.Runes Vargas, V. Base de rasgos funcionales y usos de las especies más abundantes en los sistemas agroforestales de Centroamérica (Agroforestry Tree Functional Traits). in Diversidad en sistemas agroforestales de Centroamérica una aproximación desde el enfoque functional. Master thesis, CATIE, Costa Rica (2016).60.Vázquez-Yanes, C., Batis Muñoz, A. I., Alcocer Silva, M. I., Gual Díaz, M. & Sánchez Dirzo, C. Árboles y arbustos potencialmente valiosos para la restauración ecológica y la reforestación. Reporte técnico del proyecto J084. (1999).61.Vozzo, J. A. Tropical Tree Seed Manual (U.S. Department of Agriculture, Forest Service, 2002).62.Webb, D. B., Wood, P. J., Smith, J. P. & Sian Henman, G. A Guide to Species Selection for Tropical and Sub-tropical Plantations (Unit of Tropical Silviculture, Commonwealth Forestry Institute, University of Oxford, 1984).63.Soultan, A. & Safi, K. The interplay of various sources of noise on reliability of species distribution models hinges on ecological specialisation. PLoS ONE 12, e0187906 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    64.GBIF. GBIF Occurrence Download. Accessed from R via rgbif 2020-05-18. Darwin Core Archive. https://doi.org/10.15468/dl.pstza2. (2020).65.Anderson-Teixeira, K. J. et al. CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Glob. Change Biol. 21, 528–549 (2015).Article 

    Google Scholar 
    66.CRIA. SpeciesLink (CRIA, 2012).67.Peet, R. K., Lee, M. T., Jennings, M. D. & Faber-Langendoen, D. VegBank: a permanent, open-access archive for vegetation plot data. Biodivers. Ecol. 4, 233–241 (2012).Article 

    Google Scholar 
    68.Šímová, I. et al. Spatial patterns and climate relationships of major plant traits in the New World differ between woody and herbaceous species. J. Biogeogr. 45, 895–916 (2018).Article 

    Google Scholar 
    69.US Forest Service. Forest Inventory and Analysis National Program (US Forest Service, 2013).70.de Sousa, K., van Zonneveld, M., Holmgren, M., Kindt, R. & Ordoñez, J. C. Replication data for: ‘The future of coffee and cocoa agroforestry in a warmer Mesoamerica’. Harvard Dataverse https://doi.org/10.7910/DVN/0O1GW1. (2019).71.Chamberlain, S. rgbif: Interface to the Global ‘Biodiversity’ Information Facility API. R package version 2.3. (2020).72.Maitner, B. S. et al. The BIEN R package: A tool to access the botanical information and ecology network (BIEN) database. Methods Ecol. Evol. 9, 373–379 (2018).Article 

    Google Scholar 
    73.Morales, J. F. Sinopsis of the genus Weinmannia (Cunoniaceae) in Mexico and Central America. An. Jard.ín Bot.ánico Madr. 67, 137–155 (2010).Article 

    Google Scholar 
    74.Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    75.Danielson, J. J. & Gesch, D. B. Global multi-resolution terrain elevation data 2010 (GMTED2010). http://pubs.er.usgs.gov/publication/ofr20111073 (2011).76.Hengl, T. et al. SoilGrids1km—Global Soil Information Based on Automated Mapping. PLoS ONE 9, e105992 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    77.Schmitt, S., Pouteau, R., Justeau, D., de Boissieu, F. & Birnbaum, P. SSDM—an R package to predict distribution of species richness and composition based on stacked species distribution models. Methods. Ecol. Evol. 8, 1795–1803 (2017).
    Google Scholar 
    78.Beaumont, L. J. et al. Which species distribution models are more (or less) likely to project broad-scale, climate-induced shifts in species ranges? Ecol. Model. 342, 135–146 (2016).Article 

    Google Scholar 
    79.Lay, G. L., Engler, R., Franc, E. & Guisan, A. Prospective sampling based on model ensembles improves the detection of rare species. Ecography 33, 1015–1027 (2010).Article 

    Google Scholar 
    80.Guo, C. et al. Uncertainty in ensemble modelling of large-scale species distribution: effects from species characteristics and model techniques. Ecol. Model. 306, 67–75 (2015).Article 

    Google Scholar 
    81.Naimi, B. On uncertainty in species distribution modelling https://doi.org/10.3990/1.9789036538404 (University of Twente, 2015).82.Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: how, where and how many?: How to use pseudo-absences in niche modelling? Methods Ecol. Evol. 3, 327–338 (2012).Article 

    Google Scholar 
    83.Hirzel, A. H., Le Lay, G., Helfer, V., Randin, C. & Guisan, A. Evaluating the ability of habitat suitability models to predict species presences. Ecol. Model. 199, 142–152 (2006).Article 

    Google Scholar 
    84.Naimi, B. & Araújo, M. B. sdm: a reproducible and extensible R platform for species distribution modelling. Ecography 39, 368–375 (2016).Article 

    Google Scholar 
    85.Diniz‐Filho, J. A. F. et al. Partitioning and mapping uncertainties in ensembles of forecasts of species turnover under climate change. Ecography 32, 897–906 (2009).Article 

    Google Scholar 
    86.Guillera‐Arroita, G. et al. Is my species distribution model fit for purpose? Matching data and models to applications. Glob. Ecol. Biogeogr. 24, 276–292 (2015).Article 

    Google Scholar 
    87.Phillips, S. J. & Elith, J. POC plots: calibrating species distribution models with presence-only data. Ecology 91, 2476–2484 (2010).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    88.Schwarz, J. & Heider, D. GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making. Bioinformatics 35, 2458–2465 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    89.D’Amen, M., Rahbek, C., Zimmermann, N. E. & Guisan, A. Spatial predictions at the community level: from current approaches to future frameworks: Methods for community-level spatial predictions. Biol. Rev. 92, 169–187 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    90.Lobo, J. M., Jiménez‐Valverde, A. & Real, R. AUC: a misleading measure of the performance of predictive distribution models. Glob. Ecol. Biogeogr. 17, 145–151 (2008).Article 

    Google Scholar 
    91.Lewis, O. T. Climate change, species–area curves and the extinction crisis. Philos. Trans. R. Soc. B: Biol. Sci. 361, 163–171 (2006).Article 

    Google Scholar 
    92.Griscom, H. P. & Ashton, M. S. Restoration of dry tropical forests in Central America: a review of pattern and process. For. Ecol. Manag. 261, 1564–1579 (2011).Article 

    Google Scholar 
    93.Rahman, M., Islam, M., Gebrekirstos, A. & Bräuning, A. Trends in tree growth and intrinsic water-use efficiency in the tropics under elevated CO2 and climate change. Trees 33, 623–640 (2019).Article 

    Google Scholar 
    94.Riitters, K., Wickham, J., O’Neill, R., Jones, K. B. & Smith, E. Global-scale patterns of forest fragmentation. Conservation Ecol. 4, 3 (2000).95.Morelli, T. L. et al. The fate of Madagascar’s rainforest habitat. Nat. Clim. Change 10, 89–96 (2020).Article 

    Google Scholar 
    96.Baumbach, L., Warren, D. L., Yousefpour, R. & Hanewinkel, M. Replication data for ‘Climate change may induce connectivity loss and mountaintop extinction in Central American forests’. https://doi.org/10.5281/zenodo.4835834 (2021).97.Baumbach, L., Warren, D. L., Yousefpour, R. & Hanewinkel, M. Supplementary data for ‘Climate change may induce connectivity loss and mountaintop extinction in Central American forests’. https://doi.org/10.5281/zenodo.4836270. (2021).98.Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize Implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).CAS 
    Article 

    Google Scholar  More

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    When two are better than one

    In fig gardens, trees and wasps have been locked in a delicate, 90-million-year-old eco-evolutionary dance1. Fig wasps use the fruit of the fig tree as a sweet incubator for their eggs, while fig trees rely on wasps to pollinate their flowers. Neither can live without the other. This is an example of an obligate mutualism — a bi-directional interdependency that is essential for each partner’s survival. Given how intertwined the two partners are, it’s easy to assume that obligate mutualisms are limiting; that is, one partner can live only where the other thrives, thus constraining the range of environments that support the growth of the pair. Writing in Nature Ecology & Evolution, Oña, et al.2 use synthetic microbial communities to demonstrate that quite the opposite can occur: obligate mutualists facilitate the growth of their partners and expand their range of habitable environments, including environments in which neither could survive alone. Such examples of ‘niche expansion’, as the authors define it, may provide clues as to how vast swaths of species diversity are maintained in nature. More

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    Obligate cross-feeding expands the metabolic niche of bacteria

    1.Grinnell, J. The niche-relationships of the California thrasher. Auk 34, 427–433 (1917).Article 

    Google Scholar 
    2.Elton, C. S. Animal Ecology (Univ. Chicago Press, 2001).3.Hutchinson, G. E. Concluding remarks Cold Spring Harb. Symp. Quant. Biol. 22, 415–427 (1957).4.Hutchinson, G. E. An Introduction to Population Ecology (Yale Univ. Press, 1978).5.Colwell, R. K. & Rangel, T. F. Hutchinson’s duality: the once and future niche. Proc. Natl Acad. Sci. USA 106, 19651–19658 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Polechová, J. & Storch, D. in Encyclopedia of Ecology 2nd edn, Vol. 3 (ed Fath, B.) 72–80 (Elsevier, 2018).7.Hardin, G. The competitive exclusion principle. Science 131, 1292–1297 (1960).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Hutchinson, G. E. Population studies: animal ecology and demography. Bull. Math. Biol. 53, 193–213 (1991).Article 

    Google Scholar 
    9.Odum, E. P. Fundamentals of Ecology (Saunders, 1959).10.Begon, M., Townsend, C. R. & JL., H. Ecology: From Individuals to Ecosystems (Wiley, 2006).11.Levin, S. & Carpenter, S. The Princeton Guide to Ecology (Princeton Univ. Press, 2009).12.Bruno, J. F., Stachowicz, J. J. & Bertness, M. D. Inclusion of facilitation into ecological theory. Trends Ecol. Evol. 18, 119–125 (2003).Article 

    Google Scholar 
    13.Bulleri, F., Bruno, J. F., Silliman, B. R. & Stachowicz, J. J. Facilitation and the niche: implications for coexistence, range shifts and ecosystem functioning. Funct. Ecol. 30, 70–78 (2016).Article 

    Google Scholar 
    14.Austin, M. Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecol. Modell. 157, 101–118 (2002).Article 

    Google Scholar 
    15.Soberon, J. & Peterson, A. T. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodivers. Inform. 2, 1–10 (2005).Article 

    Google Scholar 
    16.Pires, M. M. & Guimarães, P. R. Interaction intimacy organizes networks of antagonistic interactions in different ways. J. R. Soc. Interface 10, 20120649 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    17.Ashby, B., Watkins, E., Lourenço, J., Gupta, S. & Foster, K. R. Competing species leave many potential niches unfilled. Nat. Ecol. Evol. 1, 1495–1501 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Pérez-Gutiérrez, R. A. et al. Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network. ISME J. 7, 487–497 (2013).PubMed 
    Article 
    CAS 

    Google Scholar 
    19.Russel, J., Røder, H. L., Madsen, J. S., Burmølle, M. & Sørensen, S. J. Antagonism correlates with metabolic similarity in diverse bacteria. Proc. Natl Acad. Sci. USA 114, 10684–10688 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Ricklefs, R. E. Evolutionary diversification, coevolution between populations and their antagonists, and the filling of niche space. Proc. Natl Acad. Sci. USA 107, 1265–1272 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.Stadler, B. & AFG, D. Ecology and evolution of aphid–ant interactions. Annu. Rev. Ecol. Evol. Syst. 107, 345–372 (2005).Article 

    Google Scholar 
    22.Thébault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).PubMed 
    Article 
    CAS 

    Google Scholar 
    23.Rohr, R. P., Saavedra, S. & Bascompte, J. On the structural stability of mutualistic systems. Science 345, 1253497 (2014).PubMed 
    Article 
    CAS 

    Google Scholar 
    24.Hom, E. & Murray, A. Niche engineering demonstrates a latent capacity for fungal–algal mutualism. Science 345, 94–95 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    25.Klein, A. M. et al. Importance of pollinators in changing landscapes for world crops. Proc. R. Soc. B 274, 303–313 (2007).PubMed 
    Article 

    Google Scholar 
    26.Yurtsev, E. A., Conwill, A. & Gore, J. Oscillatory dynamics in a bacterial cross-protection mutualism. Proc. Natl Acad. Sci. USA 113, 6236–6241 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    27.Pereira, F. C. & Berry, D. Microbial nutrient niches in the gut. Environ. Microbiol. 19, 1366–1378 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 109 (2017).PubMed 
    Article 

    Google Scholar 
    29.Goldford, J. E. et al. Emergent simplicity in microbial community assembly. Science 361, 469–474 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    30.Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    31.Ratzke, C. & Gore, J. Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol. 16, e2004248 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    32.Matthews, B., Aebischer, T., Sullam, K. E., Lundsgaard-Hansen, B. & Seehausen, O. Experimental evidence of an eco-evolutionary feedback during adaptive divergence. Curr. Biol. 26, 483–489 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    33.Hendry, A. Eco-evolutionary Dynamics (Princeton Univ. Press, 2017).34.Wintermute, E. H. & Silver, P. A. Emergent cooperation in microbial metabolism. Mol. Syst. Biol. 6, 407 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Giri, S. et al. Metabolic dissimilarity determines the establishment of cross- feeding interactions in bacteria. Preprint at bioRxiv https://doi.org/10.1101/2020.10.09.333336 (2020).36.Preussger, D., Giri, S., Muhsal, L. K., Oña, L. & Kost, C. Reciprocal fitness feedbacks promote the evolution of mutualistic cooperation. Curr. Biol. 30, 3580–3590.e7 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Stearns, S. Trade-offs in life-history evolution. Funct. Ecol. 3, 259–268 (1989).Article 

    Google Scholar 
    38.Agrawal, A. A., Conner, J. K. & Rasmann, S. in Evolution Since Darwin (eds Bell, M. A. et al.) Ch. 10 (Sinauer Associates, 2010).39.González-Cabaleiro, R., Ofiţeru, I. D., Lema, J. M. & Rodríguez, J. Microbial catabolic activities are naturally selected by metabolic energy harvest rate. ISME J. 9, 2630–2641 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    40.Kassen, R. The experimental evolution of specialists, generalists, and the maintenance of diversity. J. Evol. Biol. 15, 173–190 (2002).Article 

    Google Scholar 
    41.Sexton, J. P., Montiel, J., Shay, J. E., Stephens, M. R. & Slatyer, R. A. Evolution of ecological niche breadth. Annu. Rev. Ecol. Evol. Syst. 48, 183–206 (2017).Article 

    Google Scholar 
    42.May, R. & Arthur, R. Niche overlap as a function of environmental variability. Proc. Natl Acad. Sci. USA 69, 1109–1113 (1972).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    43.Bono, L. M., Draghi, J. A. & Turner, P. E. Evolvability costs of niche expansion. Trends Genet. 36, 14–23 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    44.Treves, D. S., Manning, S. & Adams, J. Repeated evolution of an acetate-cross-feeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15, 789–797 (1998).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    45.Rozen, D. E., Schneider, D. & Lenski, R. E. Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J. Mol. Evol. 61, 171–180 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    46.Rakoff-Nahoum, S., Coyne, M. J. & Comstock, L. E. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr. Biol. 24, 40–49 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    47.Enke, T. N. et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr. Biol. 29, 1528–1535.e6 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Gentile, C. L. & Weir, T. L. The gut microbiota at the intersection of diet and human health. Science 362, 776–780 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    49.Ruff, W. E., Greiling, T. M. & Kriegel, M. A. Host–microbiota interactions in immune-mediated diseases. Nat. Rev. Microbiol. 18, 521–538 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    50.Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.Morris, B. E. L., Henneberger, R., Huber, H. & Moissl-Eichinger, C. Microbial syntrophy: interaction for the common good. FEMS Microbiol. Rev. 37, 384–406 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.D’Souza, G. et al. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat. Prod. Rep. 35, 455–488 (2018).PubMed 
    Article 

    Google Scholar 
    53.Johnson, W. M. et al. Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities? FEMS Microbiol. Ecol. 96, 1–14 (2020).Article 
    CAS 

    Google Scholar 
    54.Machado, D. et al. Polarization of microbial communities between competitive and cooperative metabolism. Nat. Ecol. Evol. 5, 195–203 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Bernhardsson, S., Gerlee, P. & Lizana, L. Structural correlations in bacterial metabolic networks. BMC Evol. Biol. 11, 20 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Zelezniak, A. et al. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl Acad. Sci. USA 112, 6449–6454 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    57.Hester, E. R., Jetten, M. S. M., Welte, C. U. & Lücker, S. Metabolic overlap in environmentally diverse microbial communities. Front. Genet. https://doi.org/10.3389/fgene.2019.00989 (2019).58.Mitri, S. & Richard Foster, K. The genotypic view of social interactions in microbial communities. Annu. Rev. Genet. 47, 247–273 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    59.Levine, J. M., Bascompte, J., Adler, P. B. & Allesina, S. Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546, 56–64 (2017).CAS 
    PubMed 
    Article 

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

    Google Scholar 
    61.Vanstockem, M., Michiels, K., Vanderleyden, J. & van Gool, A. P. Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum: physical analysis of Tn5 and Tn5-Mob insertion mutants. Appl. Environ. Microbiol. 53, 410–415 (1987).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    62.Thomason, L. C., Costantino, N. & Court, D. L. E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. 79, 1.17.1–1.17.8 (2007).63.Pande, S. et al. Metabolic cross-feeding via intercellular nanotubes among bacteria. Nat. Commun. 6, 6238 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    64.Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.Konkol, M. A., Blair, K. M. & Kearns, D. B. Plasmid-encoded comi inhibits competence in the ancestral 3610 strain of Bacillus subtilis. J. Bacteriol. 195, 4085–4093 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Koo, B. M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst. 4, 291–305.e7 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Thompson, I., Lilley, A., Ellis, R., Bramwell, P. & Bailey, M. Survival, colonization and dispersal of genetically modified Pseudomonas fluorescens SBW25 in the phytosphere of field grown sugar beet. Nat. Biotechnol. 13, 1493–1497 (1995).CAS 
    Article 

    Google Scholar 
    68.Rainey, P. B. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1, 243–257 (1999).CAS 
    PubMed 
    Article 

    Google Scholar 
    69.Horton, R., Hunt, H., Ho, S., Pullen, J. & Pease, L. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61–68 (1989).CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Ditta, G., Stanfield, S., Corbin, D. & Helinski, D. R. Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl Acad. Sci. USA 77, 7347–7351 (1980).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    71.Zhang, X. X. & Rainey, P. B. Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176, 2165–2176 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Lassak, J., Henche, A. L., Binnenkade, L. & Thormann, K. M. ArcS, the cognate sensor kinase in an atypical arc system of Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 76, 3263–3274 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    73.Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    74.Stecher, G., Tamura, K. & Kumar, S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    75.Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    76.Bochner, B. R. Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33, 191–205 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar  More