Philippa Kaur

van Elsas JD, Chiurazzi M, Mallon CA, Elhottovā D, Krištůfek V, Salles JF. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci USA 2012;109:1159–64.PubMed 
PubMed Central 
Article 

Google Scholar 
Bardgett RD, Van Der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.CAS 
PubMed 
Article 

Google Scholar 
George PB, Lallias D, Creer S, Seaton FM, Kenny JG, Eccles RM, et al. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat Commun. 2019;10:1–11.Article 
CAS 

Google Scholar 
Delgado-Baquerizo M, Reich PB, Trivedi C, Eldridge DJ, Abades S, Alfaro FD, et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol. 2020;4:210–20.PubMed 
Article 

Google Scholar 
Xiao E, Ning Z, Xiao T, Sun W, Jiang S. Soil bacterial community functions and distribution after mining disturbance. Soil Biol Biochem. 2021;157:108232.CAS 
Article 

Google Scholar 
Jiao S, Zhang Z, Yang F, Lin Y, Chen W, Wei G. Temporal dynamics of microbial communities in microcosms in response to pollutants. Mol Ecol. 2017;26:923–36.CAS 
PubMed 
Article 

Google Scholar 
Fajardo C, Costa G, Nande M, Botías P, García-Cantalejo J, Martín M. Pb, Cd, and Zn soil contamination: monitoring functional and structural impacts on the microbiome. Appl Soil Ecol. 2019;135:56–64.Article 

Google Scholar 
Krabbenhoft DP, Sunderland EM. Global change and mercury. Science. 2013;341:1457–8.CAS 
PubMed 
Article 

Google Scholar 
Obrist D, Kirk JL, Zhang L, Sunderland EM, Jiskra M, Selin NE. A review of global environmental mercury processes in response to human and natural perturbations: Changes of emissions, climate, and land use. Ambio. 2018;47:116–40.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Amos HM, Jacob DJ, Streets DG, Sunderland EM. Legacy impacts of all-time anthropogenic emissions on the global mercury cycle. Global Biogeochem Cycles. 2013;27:410–21.CAS 
Article 

Google Scholar 
Zhang L, Wong MH. Environmental mercury contamination in China: sources and impacts. Environ Int. 2007;33:108–21.CAS 
PubMed 
Article 

Google Scholar 
Müller AK, Westergaard K, Christensen S, Sørensen SJ. The effect of long-term mercury pollution on the soil microbial community. FEMS Microbiol Ecol. 2001;36:11–9.PubMed 
Article 

Google Scholar 
Liu YR, Wang JJ, Zheng YM, Zhang LM, He JZ. Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils. Microb Ecol. 2014;68:575–83.CAS 
PubMed 
Article 

Google Scholar 
Liu YR, Delgado-Baquerizo M, Bi L, Zhu J, He JZ. Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China. Microbiome. 2018;6:183.PubMed 
PubMed Central 
Article 

Google Scholar 
Li D, Li X, Tao Y, Yan Z, Ao Y. Deciphering the bacterial microbiome in response to long-term mercury contaminated soil. Ecotoxicol Environ Saf. 2022;229:113062.CAS 
PubMed 
Article 

Google Scholar 
Zappelini C, Karimi B, Foulon J, Lacercat-Didier L, Maillard F, Valot B, et al. Diversity and complexity of microbial communities from a chlor-alkali tailings dump. Soil Biol Biochem. 2015;90:101–10.CAS 
Article 

Google Scholar 
Baldrian P, in der Wiesche C, Gabriel J, Nerud F, Zadražil F. Influence of cadmium and mercury on activities of ligninolytic enzymes and degradation of polycyclic aromatic hydrocarbons by Pleurotus ostreatus in soil. Appl Environ Microbiol. 2000;66:2471–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Crane S, Dighton J, Barkay T. Growth responses to and accumulation of mercury by ectomycorrhizal fungi. Fungal Biol. 2010;114:873–80.CAS 
PubMed 
Article 

Google Scholar 
Johansen JL, Rønn R, Ekelund F. Toxicity of cadmium and zinc to small soil protists. Environ Pollut. 2018;242:1510–7.CAS 
PubMed 
Article 

Google Scholar 
Wanner M, Birkhofer K, Fischer T, Shimizu M, Shimano S, Puppe D. Soil testate amoebae and diatoms as bioindicators of an old heavy metal contaminated floodplain in Japan. Microb Ecol. 2020;79:123–33.CAS 
PubMed 
Article 

Google Scholar 
Zhou Y, Sun B, Xie B, Feng K, Zhang Z, Zhang Z, et al. Warming reshaped the microbial hierarchical interactions. Glob Chang Biol. 2021;27:6331–47.CAS 
PubMed 
Article 

Google Scholar 
Zhao ZB, He JZ, Geisen S, Han LL, Wang JT, Shen JP, et al. Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils. Microbiome. 2019;7:33.PubMed 
PubMed Central 
Article 

Google Scholar 
Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, et al. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev. 2018;42:293–323.CAS 
PubMed 
Article 

Google Scholar 
Jiang Y, Luan L, Hu K, Liu M, Chen Z, Geisen S, et al. Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences. Microbiome. 2020;8:1–14.CAS 
Article 

Google Scholar 
Huang X, Wang J, Dumack K, Liu W, Zhang Q, He Y, et al. Protists modulate fungal community assembly in paddy soils across climatic zones at the continental scale. Soil Biol Biochem. 2021;160:108358.CAS 
Article 

Google Scholar 
Grossmann L, Jensen M, Heider D, Jost S, Glücksman E, Hartikainen H, et al. Protistan community analysis: key findings of a large-scale molecular sampling. ISME J. 2016;10:2269–79.PubMed 
PubMed Central 
Article 

Google Scholar 
Jassey VE, Signarbieux C, Hättenschwiler S, Bragazza L, Buttler A, Delarue F, et al. An unexpected role for mixotrophs in the response of peatland carbon cycling to climate warming. Sci Rep. 2015;5:1–10.Article 
CAS 

Google Scholar 
Thakur MP, Geisen S. Trophic regulations of the soil microbiome. Trends Microbiol. 2019;27:771–80.CAS 
PubMed 
Article 

Google Scholar 
Geisen S, Hu S, Dela Cruz TEE, Veen GFC. Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes. ISME J. 2021;15:618–21.CAS 
PubMed 
Article 

Google Scholar 
Guo S, Xiong W, Hang X, Gao Z, Jiao Z, Liu H, et al. Protists as main indicators and determinants of plant performance. Microbiome. 2021;9:64.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Feng X, Li P, Qiu G, Wang S, Li G, Shang L, et al. Human exposure to methylmercury through rice intake in mercury mining areas, Guizhou Province, China. Environ Sci Technol. 2008;42:326–32.CAS 
PubMed 
Article 

Google Scholar 
Meng M, Li B, Shao JJ, Wang T, He B, Shi JB, et al. Accumulation of total mercury and methylmercury in rice plants collected from different mining areas in China. Environ Pollut. 2014;184:179–86.CAS 
PubMed 
Article 

Google Scholar 
Liu YR, Dong JX, Zhang QG, Wang JT, Han LL, Zeng J, et al. Longitudinal occurrence of methylmercury in terrestrial ecosystems of the Tibetan Plateau. Environ Pollut. 2016;218:1342–9.CAS 
PubMed 
Article 

Google Scholar 
Walkley A, Black IA. An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci. 1934;37:29–38.CAS 
Article 

Google Scholar 
Jones D, Willett V. Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biol Biochem. 2006;38:991–9.CAS 
Article 

Google Scholar 
Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun. 2016;7:1–8.Article 
CAS 

Google Scholar 
Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2:113–8.CAS 
PubMed 
Article 

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

Google Scholar 
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.CAS 
PubMed 
Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D6.CAS 
PubMed 
Article 

Google Scholar 
Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019;47:D259–D64.CAS 
PubMed 
Article 

Google Scholar 
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013;41:D597–604.CAS 
PubMed 
Article 

Google Scholar 
Oliverio AM, Geisen S, Delgado-Baquerizo M, Maestre FT, Turner BL, Fierer N. The global-scale distributions of soil protists and their contributions to belowground systems. Sci Adv. 2020;6:eaax8787.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Finland MotE: Government decree on the assessment of soil contamination and remediation needs (214/2007). In.: Ministry of the Environment Helsinki (FI); 2007.Carlon C. Derivation methods of soil screening values in europe: A review of national procedures towards harmonisation: A report of the ENSURE action. EUR-OP. 2007.Toth G, Hermann T, Da Silva MR, Montanarella L. Heavy metals in agricultural soils of the European Union with implications for food safety. Environ Int. 2016;88:299–309.CAS 
PubMed 
Article 

Google Scholar 
De Caceres M, Jansen F. Relationship between species and groups of sites. Package ‘indicspecies’, version 1.7.6. 2016.Frossard A, Donhauser J, Mestrot A, Gygax S, Bååth E, Frey B. Long-and short-term effects of mercury pollution on the soil microbiome. Soil Biol Biochem. 2018;120:191–9.CAS 
Article 

Google Scholar 
Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Langfelder P, Horvath S. Fast R functions for robust correlations and hierarchical clustering. J Stat Softw. 2012;46:1–17.Article 

Google Scholar 
Luo F, Zhong J, Yang Y, Scheuermann RH, Zhou J. Application of random matrix theory to biological networks. Phys Lett A. 2006;357:420–3.CAS 
Article 

Google Scholar 
Deng Y, Jiang YH, Yang YF, He ZL, Luo F, Zhou JZ. Molecular ecological network analyses. BMC Bioinform. 2012;13:1–20.Article 

Google Scholar 
Benjamini Y, Krieger AM, Yekutieli D. Adaptive linear step-up procedures that control the false discovery rate. Biometrika. 2006;93:491–507.Article 

Google Scholar 
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Proceedings of the International AAAI Conference on Web and Social Media. 2009;3:361–2.Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.
Google Scholar 
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O’Hara R, et al. Vegan: community ecology package. Ordination methods, diversity analysis and other functions for community and vegetation ecologists. R Package Ver. 2015;2:3–1.
Google Scholar 
Chen B, Xiong W, Qi J, Pan H, Chen S, Peng Z, et al. Trophic interrelationships drive the biogeography of protistan community in agricultural ecosystems. Soil Biol Biochem. 2021;163:108445.CAS 
Article 

Google Scholar 
Jiao S, Lu Y, Wei G. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. Glob Chang Biol. 2022;28:140–53.Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.PubMed 
Article 
CAS 

Google Scholar 
Revelle WR. psych: Procedures for personality and psychological research. 2017.Archer E. rfPermute: estimate permutation p-values for random forest importance metrics. R package version. 2016;1(2).Wang JT, Zheng YM, Hu HW, Li J, Zhang LM, Chen BD, et al. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems. Sci Rep. 2016;6:1–7.Article 
CAS 

Google Scholar 
Schermelleh-Engel K, Moosbrugger H, Müller H. Evaluating the fit of structural equation models: Tests of significance and descriptive goodness-of-fit measures. Methods Psychol Res Online. 2003;8:23–74.
Google Scholar 
Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, et al. Body size determines soil community assembly in a tropical forest. Mol Ecol. 2019;28:528–43.CAS 
PubMed 
Article 

Google Scholar 
Stefan G, Cornelia B, Jörg R, Michael B. Soil water availability strongly alters the community composition of soil protists. Pedobiologia. 2014;57:205–13.Article 

Google Scholar 
Luan L, Jiang Y, Cheng M, Dini-Andreote F, Sui Y, Xu Q, et al. Organism body size structures the soil microbial and nematode community assembly at a continental and global scale. Nat Commun. 2020;11:6406.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Qi Q, Hu C, Lin J, Wang X, Tang C, Dai Z, et al. Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks. Environ Pollut. 2022;306:119406.CAS 
PubMed 
Article 

Google Scholar 
Wu W, Lu HP, Sastri A, Yeh YC, Gong GC, Chou WC, et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 2018;12:485–94.PubMed 
Article 

Google Scholar 
Villarino E, Watson JR, Jönsson B, Gasol JM, Salazar G, Acinas SG, et al. Large-scale ocean connectivity and planktonic body size. Nat Commun. 2018;9:1–13.CAS 
Article 

Google Scholar 
Mitsch WJ, Gosselink JG Wetlands. John Wiley & Sons; 2015.Margesin R, Feller G, Gerday C, Russell N. The Encyclopedia of Environmental Microbiology. 2002;2.Liu YR, Johs A, Bi L, Lu X, Hu HW, Sun D, et al. Unraveling microbial communities associated with methylmercury production in paddy soils. Environ Sci Technol. 2018;52:13110–8.CAS 
PubMed 
Article 

Google Scholar 
Hall B, St Louis V, Rolfhus K, Bodaly R, Beaty K, Paterson M, et al. Impacts of reservoir creation on the biogeochemical cycling of methyl mercury and total mercury in boreal upland forests. Ecosystems. 2005;8:248–66.CAS 
Article 

Google Scholar 
Clarholm M. Protozoan grazing of bacteria in soil-impact and importance. Microb Ecol. 1981;7:343–50.CAS 
PubMed 
Article 

Google Scholar 
Asiloglu R, Shiroishi K, Suzuki K, Turgay OC, Harada N. Soil properties have more significant effects on the community composition of protists than the rhizosphere effect of rice plants in alkaline paddy field soils. Soil Biol Biochem. 2021;161:108397.CAS 
Article 

Google Scholar 
Asiloglu R, Kenya K, Samuel SO, Sevilir B, Murase J, Suzuki K, et al. Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil. Soil Biol Biochem. 2021;156:108186.CAS 
Article 

Google Scholar 
Nguyen BAT, Chen QL, He JZ, Hu HW. Livestock manure spiked with the antibiotic tylosin significantly altered soil protist functional groups. J Hazard Mater. 2021;427:127867.Nguyen BAT, Chen QL, He JZ, Hu HW. Oxytetracycline and ciprofloxacin exposure altered the composition of protistan consumers in an agricultural soil. Environ Sci Technol. 2020;54:9556–63.CAS 
PubMed 
Article 

Google Scholar 
Nguyen BAT, Chen QL, Yan ZZ, Li CY, He JZ, Hu HW. Distinct factors drive the diversity and composition of protistan consumers and phototrophs in natural soil ecosystems. Soil Biol Biochem. 2021;160:108317.CAS 
Article 

Google Scholar 
Wu S, Dong Y, Deng Y, Cui L, Zhuang X. Protistan consumers and phototrophs are more sensitive than bacteria and fungi to pyrene exposure in soil. Sci Total Environ. 2022;822:153539.CAS 
PubMed 
Article 

Google Scholar 
Potts LD, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, et al. Chronic environmental perturbation influences microbial community assembly patterns. Environ Sci Technol. 2022;56:2300–11.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ge AH, Liang ZH, Xiao JL, Zhang Y, Zeng Q, Xiong C, et al. Microbial assembly and association network in watermelon rhizosphere after soil fumigation for Fusarium wilt control. Agric Ecosyst Environ. 2021;312:107336.CAS 
Article 

Google Scholar 
Pernthaler J, Sattler B, Simek K, Schwarzenbacher A, Psenner R. Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community. Aquat Microb Ecol. 1996;10:255–63.Article 

Google Scholar 
Holtze MS, Ekelund F, Rasmussen LD, Jacobsen CS, Johnsen K. Prey-predator dynamics in communities of culturable soil bacteria and protozoa: differential effects of mercury. Soil Biol Biochem. 2003;35:1175–81.CAS 
Article 

Google Scholar 
Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459:193–9.CAS 
PubMed 
Article 

Google Scholar 
Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, et al. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol. 2022;73:171–8.CAS 
PubMed 
Article 

Google Scholar  More

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Roberson, L. A., Watson, R. A. & Klein, C. J. Over 90 endangered fish and invertebrates are caught in industrial fisheries. Nat. Commun. 11, 1–8 (2020).Article 
CAS 

Google Scholar 
Pacoureau, N. et al. Half a century of global decline in oceanic sharks and rays. Nature 589, 567–571 (2021).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Dulvy, N. K. et al. Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Curr. Biol. 31, 1–15 (2021).Article 
CAS 

Google Scholar 
MacNeil, M. A. et al. Global status and conservation potential of reef sharks. Nature 583, 801–806 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Dent, F. & Clarke, S. State of the global market for shark products. FAO Fish. Aquac. Tech. Pap. No. 590. 187 (2015).FAO. 2008. The State of World Fisheries and Aquaculture. Food and Agriculture Organization of the United Nations, Rome (2008).Davidson, L. N. K., Krawchuk, M. A. & Dulvy, N. K. Why have global shark and ray landings declined: improved management or over fishing? Fish Fish 17, 438–458 (2016).Article 

Google Scholar 
Clarke, S. C. et al. Global estimates of shark catches using trade records from commercial markets. Ecol. Lett. 9, 1115–1126 (2006).PubMed 
Article 

Google Scholar 
Dulvy, N. K. et al. Extinction risk and conservation of the world’ s sharks and rays. Elife 3, 1–35 (2014).Article 

Google Scholar 
FAO. The State of World Fisheries and Aquaculture. Sustainability in action. Rome https://doi.org/10.4060/ca9229en (2020).Smith, H. et al. Ecology and the science of small-scale fisheries: A synthetic review of research effort for the Anthropocene. Biol. Conserv. 254, 108895 (2021).Article 

Google Scholar 
Worm, B. et al. Global catches, exploitation rates, and rebuilding options for sharks. Mar. Policy 40, 194–204 (2013).Article 

Google Scholar 
Queiroz, N. et al. Global spatial risk assessment of sharks under the footprint of fisheries. Nature 572, 461–466 (2019).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Leurs, G. et al. Industrial fishing near West African marine protected areas and its potential effects on mobile marine predators. Fron. Mar. Sci. 8, 1–13 (2021).ADS 

Google Scholar 
White, W. T. et al. Shark longline fishery of Papua New Guinea: Size and species composition and spatial variation of the catches. Mar. Freshw. Res. 71, 662–669 (2020).Article 

Google Scholar 
Jacquet, J. & Pauly, D. Funding priorities: Big barriers to small-scale fisheries. Conserv. Biol. 22, 832–835 (2008).PubMed 
Article 

Google Scholar 
Moore, J. E. et al. An interview-based approach to assess marine mammal and sea turtle captures in artisanal fisheries. Biol. Conserv. 143, 795–805 (2010).Article 

Google Scholar 
Soykan, C. U. et al. Why study bycatch? An introduction to the Theme Section on fisheries bycatch. Endanger. Species Res. 5, 91–102 (2008).Article 

Google Scholar 
Haque, A. B. et al. Socio-ecological approach on the fishing and trade of rhino rays (Elasmobranchii: Rhinopristiformes) for their biological conservation in the Bay of Bengal, Bangladesh. Ocean Coast. Manag. 210, 105690 (2021).Article 

Google Scholar 
Barausse, A. et al. The role of fisheries and the environment in driving the decline of elasmobranchs in the nor-thern Adriatic Sea. ICES J. Mar. Sci. 71, 1593–1603 (2014).Article 

Google Scholar 
Pérez-Jiménez, J. C. & Mendez-Loeza, I. The small-scale shark fisheries in the southern Gulf of Mexico: Understanding their heterogeneity to improve their management. Fish. Res. 172, 96–104 (2015).Article 

Google Scholar 
Saidi, B., Enajjar, S. & Bradai, M. N. Elasmobranch captures in shrimps trammel net fishery off the Gulf of Gabès (Southern Tunisia, Mediterranean Sea). J. Appl. Ichthyol. 32, 421–426 (2016).Article 

Google Scholar 
Vögler, R., González, C. & Segura, A. M. Spatio-temporal dynamics of the fish community associated with artisanal fisheries activities within a key marine protected area of the Southwest Atlantic (Uruguay). Ocean Coast. Manag. 190, 105175 (2020).Dulvy, N. K. et al. Challenges and priorities in Shark and Ray conservation. Curr. Biol. 27, R565–R572 (2017).CAS 
PubMed 
Article 

Google Scholar 
Davidson, L. N. K. & Dulvy, N. K. Global marine protected areas to prevent extinctions. Nat. Ecol. Evol. 1, 1–6 (2017).Article 

Google Scholar 
Edgar, G. J. et al. Global conservation outcomes depend on marine protected areas with five key features. Nature 506, 216–220 (2014).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Giakoumi, S. et al. Ecological effects of full and partial protection in the crowded Mediterranean Sea: A regional meta-analysis. Sci. Rep. 7, 1–12 (2017).ADS 
CAS 
Article 

Google Scholar 
Grorud-Colvert, K. et al. The MPA Guide: A framework to achieve global goals for the ocean. Science 373, 6560 (2021).Article 
CAS 

Google Scholar 
Di Franco, A. et al. Five key attributes can increase marine protected areas performance for small-scale fisheries management. Sci. Rep. 6, 38135 (2016).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Ban, N. C., Kushneryk, K., Falk, J., Vachon, A. & Sleigh, L. Improving compliance of recreational fishers with Rockfish Conservation Areas: community–academic partnership to achieve and evaluate conservation. ICES J. Mar. Sci. 77, 2308–2318 (2019).Di Lorenzo, M., Guidetti, P., Di Franco, A., Calò, A. & Claudet, J. Assessing spillover from marine protected areas and its drivers: A meta-analytical approach. Fish Fish. 15, 1–10 (2020).Belharet, M. et al. Extending full protection inside existing marine protected areas, or reducing fishing effort outside, can reconcile conservation and fisheries goals. J. Appl. Ecol. 57, 1948–1957 (2020).Article 

Google Scholar 
McCauley, D. J. et al. Marine defaunation: Animal loss in the global ocean. Science 347, 247–254 (2015).CAS 
Article 

Google Scholar 
Di Franco, A. et al. Linking home ranges to protected area size: The case study of the Mediterranean Sea. Biol. Conserv. 221, 175–181 (2018).MacKeracher, T., Diedrich, A. & Simpfendorfer, C. A. Sharks, rays and marine protected areas: A critical evaluation of current perspectives. Fish Fish 20, 255–267 (2019).Article 

Google Scholar 
Ward-Paige, C. A., Keith, D. M., Worm, B. & Lotze, H. K. Recovery potential and conservation options for elasmobranchs. J. Fish. Biol. 80, 1844–1869 (2012).CAS 
PubMed 
Article 

Google Scholar 
Lester, S. E. et al. Biological effects within no-take marine reserves: a global synthesis. MEPS 384, 33–46 (2009).ADS 
Article 

Google Scholar 
O’Leary, B. C. et al. Addressing criticisms of large-scale marine protected areas. Bioscience 68, 359–370 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Collins, C. et al. Understanding persistent non-compliance in a remote, large-scale marine protected area. Front. Mar. Sci. 8, 1–13 (2021).ADS 
Article 

Google Scholar 
White, T. D. et al. Assessing the effectiveness of a large marine protected area for reef shark conservation. Biol. Conserv. 207, 64–71 (2017).Article 

Google Scholar 
Speed, C. W., Cappo, M. & Meekan, M. G. Evidence for rapid recovery of shark populations within a coral reef marine protected area. Biol. Conserv. 220, 308–319 (2018).Article 

Google Scholar 
Escalle, L. et al. Restricted movements and mangrove dependency of the nervous shark Carcharhinus cautus in nearshore coastal waters. J. Fish. Biol. 87, 323–341 (2015).CAS 
PubMed 
Article 

Google Scholar 
O’Leary, B. C. et al. Effective coverage targets for ocean protection. Conserv. Lett. 9, 398–404 (2016).Article 

Google Scholar 
Guidetti, P., Danovaro, R., Bottaro, M. & Ciccolella, A. Marine protected areas and endangered shark conservation. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 2671–2672 (2021).Article 

Google Scholar 
Lubchenco, J. & Grorud-Colvert, K. Making waves: The science and politics of ocean protection. Science 350, 382–383 (2015).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Zupan, M. et al. Marine partially protected areas: drivers of ecological effectiveness. Front. Ecol. Environ. 16, 381–387 (2018).Article 

Google Scholar 
Dulvy, N. K., Allen, D. J., Ralph, G. M. & Walls, R. H. L. The Conservation Status of Sharks, Rays, and Chimaeras in the Mediterranean Sea. IUCN, Malaga, Spain. pp. 236 (2016).Morales-Muñiz, A. & Roselló, E. 20,000 years of fishing in the Strait: archaeological fish and shellfish assemblages from southern Iberia. In Human Impacts on Ancient Marine Ecysosytems: a Global Perspective (eds Torben, R. C. & Erlandson, J. M.), pp. 243–278 (University of California Press, Berkeley, 2008).Coll, M. et al. The biodiversity of the Mediterranean Sea: estimates, patterns, and threats. PLoS One 5, e11842 (2010).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Cashion, M. S., Bailly, N. & Pauly, D. Official catch data underrepresent shark and ray taxa caught in Mediterranean and Black Sea fisheries. Mar. Pol. 105, 1–9 (2019).Article 

Google Scholar 
Ferretti, F., Myers, R. A., Serena, F. & Lotze, H. K. Loss of large predatory sharks from the Mediterranean Sea. Conserv. Biol. 22, 952–964 (2008).PubMed 
Article 

Google Scholar 
Colloca, F., Enea, M., Ragonese, S. & Di Lorenzo, M. A century of fishery data documenting the collapse of smooth-hounds (Mustelus spp.) in the Mediterranean Sea. Aquat. Conserv. Mar. Freshw. Ecosyst. 27, 1145–1155 (2017).Article 

Google Scholar 
Colloca, F., Carrozzi, V., Simonetti, A. & Lorenzo, M. D. Using local ecological knowledge of fishers to reconstruct abundance trends of Elasmobranch populations in the Strait of Sicily. Front. Mar. Sci. 7, 1–8 (2020).Article 

Google Scholar 
FAO. The State of World Fisheries and Aquaculture.Contributing to food security and nutrition for all. Rome. pp 200 (2016).Milazzo, M., Cattano, C., Al Mabruk, S. A. A. & Giovos, I. Mediterranean sharks and rays need action. Science 371, 355–356 (2021).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Claudet, J., Loiseau, C., Sostres, M. & Zupan, M. Underprotected marine protected areas in a global biodiversity hotspot. One Earth 2, 380–384 (2020).ADS 
Article 

Google Scholar 
Maynou, F. et al. Estimating trends of population decline in long-lived marine species in the Mediterranean Sea based on fishers’ perceptions. PLoS One 6, e21818 (2011).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Serena, F. et al. Species diversity, taxonomy and distribution of Chondrichthyes in the Mediterranean and Black Sea. Eur. Zool. J. 87, 497–536 (2020).Article 

Google Scholar 
Morey, G., Moranta, J., Riera, F., Grau, A. M. & Morales-NIN, B. Elasmobranchs in trammel net fishery associated to marine reserves in the Balearic Islands (NW Mediterranean). Cybium 30, 125–132 (2006).
Google Scholar 
Temple, A. J. et al. Marine megafauna interactions with small-scale fisheries in the southwestern Indian Ocean: a review of status and challenges for research and management. Rev. Fish. Biol. Fish. 28, 89–115 (2018).Article 

Google Scholar 
Siskey, M. R., Shipley, O. N. & Frisk, M. G. Skating on thin ice: Identifying the need for species- ­ specific data and defined migration ecology of Rajidae spp. Fish Fish 20, 286–302 (2019).Article 

Google Scholar 
Chapman, D. D., Feldheim, K. A., Papastamatiou, Y. P. & Hueter, R. E. There and back again: a review of residency and return migrations in Sharks, with implications for population structure and management. Ann. Rev. Mar. Sci. 7, 547–570 (2015).PubMed 
Article 

Google Scholar 
Heupel, M. R., Carlson, J. K. & Simpfendorfer, C. A. Shark nursery areas: Concepts, definition, characterization and assumptions. Mar. Ecol. Prog. Ser. 337, 287–297 (2007).ADS 
Article 

Google Scholar 
Speed, C., Field, I., Meekan, M. & Bradshaw, C. Complexities of coastal shark movements and their implications for management. Mar. Ecol. Prog. Ser. 408, 275–293 (2010).ADS 
Article 

Google Scholar 
Knip, D. M., Heupel, M. R. & Simpfendorfer, C. A. Mortality rates for two shark species occupying a shared coastal environment. Fish. Res. 125–126, 184–189 (2012).Article 

Google Scholar 
Espinoza, M., Farrugia, T. J. & Lowe, C. G. Habitat use, movements and site fidelity of the gray smooth-hound shark (Mustelus californicus Gill 1863) in a newly restored southern California estuary. J. Exp. Mar. Bio. Ecol. 401, 63–74 (2011).Article 

Google Scholar 
Myers, R. A. & Mertz, G. The limits of exploitation: A precautionary approach. Ecol. Appl. 8, 165–169 (1998).Article 

Google Scholar 
Ferretti, F., Osio, G., Jenkins, C., Rosenberg, A. A. & Lotze, H. K. Long-term change in a meso-predator community in response to prolonged and heterogeneous human impact. Sci. Rep. 3, 1057 (2013).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Lotze, H. K. et al. Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312, 1806–1809 (2006).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Di Lorenzo, M. et al. Ontogenetic trophic segregation between two threatened smooth ‑ hound sharks in the Central Mediterranean Sea. Sci. Rep. 10, 1–15 (2020).Article 
CAS 

Google Scholar 
Mulas, A. et al. Resource partitioning among sympatric elasmobranchs in the central-western Mediterranean continental shelf. Mar. Biol. 166, 1–16 (2019).Article 

Google Scholar 
Silva, P. M., Teixeira, C. M., Pita, C., Cabral, H. N. & França, S. Portuguese artisanal fishers’ knowledge about Elasmobranchs—A case study. Front. Mar. Sci. 8, 1–9 (2021).
Google Scholar 
Cortés, E. & Brooks, E. N. Stock status and reference points for sharks using data-limited methods and life history. Fish Fish 19, 1110–1129 (2018).Article 

Google Scholar 
Prince, J. D. Gauntlet fisheries for elasmobranchs – The secret of sustainable shark fisheries. J. Northwest Atl. Fish. 37, 407–416 (2005).Article 

Google Scholar 
Booth, H., Squires, D. & Milner-Gulland, E. J. The neglected complexities of shark fisheries, and priorities for holistic risk-based management. Ocean Coast. Manag. 182, 104994 (2019).Article 

Google Scholar 
Juhel, J. B. et al. Reef accessibility impairs the protection of sharks. J. Appl. Ecol. 55, 673–683 (2018).Article 

Google Scholar 
Espinoza, M., Cappo, M., Heupel, M. R., Tobin, A. J. & Simpfendorfer, C. A. Quantifying shark distribution patterns and species-habitat associations: Implications of Marine Park zoning. PLoS One 9, e106885 (2014).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Cattano, C., Turco, G., Di Lorenzo, M., Visconti, G. & Milazzo, M. Sandbar shark aggregation in the central Mediterranean Sea and potential effects of tourism. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 1420–1428 (2021).Article 

Google Scholar 
O’Connell, C. P., Stroud, E. M. & He, P. The emerging field of electrosensory and semiochemical shark repellents: Mechanisms of detection, overview of past studies, and future directions. Ocean Coast. Manag. 97, 2–11 (2014).Article 

Google Scholar 
Barbato, M. et al. The use of fishers’ Local Ecological Knowledge to reconstruct fish behavioural traits and fishers’ perception of conservation relevance of elasmobranchs in the Mediterranean Sea. Mediterr. Mar. Sci. 22, 603–622 (2021).Article 

Google Scholar 
Gill, D. A. et al. Capacity shortfalls hinder the performance of marine protected areas globally. Nature 543, 665–669 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Booth, H., Squires, D. & Milner-Gulland, E. J. The mitigation hierarchy for sharks: A risk-based framework for reconciling trade-offs between shark conservation and fisheries objectives. Fish Fish 21, 269–289 (2020).Article 

Google Scholar 
Sala, E. et al. Author correction: protecting the global ocean for biodiversity, food and climate. Nature 592, 397–402 (2021).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Di Franco, A. et al. Improving marine protected area governance through collaboration and co-production. J. Environ. Manag. 269, 110757 (2020).Article 

Google Scholar 
Abràmoff, M. D., Magalhães, P. J. & Ram, S. J. Image processing with imageJ. Biophotonics Int 11, 36–41 (2004).
Google Scholar 
Froese, R., & Pauly, D. FishBase. https://www.fishbase.org (2021).Micheli, F. et al. Cumulative human impacts on Mediterranean and Black Sea marine ecosystems: assessing current pressures and opportunities. PLoS ONE 8, e79889 (2013).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Atwood, T. B. et al. Herbivores at the highest risk of extinction among mammals, birds, and reptiles. Sci. Adv. 6, eabb8458 (2020).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Munstermann, M. J. et al. A global ecological signal of extinction risk in terrestrial vertebrates. Cons. Biol. 36, 1–13 (2021).
Google Scholar 
Martin, T. G., Wintle, A., Rhodes, J. R., Field, A. & Low-choy, S. J. REVIEWS AND Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecol. Lett. 8, 1235–1246 (2005).PubMed 
Article 

Google Scholar 
Rigby, R. A., Stasinopoulos, D. M. & Lane, P. W. Generalized additive models for location, scale and shape. J. R. Stat. Soc. Ser. C. Appl. Stat. 54, 507–554 (2005).MathSciNet 
MATH 
Article 

Google Scholar 
Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org (2016).Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14 (2010).Article 

Google Scholar 
Akaike, H. A new look at the Statistical Model Identification. IEEE Trans. Autom. Contr. 19, 716–723 (1974).ADS 
MathSciNet 
MATH 
Article 

Google Scholar 
Kariya, T. Institute of Mathematical Statistics is collaborating with JSTOR to digitize, preserve, and extend access to The Annals of Statistics. Ann. Stat. 19, 1403–1433, www.jstor.org (1991). ®.
Google Scholar 
Stasinopoulos, D. M. & Rigby, R. A. Generalized additive models for location scale and shape (GAMLSS) in R. J. Stat. Softw. 23, 1–46 (2007).Article 

Google Scholar 
Van Buuren, S. & Fredriks, M. Worm plot: A simple diagnostic device for modelling growth reference curves. Stat. Med. 20, 1259–1277 (2001).PubMed 
Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. (2020).Legendre, P. & Legendre, L. Numerical ecology, 2nd English edn. Elsevier, Amsterdam (1998).Peres-Neto, P. R., Legendre, P., Dray, S. & Borcard, D. Variation partitioning of species data matrices: Estimation and comparison of fractions. Ecology 87, 2614–2625 (2006).PubMed 
Article 

Google Scholar 
Oksanen, A. J. et al. Vegan: Community Ecology Package. R package Version 2.0-2 (2011). Available at: http://cran.r-project.org/. (2012).Di Lorenzo et al. Dataset1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318878.v1 (2022).Di Lorenzo et al. Dataset2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318881.v3 (2022).Di Lorenzo et al. Dataset3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318884.v1 (2022).Di Lorenzo et al. Dataset4: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318887.v1 (2022).Di Lorenzo et al. Code1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318875.v2 (2022).Di Lorenzo et al. Code2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318890.v1 (2022).Di Lorenzo et al. Code3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318893.v1 (2022). More

Arias PA, Bellouin N, Coppola E, Jones RG, Krinner G, Marotzke J, et al. Technical Summary. In Climate Change 2021: The Physical Science Basis, the Working Group I contribution to the Sixth Assessment Report. Cambridge University Press: Cambridge, UK; New York, NY, USA, 2021. 42–4.Donhauser J, Frey B. Alpine soil microbial ecology in a changing world. FEMS Microbiol Ecol. 2018;94:1–31.Article 
CAS 

Google Scholar 
Bradley JA, Singarayer JS, Anesio AM. Microbial community dynamics in the forefield of glaciers. Proc R Soc B. 2014; 281.Hood E, Battin TJ, Fellman J, O’neel S, Spencer RGM. Storage and release of organic carbon from glaciers and ice sheets. Nat Geosci. 2015;8:91–96.CAS 
Article 

Google Scholar 
Harden JW, Mark RK, Sundquist ET, Stallard RF. Dynamics of Soil Carbon During Deglaciation of the Laurentide Ice Sheet. Science. 1992;258:1921–4.CAS 
PubMed 
Article 

Google Scholar 
Egli M, Favilli F, Krebs R, Pichler B, Dahms D. Soil organic carbon and nitrogen accumulation rates in cold and alpine environments over 1 Ma. Geoderma. 2012;183-4:109–23.Article 
CAS 

Google Scholar 
Khedim N, Cécillon L, Poulenard J, Barré P, Baudin F, Marta S, et al. Topsoil organic matter build-up in glacier forelands around the world. Glob Chang. Biol. 2021;27:1662–77.
Google Scholar 
Amico MED, Freppaz M, Filippa G, Zanini E. Vegetation in fluence on soil formation rate in a proglacial chronosequence (Lys Glacier, NW Italian Alps). Catena. 2014;113:122–37.Article 
CAS 

Google Scholar 
Mateos-Rivera A, Yde JC, Wilson B, Finster KW, Reigstad LJ, Øvreås L The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway). FEMS Microbiol Ecol. 2016; 92. https://doi.org/10.1093/femsec/fiw038.Vilmundardóttir OK, Gísladóttir G, Lal R. Soil carbon accretion along an age chronosequence formed by the retreat of the Skaftafellsjökull glacier. SE-Iceland. Geomorphology. 2015;228:124–33.Article 

Google Scholar 
Strauss SL, Ruhland CT, Day TA. Trends in soil characteristics along a recently deglaciated foreland on Anvers Island, Antarctic Peninsula. Polar Biol. 2009;32:1779–88.Article 

Google Scholar 
Kabala C, Zapart J. Initial soil development and carbon accumulation on moraines of the rapidly retreating Werenskiold Glacier, SW Spitsbergen, Svalbard archipelago. Geoderma. 2012;175-6:9–20.Article 
CAS 

Google Scholar 
Fernández-martínez MA, Pointing SB, Pérez-ortega S, Arróniz-crespo M, Green TGA, Rozzi R, et al. Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile). Int Microbiol. 2016;19:161–73.PubMed 

Google Scholar 
Kazemi S, Hatam I, Lanoil B. Bacterial community succession in a high-altitude subarctic glacier foreland is a three-stage process. Mol Ecol. 2016;25:5557–67.CAS 
PubMed 
Article 

Google Scholar 
He L, Tang Y. Soil development along primary succession sequences on moraines of Hailuogou Glacier, Gongga Mountain, Sichuan, China. Catena. 2008;72:259–69.Article 

Google Scholar 
Zhou J, Bing HJ, Wu YH, Yang ZJ, Wang JP, Sun HY, et al. Rapid weathering processes of a 120-year-old chronosequence in the Hailuogou Glacier foreland, Mt. Gongga, SW China Jun. Geoderma. 2016;267:78–91.CAS 
Article 

Google Scholar 
Zeng J, Lou K, Zhang CJ, Wang JT, Hu HW, Shen JP, et al. Primary succession of nitrogen cycling microbial communities along the deglaciated forelands of Tianshan Mountain, China. Front Microbiol. 2016; 7. https://doi.org/10.3389/fmicb.2016.01353.Wei TF, Shangguan DH, Yi SH, Ding YJ. Characteristics and controls of vegetation and diversity changes monitored with an unmanned aerial vehicle (UAV) in the foreland of the Urumqi Glacier No. 1, Tianshan, China. Sci Total Environ. 2021;771:145433.CAS 
PubMed 
Article 

Google Scholar 
Huang MH, Shi YF. Progress in the study on basic features of glaciers in China in the last thirty years. J Glaciol Geocryol. 1988;10:228–37.
Google Scholar 
Xu XK, Pan BL, Hu E, Li YJ, Liang YH. Responses of two branches of Glacier No. 1 to climate change from 1993 to 2005, Tianshan, China. Quat Int. 2011;236:143–50.Article 

Google Scholar 
Liu YS, Qin X, Chen JZ, Li ZL, Wang J, Du WT, et al. Variations of Laohugou Glacier No. 12 in the western Qilian Mountains, China, from 1957 to 2015. J Mt Sci. 2018;15:25–32.Article 

Google Scholar 
Schulz S, Brankatschk R, Dümig A, Kögel-Knabner I, Schloter M, Zeyer J. The role of microorganisms at different stages of ecosystem development for soil formation. Biogeosciences. 2013;10:3983–96.Article 

Google Scholar 
Odum EP. The strategy of ecosystem development. Science. 1969;164:262–70.CAS 
PubMed 
Article 

Google Scholar 
Schmidt SK, Reed SC, Nemergut DR, Grandy AS, Cleveland CC, Weintraub MN, et al. The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils. Proc R Soc B. 2008;275:2793–802.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Knelman JE, Legg TM, O’Neill SP, Washenberger CL, González A, Cleveland CC, et al. Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biol Biochem. 2012;46:172–80.CAS 
Article 

Google Scholar 
Rime T, Hartmann M, Frey B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. ISME J. 2016;10:1625–41.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54.CAS 
PubMed 
Article 

Google Scholar 
Chen H, Wang F, Kong WD, Jia HZ, Zhou TQ, Xu R, et al. Soil microbial CO2 fixation plays a significant role in terrestrial carbon sink in a dryland ecosystem: A four-year small-scale field-plot observation on the Tibetan Plateau. Sci Total Environ. 2021; 761. https://doi.org/10.1016/j.scitotenv.2020.143282.Bond-lamberty B, Wang CK, Gower ST. A global relationship between the heterotrophic and autotrophic components of soil respiration? Gloal Chang. Biol. 2004;10:1756–66.
Google Scholar 
Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci USA. 2021; 118. https://doi.org/10.1073/pnas.2115292118/-/DCSupplemental.Published.Margesin R, Jud M, Tscherko D, Schinner F. Microbial communities and activities in alpine and subalpine soils. FEMS Microbiol Ecol. 2009;67:208–18.CAS 
PubMed 
Article 

Google Scholar 
Zhou ZH, Wang CK, Luo YQ. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun. 2020;11:3072.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Guelland K, Hagedorn F, Smittenberg RH, Göransson H, Bernasconi SM, Hajdas I, et al. Evolution of carbon fluxes during initial soil formation along the forefield of Damma glacier, Switzerland. Biogeochemistry. 2013;113:545–61.CAS 
Article 

Google Scholar 
Chen QL, Ding J, Li CY, Yan ZZ, He JZ, Hu HW. Microbial functional attributes, rather than taxonomic attributes, drive top soil respiration, nitrification and denitrification processes. Sci Total Environ. 2020;734:139479.CAS 
PubMed 
Article 

Google Scholar 
Zheng BX, Zhu YG, Sardans J, Peñuelas J, Su JQ. QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling. Sci China (Life Sciences). 2018;61:1451–62.CAS 
Article 

Google Scholar 
Fan KK, Delgado-Baquerizo M, Guo XS, Wang DZ, Zhu YG, Chu HY. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME J. 2021;15:550–61.CAS 
PubMed 
Article 

Google Scholar 
Zhou JZ, Xue K, Xie JP, Deng Y, Wu LY, Cheng XH, et al. Microbial mediation of carbon-cycle feedbacks to climate warming. Nat Clim Chang. 2012;2:106–10.CAS 
Article 

Google Scholar 
Chen JZ, Qin X, Kang SC, Du WT, Sun WJ, Liu YS. Potential effect of black carbon on glacier mass balance during the past 55 years of Laohugou Glacier No. 12, western Qilian Mountains. J Earth Sci. 2020;31:410–8.CAS 
Article 

Google Scholar 
Zhang LN, Jiang Y, Zhao SD, Jiao L, Wen Y. Relationships between tree age and climate sensitivity of radial growth in different drought conditions of Qilian Mountains, northwestern China. Forests. 2018; 9. https://doi.org/10.3390/f9030135.Sun WJ, Qin X, Ren JW, Yang XG, Zhang T, Liu YS, et al. The surface energy budget in the accumulation zone of the laohugou glacier No. 12 in the western Qilian mountains, China, in summer 2009. Arctic, Antarct Alp Res. 2012;44:296–305.Article 

Google Scholar 
Wang YW, Ma AZ, Liu GH, Ma JP, Wei J, Zhou HC, et al. Potential feedback mediated by soil microbiome response to warming in a glacier forefield. Glob Chang Biol. 2020;26:697–708.PubMed 
Article 

Google Scholar 
Harris D, Horwa WR, Van Kessel C. Acid fumigation of soils to remove carbonates prior to total organic carbon or carbon-13 isotopic analysis. Soil Sci Soc Am J.2001;65:1853–6.CAS 
Article 

Google Scholar 
Zhou HC, Ma AZ, Liu GH, Zhou XR, Yin J, Liang Y, et al. Reduced interactivity during microbial community degradation leads to the extinction of Tricholomas matsutake. L Degrad Dev. 2021;32:5118–28.Article 

Google Scholar 
Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol. 2016;92:fiw018.PubMed 
Article 
CAS 

Google Scholar 
Feng K, Zhang ZJ, Cai WW, Liu WZ, Xu MY, Yin HQ, et al. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol. 2017;26:6170–82.PubMed 
Article 

Google Scholar 
McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.CAS 
PubMed 
Article 

Google Scholar 
Mackelprang R, Burkert A, Haw M, Mahendrarajah T, Conaway CH, Douglas TA, et al. Microbial survival strategies in ancient permafrost: insights from metagenomics. ISME J. 2017;11:2305–18.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wang YW, Ma AZ, Zhong GS, Xie F, Zhou HC, Liu GH, et al. Effect of Simulated Warming on Microbial Community in Glacier Forefield. Environ Sci. 2020;41:2918–23.
Google Scholar 
Lei YB, Zhou J, Xiao HF, Duan BL, Wu YH, Korpelainen H, et al. Soil nematode assemblages as bioindicators of primary succession along a 120-year-old chronosequence on the Hailuogou Glacier forefield, SW China. Soil Biol Biochem. 2015;88:362–71.CAS 
Article 

Google Scholar 
Sigler WV, Crivii S, Zeyer J. Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics. Microb Ecol. 2002;44:306–16.CAS 
PubMed 
Article 

Google Scholar 
Hu WM, Schmidt SK, Sommers P, Darcy JL, Porazinska DL. Multiple-trophic patterns of primary succession following retreat of a high-elevation glacier. Ecosphere. 2021; 12. https://doi.org/10.1002/ecs2.3400.Nemergut DR, Anderson SP, Cleveland CC, Martin AP, Miller AE, Seimon A, et al. Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol. 2007;53:110–22.PubMed 
Article 

Google Scholar 
Whelan P, Bach AJ. Retreating glaciers, incipient soils, emerging forests: 100 years of landscape change on Mount Baker, Washington, USA. Ann Am Assoc Geogr. 2017;107:336–49.
Google Scholar 
Cleveland CC, Liptzin ÆD. C:N:P stoichiometry in soil: is there a ‘Redfield ratio’ for the microbial biomass? Biogeochemistry. 2007;85:235–52.Article 

Google Scholar 
Manzoni S, Taylor P, Richter A, Porporato A, Ågren GI. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 2012;196:79–91.CAS 
PubMed 
Article 

Google Scholar 
Tian J, Zong N, Hartley IP, He NP, Zhang JJ, Powlson D, et al. Microbial metabolic response to winter warming stabilizes soil carbon. Gloal Chang Biol. 2021;27:2011–28.CAS 
Article 

Google Scholar 
Zhu XF, Liang C, Masters MD, Kantola IB, DeLucia EH. The impacts of four potential bioenergy crops on soil carbon dynamics as shown by biomarker analyses and DRIFT spectroscopy. Glob Chang Biol Bioenergy. 2018;10:489–500.CAS 
Article 

Google Scholar 
Evans MCW, Buchanan BB, Arnon DI. A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Biochemistry. 1966;55:928–34.CAS 

Google Scholar 
Menendez C, Bauer Z, Huber H, Gad’on N, Stetter K, Fuchs G. Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation. J Bacteriol. 1999;181:1088–98.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li Y, Cha QQ, Dang YR, Chen XL, Wang M, Mcminn A, et al. Reconstruction of the functional ecosystem in the high light, low temperature union glacier region, Antarctica. Front Microbiol. 2019;10:1–14.Article 

Google Scholar 
Lazzaro A, Hilfiker D, Zeyer J. Structures of microbial communities in alpine soils: Seasonal and elevational effects. Front Microbiol. 2015; 6. https://doi.org/10.3389/fmicb.2015.01330.Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, et al. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol. 2013;79:3724–33.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bardgett RD, Freeman C, Ostle NJ. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2008;2:805–14.CAS 
PubMed 
Article 

Google Scholar 
Liang C, Schimel JP, Jastrow JD. The importance of anabolism in microbial control over soil carbon storage. Nat Microbiol. 2017;2:17105.CAS 
PubMed 
Article 

Google Scholar 
Schäfer A, Konrad R, Kuhnigk T, Kämpfer P, Hertel H, König H. Hemicellulose-degrading bacteria and yeasts from the termite gut. J Appl Bacteriol. 1996;80:471–8.PubMed 
Article 

Google Scholar 
Lange M, Roth V-N, Nico E, Roscher C, Thorsten D, Fischer-bedtke C, et al. Plant diversity enhances production and downward transport of biodegradable dissolved organic matter. J Ecol. 2021;109:1284–97.CAS 
Article 

Google Scholar 
Ho A, Di Lonardo DP, Bodelier PLE. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol. 2017;93:1–14.CAS 

Google Scholar 
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.PubMed 
Article 

Google Scholar 
Jansson JK, Hofmockel KS. Soil microbiomes and climate change. Nat Rev Microbiol. 2020;18:35–46.CAS 
PubMed 
Article 

Google Scholar 
Yan BS, Sun LP, Li JJ, Liang CQ, Wei FR, Xue S, et al. Change in composition and potential functional genes of soil bacterial and fungal communities with secondary succession in Quercus liaotungensis forests of the Loess Plateau, western China. Geoderma. 2020;364:114199.CAS 
Article 

Google Scholar 
Wu MH, Chen SY, Chen JW, Xue K, Chen SL, Wang XM, et al. Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation. Proc Natl Acad Sci USA. 2021;118:1–9.
Google Scholar  More

All crops have been modified through some form of improvement, whether to enhance yield, taste, resilience or another factor. My passion is to continue accelerating the development of crop varieties that are more resistant to climate change and pests. This will make food supplies more secure and will also improve the quality of life for small-hold farmers in Africa and Asia, whose livelihoods can be devastated by crop failure.The goal of crop breeding is not only to develop new varieties, but also to produce genetically superior parents with a range of desirable traits that will be useful in future generations. Complex traits, such as yield or climate resilience, are often regulated by many genes. To speed up crop breeding for those traits, we use genomic data to select the best parental combinations, and then cameras and digital tools to identify the best progeny.In this photo, I’m in a greenhouse in Peru owned by my employer, the International Potato Center (CIP), inspecting potential sweet potato (Ipomoea batatas) breeding parents for cross-pollination. CIP is one of 13 gene banks and research facilities around the world, known collectively as One CGIAR, which protect and utilize crop genetic diversity. I’ve worked at CIP since 2016; before then, I worked in industry, where I developed crops such as drought-tolerant corn hybrids.Because potatoes don’t have seeds that can be preserved for decades, we must reproduce them by growing small parts of plant organs, such as a root, a tuber or part of a stem, in tissue culture. Nearly 85% of the unique potato populations stored at CIP are also cryopreserved in liquid nitrogen to maintain a long-term backup.I can’t think of a nobler mission than working on food security. I hope that more young scientists — especially women — will focus their talents on crop breeding for the future. More

Nature Positive is an aspirational term that is increasingly being used by businesses, governments and NGOs, but there is a danger that its meaning is being diluted away from measurable overall net gain in biodiversity towards merely any action that benefits nature, argues E.J. Milner-Gulland.The term is appealing because it suggests an optimistic, intuitive and clear summary of where society needs to get to, and it can be used equally by business, government and civil society to describe their aspirations to protect and recover nature. However, once terms start gaining traction, particularly relatively general terms like Nature Positive, there is a risk of slippage and loss of meaning. It is already starting to feel like any actions that increase biodiversity anywhere, and by any amount, can be called Nature Positive. This trend has to be resisted. More

Alroy J. Effects of habitat disturbance on tropical forest biodiversity. Proc Natl Acad Sci USA. 2017;114:6056–61.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gatti LV, Basso LS, Miller JB, Gloor M, Gatti Domingues L, Cassol HLG, et al. Amazonia as a carbon source linked to deforestation and climate change. Nature. 2021;595:388–93.CAS 
PubMed 
Article 

Google Scholar 
Ellwanger JH, Kulmann-Leal B, Kaminski VL, Valverde-Villegas JM, Veiga ABGDA, Spilki FR, et al. Beyond diversity loss and climate change: impacts of Amazon deforestation on infectious diseases and public health. An Acad Bras Cienc. 2020;92:e20191375.CAS 
PubMed 
Article 

Google Scholar 
Morand S, Lajaunie C. Outbreaks of vector-borne and zoonotic diseases are associated with changes in forest cover and oil palm expansion at global scale. Front Vet Sci. 2021;8:661063.PubMed 
PubMed Central 
Article 

Google Scholar 
Keenan RJ, Reams GA, Achard F, de Freitas JV, Grainger A, Lindquist E. Dynamics of global forest area: results from the FAO Global Forest Resources Assessment 2015. For Ecol Manage. 2015;352:9–20.Article 

Google Scholar 
Rezende CL, Scarano FR, Assad ED, Joly CA, Metzger JP, Strassburg BBN, et al. From hotspot to hopespot: an opportunity for the Brazilian Atlantic Forest. Perspectives in Ecology and Conservation. 2018;16:208–14.Article 

Google Scholar 
Yarwood SA. The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review. FEMS Microbiol Ecol. 2018;94: https://doi.org/10.1093/femsec/fiy175.Kock RA, Orynbayev M, Robinson S, Zuther S, Singh NJ, Beauvais W, et al. Saigas on the brink: multidisciplinary analysis of the factors influencing mass mortality events. Sci Adv. 2018;4:eaao2314.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Murdock CC, Blanford S, Hughes GL, Rasgon JL, Thomas MB. Temperature alters Plasmodium blocking by Wolbachia. Sci Rep. 2014;4:3932.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
MacArthur RH, Wilson EO. An equilibrium theory of insular zoogeography. Evolution. 1963;17:373–87.Article 

Google Scholar 
Krasnov BR, Shenbrot GI, Medvedev SG. Host–habitat relations as an important determinant of spatial distribution of flea assemblages (Siphonaptera) on rodents in the Negev Desert. Parasitology. 1997;114:159–73.Poulin R. Are there general laws in parasite ecology? Parasitology 2007;134:63–776Speer KA, Dheilly NM, Perkins SL. Microbiomes are integral to conservation of parasitic arthropods. Biol Conserv. 2020;250:108695.Bell T, Ager D, Song J-I, Newman JA, Thompson IP, Lilley AK, et al. Larger islands house more bacterial taxa. Science. 2005;308:1884.CAS 
PubMed 
Article 

Google Scholar 
Zinger L, Boetius A, Ramette A. Bacterial taxa-area and distance-decay relationships in marine environments. Mol Ecol. 2014;23:954–64.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12.CAS 
PubMed 
Article 

Google Scholar 
Carbonero F, Oakley BB, Purdy KJ. Metabolic flexibility as a major predictor of spatial distribution in microbial communities. PLoS One. 2014;9:e85105.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
van der Gast CJ. Microbial biogeography: the end of the ubiquitous dispersal hypothesis? Environ Microbiol. 2015;17:544–6.PubMed 
Article 

Google Scholar 
Weiss B, Aksoy S. Microbiome influences on insect host vector competence. Trends Parasitol. 2011;27:514–22.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gupta A, Nair S. Dynamics of insect-microbiome interaction influence host and microbial symbiont. Front Microbiol. 2020;11:1357.PubMed 
PubMed Central 
Article 

Google Scholar 
Dick CW, Dittmar K. Parasitic bat Flies (Diptera: Streblidae and Nycteribiidae): Host specificity and potential as vectors. In: Klimpel S, Mehlhorn H (eds). Bats (Chiroptera) as Vectors of Diseases and Parasites. 2014. Springer, Berlin, Heidelberg, pp 131–55.Speer KA, Luetke E, Bush E, Sheth B, Gerace A, Quicksall Z, et al. A fly on the cave wall: Parasite genetics reveal fine-scale dispersal patterns of bats. 2019;105:555-66.Patterson BD, Dick CW, Dittmar K. Sex biases in parasitism of neotropical bats by bat flies (Diptera: Streblidae). J Trop Ecol. 2008;24:387–96.Article 

Google Scholar 
Hiller T, Brändel SD, Honner B, Page RA, Tschapka M. Parasitization of bats by bat flies (Streblidae) in fragmented habitats. Biotropica. 2020;72:617.
Google Scholar 
Kikuchi Y, Tada A, Musolin DL, Hari N, Hosokawa T, Fujisaki K, et al. Collapse of insect gut symbiosis under simulated climate change. MBio. 2016;7:e01578-16.Thapa S, Zhang Y, Allen MS. Effects of temperature on bacterial microbiome composition in Ixodes scapularis ticks. Microbiologyopen. 2019;8:e00719.PubMed 
Article 
CAS 

Google Scholar 
Teixeira TSM. Bats in a fragmented world. 2019. Queen Mary University of London.Emmons L, Feer F. Neotropical rainforest mammals: a field guide. 1997. sidalc.net.Reis NR, Fregonezi MN, Peracchi AL, Shibatta OA. Morcegos do Brasil: guia de campo. 2013. Technical Books Editora.Sikes RS, Care A, of Mammalogists UC of TAS. 2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education. J Mammal. 2016;97:663–88.PubMed 
PubMed Central 
Article 

Google Scholar 
Wenzel RL. The streblid batflies of Venezuela (Diptera: Streblidae). Brigham Young University Science Bulletin. Biological Series. 1976;20:1.
Google Scholar 
Graciolli G, de Carvalho CJB. Moscas ectoparasitas (Diptera, Hippoboscoidea) de morcegos (Mammalia, Chiroptera) do Estado do Paraná. 11. Streblidae. Chave pictórica para gêneros e espécies 1. RevIa bras Zool. 2001;18:907–60.Article 

Google Scholar 
Graciolli G, de Carvalho CJB. Moscas ectoparasitas (Diptera, Hippoboscoidea, Nycteribiidae) de morcegos (Mammalia, Chiroptera) do Estado do Paraná, Brasil. I. Basilia, taxonomia e chave pictórica para as espécies 1. RevIa bras Zool. 2001;18:33–49.Article 

Google Scholar 
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 1994;3:294–9.CAS 
PubMed 

Google Scholar 
Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B: Biological Sciences. 2003;270:313–21.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gustafson EJ, Parker GR. Relationships between landcover proportion and indices of landscape spatial pattern. Landsc Ecol. 1992;7:101–10.Article 

Google Scholar 
McGarigal K, Cushman SA, Neel MC, Ene E. FRAGSTATS: spatial pattern analysis program for categorical maps. 2002. University of Massachusetts.Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, et al. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010;3:243–8.PubMed 
PubMed Central 
Article 

Google Scholar 
Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12:69.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Apprill A, McNally S, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol. 2015;75:129–37.Article 

Google Scholar 
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.CAS 
PubMed 
Article 

Google Scholar 
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10–12.Article 

Google Scholar 
Katoh K, Misawa K, Kuma K-I, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Katoh K, Kuma K-I, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Katoh K, Toh H. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics. 2007;23:372–4.CAS 
PubMed 
Article 

Google Scholar 
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.PubMed 
PubMed Central 
Article 
CAS 

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

Google Scholar 
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hosokawa T, Nikoh N, Koga R, Satô M, Tanahashi M, Meng X-Y, et al. Reductive genome evolution, host–symbiont co-speciation and uterine transmission of endosymbiotic bacteria in bat flies. ISME J. 2012;6:577–87.CAS 
PubMed 
Article 

Google Scholar 
Duron O, Schneppat UE, Berthomieu A, Goodman SM, Droz B, Paupy C, et al. Origin, acquisition and diversification of heritable bacterial endosymbionts in louse flies and bat flies. Mol Ecol. 2014;23:2105–17.PubMed 
Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.CAS 
PubMed 
Article 

Google Scholar 
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42:D643–8.CAS 
PubMed 
Article 

Google Scholar 
Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, et al. 25 years of serving the community with ribosomal RNA gene reference databases and tools. J Biotechnol. 2017;261:169–76.PubMed 
Article 
CAS 

Google Scholar 
Nováková E, Hypsa V, Moran NA. Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution. BMC Microbiol. 2009;9:143.PubMed 
PubMed Central 
Article 

Google Scholar 
Bressan A, Terlizzi F, Credi R. Independent origins of vectored plant pathogenic bacteria from arthropod-associated Arsenophonus endosymbionts. Microb Ecol. 2012;63:628–38.PubMed 
Article 

Google Scholar 
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Weiss S, Amir A, Hyde ER, Metcalf JL, Song SJ, Knight R. Tracking down the sources of experimental contamination in microbiome studies. Genome Biol. 2014;15:564.PubMed 
PubMed Central 
Article 

Google Scholar 
Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. Contamination in low microbial biomass microbiome studies: Issues and recommendations. Trends Microbiol. 2019;27:105–17.CAS 
PubMed 
Article 

Google Scholar 
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6:226.PubMed 
PubMed Central 
Article 

Google Scholar 
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10:57–59.CAS 
PubMed 
Article 

Google Scholar 
Alberdi A, Aizpurua O, Gilbert MTP, Bohmann K. Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods Ecol Evol. 2018;9:134–47.Article 

Google Scholar 
McMurdie PJ, Holmes S. Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data. Pac Symp Biocomput 2012; 235–46.McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: community ecology package. R package version 2.4–4. 2017. 2018.Wickham H. ggplot2: Elegant Graphics for Data Analysis. 2016. Springer.Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB. Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome. 2014;2:15.PubMed 
PubMed Central 
Article 

Google Scholar 
Gloor GB, Reid G. Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data. Can J Microbiol. 2016;62:692–703.CAS 
PubMed 
Article 

Google Scholar 
Tsilimigras MCB, Fodor AA. Compositional data analysis of the microbiome: fundamentals, tools, and challenges. Ann Epidemiol. 2016;26:330–5.PubMed 
Article 

Google Scholar 
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: And this is not optional. Front Microbiol. 2017;8:2224.PubMed 
PubMed Central 
Article 

Google Scholar 
Silverman JD, Washburne AD, Mukherjee S, David LA. A phylogenetic transform enhances analysis of compositional microbiota data. Elife 2017;6.Xia Y, Sun J. Hypothesis testing and statistical analysis of microbiome. Genes Dis. 2017;4:138–48.PubMed 
PubMed Central 
Article 

Google Scholar 
Anderson MJ, Walsh DCI. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing? Ecol Monogr. 2013;83:557–74.Article 

Google Scholar 
Anderson MJ. Permutational Multivariate Analysis of Variance (PERMANOVA). In: Balakrishnan N, Colton T, Everitt B, Piegorsch W, Ruggeri F, Teugels JL (eds). Wiley StatsRef: Statistics Reference Online. 2014. John Wiley & Sons, Ltd, Chichester, UK, pp 1–15.Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11:e1004226.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Liu H, Roeder K, Wasserman L. Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models. Adv Neural Inf Process Syst. 2010;24:1432–40.PubMed 
PubMed Central 

Google Scholar 
Röttjers L, Faust K. From hairballs to hypotheses-biological insights from microbial networks. FEMS Microbiol Rev. 2018;42:761–80.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Freeman LC. Centrality in social networks conceptual clarification. Soc Networks. 1978;1:215–39.Article 

Google Scholar 
Brandes U. A faster algorithm for betweenness centrality. J Math Sociol. 2001;25:163–77.Article 

Google Scholar 
Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. Complex Systems. 2006;1695:1–9.
Google Scholar 
Newman MEJ. Finding community structure in networks using the eigenvectors of matrices. Phys Rev E Stat Nonlin Soft Matter Phys. 2006;74:036104.CAS 
PubMed 
Article 

Google Scholar 
Delmas E, Besson M, Brice M-H, Burkle LA, Dalla Riva GV, Fortin M-J, et al. Analysing ecological networks of species interactions: Analyzing ecological networks. Biol Rev. 2019;94:16–36.Article 

Google Scholar 
Fortunato S, Hric D. Community detection in networks: A user guide. arXiv [physics.soc-ph]. 2016.Singh A, Humphries MD. Finding communities in sparse networks. Sci Rep. 2015;5:8828.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yaveroğlu ÖN, Malod-Dognin N, Davis D, Levnajic Z, Janjic V, Karapandza R, et al. Revealing the hidden language of complex networks. Sci Rep. 2014;4:4547.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Przulj N. Biological network comparison using graphlet degree distribution. Bioinformatics. 2007;23:e177–83.CAS 
PubMed 
Article 

Google Scholar 
Hočevar T, Demšar J. Computation of graphlet orbits for nodes and edges in sparse graphs. J Stat Softw 2016;71.Müller CL, Bonneau R, Kurtz Z. Generalized stability approach for regularized graphical models. arXiv [statME]. 2016.Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med. 2016;8:48.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, et al. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nat Commun. 2017;8:518.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 2013;7:1344–53.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Avena CV, Parfrey LW, Leff JW, Archer HM, Frick WF, Langwig KE, et al. Deconstructing the bat skin microbiome: Influences of the host and the environment. Front Microbiol. 2016;7:1753.PubMed 
PubMed Central 
Article 

Google Scholar 
Becker CG, Longo AV, Haddad CFB, Zamudio KR. Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome. Proc Biol Sci 2017;284.Ingala MR, Becker DJ, Bak Holm J, Kristiansen K, Simmons NB. Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats. Ecol Evol. 2019;9:6508–23.PubMed 
PubMed Central 
Article 

Google Scholar 
Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM, Weiss BL, et al. Analysis of multiple tsetse fly populations in Uganda reveals limited diversity and species-specific gut microbiota. Appl Environ Microbiol. 2014;80:4301–12.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mello RM, Laurindo RS, Silva LC, Pyles MV, Mancini MCS, Dáttilo W, et al. Landscape configuration and composition shape mutualistic and antagonistic interactions among plants, bats, and ectoparasites in human-dominated tropical rainforests. Acta Oecol. 2021;112:103769.Article 

Google Scholar 
Cirimotich CM, Ramirez JL, Dimopoulos G. Native microbiota shape insect vector competence for human pathogens. Cell Host Microbe. 2011;10:307–10.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sassera D, Epis S, Pajoro M, Bandi C. Microbial symbiosis and the control of vector-borne pathogens in tsetse flies, human lice, and triatomine bugs. Pathog Glob Health. 2013;107:285–92.PubMed 
PubMed Central 
Article 

Google Scholar 
Weiss BL, Wang J, Maltz MA, Wu Y, Aksoy S. Trypanosome infection establishment in the tsetse fly gut is influenced by microbiome-regulated host immune barriers. PLoS Pathog. 2013;9:e1003318.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Obame-Nkoghe J, Rahola N, Bourgarel M, Yangari P, Prugnolle F, Maganga GD, et al. Bat flies (Diptera: Nycteribiidae and Streblidae) infesting cave-dwelling bats in Gabon: diversity, dynamics and potential role in Polychromophilus melanipherus transmission. Parasit Vectors. 2016;9:333.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Krause AE, Frank KA, Mason DM, Ulanowicz RE, Taylor WW. Compartments revealed in food-web structure. Nature. 2003;426:282–5.CAS 
PubMed 
Article 

Google Scholar 
Stouffer DB, Bascompte J. Understanding food-web persistence from local to global scales. Ecol Lett. 2010;13:154–61.PubMed 
Article 

Google Scholar 
Trowbridge RE, Dittmar K, Whiting MF. Identification and phylogenetic analysis of Arsenophonus- and Photorhabdus-type bacteria from adult Hippoboscidae and Streblidae (Hippoboscoidea). J Invertebr Pathol. 2006;91:64–68.PubMed 
Article 

Google Scholar 
Morse SF, Bush SE, Patterson BD, Dick CW, Gruwell ME, Dittmar K. Evolution, multiple acquisition, and localization of endosymbionts in bat flies (Diptera: Hippoboscoidea: Streblidae and Nycteribiidae). Appl Environ Microbiol. 2013;79:2952–61.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wilkinson DA, Duron O, Cordonin C, Gomard Y, Ramasindrazana B, Mavingui P, et al. The bacteriome of bat flies (Nycteribiidae) from the Malagasy Region: a community shaped by host ecology, bacterial transmission mode, and host-vector specificity. Appl Environ Microbiol. 2016;82:1778–88.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Graciolli G, Dick CW. Checklist of World Nycteribiidae (Diptera: Hippoboscoidea). https://www.researchgate.net/publication/322579074_CHECKLIST_OF_WORLD_NYCTERIBIIDAE_DIPTERA_HIPPOBOSCOIDEA.Graciolli G, Dick CW. Checklist of World Streblidae (Diptera: Hippoboscoidea). https://www.researchgate.net/publication/322578987_CHECKLIST_OF_WORLD_STREBLIDAE_DIPTERA_HIPPOBOSCOIDEA.Breitschwerdt EB, Kordick DL. Bartonella infection in animals: carriership, reservoir potential, pathogenicity, and zoonotic potential for human infection. Clin Microbiol Rev. 2000;13:428–38.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jiggins FM. Male-killing Wolbachia and mitochondrial DNA: selective sweeps, hybrid introgression and parasite population dynamics. Genetics. 2003;164:5–12.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hosokawa T, Koga R, Kikuchi Y, Meng X-Y, Fukatsu T. Wolbachia as a bacteriocyte-associated nutritional mutualist. Proc Natl Acad Sci USA. 2010;107:769–74.CAS 
PubMed 
Article 

Google Scholar 
Lack JB, Nichols RD, Wilson GM, Van Den Bussche RA. Genetic signature of reproductive manipulation in the phylogeography of the bat fly, Trichobius major. J Hered. 2011;102:705–18.CAS 
PubMed 
Article 

Google Scholar 
Morse SF, Olival KJ, Kosoy M, Billeter S, Patterson BD, Dick CW, et al. Global distribution and genetic diversity of Bartonella in bat flies (Hippoboscoidea, Streblidae, Nycteribiidae). Infect Genet Evol. 2012;12:1717–23.PubMed 
Article 

Google Scholar 
Nikoh N, Hosokawa T, Moriyama M, Oshima K, Hattori M, Fukatsu T. Evolutionary origin of insect-Wolbachia nutritional mutualism. Proc Natl Acad Sci USA. 2014;111:10257–62.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stuckey MJ, Chomel BB, de Fleurieu EC, Aguilar-Setién A, Boulouis H-J, Chang C-C. Bartonella, bats and bugs: A review. Comp Immunol Microbiol Infect Dis. 2017;55:20–29.PubMed 
Article 

Google Scholar 
Gibson CM, Hunter MS. Extraordinarily widespread and fantastically complex: comparative biology of endosymbiotic bacterial and fungal mutualists of insects. Ecol Lett. 2010;13:223–34.PubMed 
Article 

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Distribution of nitrogen-cycling pathways in groundwaterDifferences in nitrogen-cycling processes based on oxygen and nitrate concentrationsSixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3) concentrations (Fig. 1A; Table S1). Nitrate concentrations were pristine (site C) to N-contaminated (sites A, B, D) [4]. Sites A–C were oxic and had low DOC (typical of groundwaters), whereas site D was dysoxic with relatively high DOC. Metagenomes from groundwater wells comprised pairs, representing the planktonic and sediment-attached fractions. Over 70 Gbp of raw sequence was generated per site (390 Gbp overall, 322 Gbp trimmed). However, 2Kb long and only 0.64–8.14% of reads (3.8% on average) mapped to MAGs (Table S4), reflecting the complexity of microbial communities in the terrestrial subsurface [11]. To capture this diversity, metagenomic reads are first used here to determine the distribution of N metabolisms.Fig. 1: Geochemistry and protein-coding sequences (based on reads) involved in nitrogen cycling that are significantly different among sites used for metagenomics.A Bar plots showing geochemical data from groundwater samples, coloured according to site. Solid bar colour = groundwater samples. Grid lines = attached-fraction enriched groundwater. All samples from site D were characterized as dysoxic, although gwj15-16 contained 0.37 mg/L DO, which are near suboxic levels (i.e. More