Philippa Kaur

Bedrock composition can play a critical role in determining the structure and water demand of forests, influencing their vulnerability to drought. The properties of bedrock can help explain within-region patterns of tree mortality in the 2011–2017 California drought.Montane forests are iconic natural resources that provide habitat, carbon sequestration, regulation of water, and, for many cultures, profound meaning. A warming climate and prolonged droughts threaten these forests, as shown by the 2011–2017 drought in California, USA, which killed over 140 million trees. However, the vulnerability of forests to climate-driven risks is not evenly distributed across these landscapes. In the 2011–2017 drought, some contiguous forested areas (or forest stands) suffered more than 70% mortality while forests in other locations experienced few or no losses1. Understanding these spatial patterns is critical for the projection of future risks and for targeted forest management. Writing in Nature Geoscience, Callahan and colleagues look beneath the surface at the composition of bedrock and find a link to these patterns of drought mortality in the California Sierra2. More

Zaneveld, J. R., McMinds, R. & Thurber, R. V. Stress and stability: Applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2, 1–8 (2017).Article 
CAS 

Google Scholar 
Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B 286, 2018–2448 (2019).Article 

Google Scholar 
Bennett, A. G. On the occurrence of diatoms on the skin of whales. Proc. R. Soc. Lond. B 91, 352–357 (1920).ADS 
Article 

Google Scholar 
Denys, L. Morphology and taxonomy of epizoic diatoms (Epiphalaina and Tursiocola) on a sperm whale (Physeter macrocephalus) stranded on the coast of Belgium. Diatom. Res. 12, 1–18 (1997).Article 

Google Scholar 
Majewska, R. Tursiocola neliana sp. nov (Bacillariophyceae) epizoic on South African leatherback sea turtles (Dermochelys coriacea) and new observations on the genus Tursiocola. Phytotaxa 453, 1–15 (2020).Article 

Google Scholar 
Majewska, R. et al. Chelonicola and Poulinea, two new gomphonemoid genera living on marine turtles from Costa Rica. Phytotaxa 233, 236–250 (2015).Article 

Google Scholar 
Majewska, R. et al. Shared epizoic taxa and differences in diatom community structure between green turtles (Chelonia mydas) from distant habitats. Microb Ecol. 74, 969–978 (2017).PubMed 
Article 

Google Scholar 
Majewska, R. et al. Two new epizoic Achnanthes species (Bacillariophyta) living on marine turtles from Costa Rica. Bot. Mar. 60, 303–318 (2017).Article 

Google Scholar 
Majewska, R., De Stefano, M. & Van de Vijver, B. Labellicula lecohuiana, a new epizoic diatom species living on green turtles in Costa Rica. Nova Hedwig Beih. 146, 23–31 (2018).Article 

Google Scholar 
Majewska, R. et al. Craspedostauros alatus sp. nov., a new diatom (Bacillariophyta) species found on museum sea turtle specimens. Diatom Res. 33, 229–240 (2018).Article 

Google Scholar 
Majewska, R. et al. Six new epibiotic Proschkinia (Bacillariophyta) species and new insights into the genus phylogeny. Eur. J. Phycol. 54, 609–631 (2019).Article 

Google Scholar 
Majewska, R., Robert, K., Van de Vijver, B. & Nel, R. A new species of Lucanicum (Cyclophorales, Bacillariophyta) associated with loggerhead sea turtles from South Africa. Bot. Lett. 167, 7–14 (2020).Article 

Google Scholar 
Frankovich, T. A., Sullivan, M. J. & Stacy, N. I. Tursiocola denysii sp. Nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta). Phytotaxa 234, 227–236 (2015).Article 

Google Scholar 
Frankovich, T. A., Ashworth, M. P., Sullivan, M. J., Vesela, J. & Stacy, N. I. Medlinella amphoroidea gen. et sp. Nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta). Phytotaxa 272, 101–114 (2016).Article 

Google Scholar 
Riaux-Gobin, C. et al. New epizoic diatom (Bacillariophyta) species from sea turtles in the Eastern Caribbean and South Pacific. Diatom Res. 32, 109–125 (2017).Article 

Google Scholar 
Riaux-Gobin, C., Witkowski, A., Chevallier, D. & Daniszewska-Kowalczyk, G. Two new Tursiocola species (Bacillariophyta) epizoic on green turtles (Chelonia mydas) in French Guiana and Eastern Caribbean. Fottea Olomouc 17, 150–163 (2017).Article 

Google Scholar 
Riaux-Gobin, C., Witkowski, A., Kociolek, J. P. & Chevallier, D. Navicula dermochelycola sp. Nov., presumably an exclusively epizoic diatom on sea turtles Dermochelys coriacea and Lepidochelys olivacea from French Guiana. Oceanol. Hydrobiol. Stud. 49, 132–139 (2020).CAS 
Article 

Google Scholar 
Robert, K., Bosak, S. & Van de Vijver, B. Catenula exigua sp. nov., a new marine diatom (Bacillariophyta) species from the Adriatic Sea. Phytotaxa 414, 113–118 (2019).Article 

Google Scholar 
Van de Vijver, B. & Bosak, S. Planothidium kaetherobertianum, a new marine diatom (Bacillariophyta) species from the Adriatic Sea. Phytotaxa 425, 105–112 (2019).Article 

Google Scholar 
Robinson, N. J. et al. Epibiotic diatoms are universally present on all sea turtle species. PLoS ONE 11, e0157011 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Van de Vijver, B. et al. Diversity of diatom communities (Bacillariophyta) associated with loggerhead sea turtles. PLoS ONE 15, e0236513 (2020).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Van de Vijver, B., Robert, K., Witkowski, A. & Bosak, S. Majewskaea gen. nov. (Bacillariophyta), a new marine benthic diatom genus from the Adriatic Sea. Fottea 20, 112–120 (2020).Article 

Google Scholar 
Majewska, R. Nagumoea hydrophicola sp. Nov. (Bacillariophyta), the first diatom species described from sea snakes. Diatom Res. 36, 49–59 (2021).Article 

Google Scholar 
Frankovich, T. A., Sullivan, M. J. & Stacey, N. I. Three new species of Tursiocola (Bacillariophyta) from the skin of the West Indian manatee (Trichechus manatus). Phytotaxa 204, 33–48 (2015).Article 

Google Scholar 
Frankovich, T. A., Ashworth, M. P., Sullivan, M. J., Theriot, E. C. & Stacy, N. I. Epizoic and apochlorotic Tursiocola species (Bacillariophyta) from the skin of Florida manatees (Trichechus manatus latirostris). Protist 169, 539–568 (2018).PubMed 
Article 

Google Scholar 
Azari, M. et al. Diatoms on sea turtles and floating debris in the Persian Gulf (Western Asia). Phycologia 59, 292–304 (2020).Article 

Google Scholar 
Majewska, R. & Goosen, W. E. For better, for worse: Manatee-associated Tursiocola (Bacillariophyta) remain faithful to their host. J. Phycol. 56, 1019–1027 (2020).CAS 
PubMed 
Article 

Google Scholar 
Smol, J. P. & Stoermer, E. F. The Diatoms: Applications for the Environmental and Earth Sciences (Cambridge University Press, 2010).Book 

Google Scholar 
Rivera, S. F. et al. DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior. PLoS ONE 13, e0195770 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Majewska, R. et al. On sea turtle-associated Craspedostauros with description of three novel species. J Phycol. 57, 199–208 (2021).CAS 
PubMed 
Article 

Google Scholar 
Holmes, R. W. The morphology of diatoms epizoic on cetaceans and their transfer from Cocconeis to two new genera, Bennettella and Epipellis. Br. Phycol. J. 20, 43–57 (1985).Article 

Google Scholar 
Woodworth, K. A., Frankovich, T. A. & Freshwater, D. W. Melanothamnus maniticola (Ceramiales, Rhodophyta): An epizoic species evolved for life on the West Indian Manatee. J. Phycol. 55, 1239–1245 (2019).CAS 
PubMed 
Article 

Google Scholar 
Vitt, L. J. & Caldwell, J. P. Herpetology: An Introductory Biology of Amphibians and Reptiles (Academic Press, 2013).
Google Scholar 
Pitman, L. R. et al. Skin in the game: Epidermal molt as a driver of long-distance migration in whales. Mar. Mamm. Sci. 36, 565–594 (2020).Article 

Google Scholar 
Pope, D. H. & Berger, L. R. Algal photosynthesis at increased hydrostatic pressure and constant pO2. Arch. Microbiol. 89, 321–325 (1973).CAS 

Google Scholar 
Calcagno, V., Jarne, P., Loreau, M., Mouquet, N. & David, P. Diversity spurs diversification in ecological communities. Nat. Commun. 8, 15810 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Robinson, N. J. & Pfaller, J. B. Sea turtle epibiosis: Global patterns and knowledge gaps. Trends Evol. Ecol. 10, 844021 (2021).
Google Scholar 
Conant, T. A., Dutton, P. H., Eguchi, T., Epperly, S. P., Fahy, C. C., Godfrey, M. H., MacPherson, S. L., Possardt, E. E., Schroeder, B. A., Seminoff, J. A., Snover, M. L. Loggerhead sea turtle (Caretta caretta) 2009 status review under the US Endangered Species Act. In Report of the loggerhead biological review Team to the National Marine Fisheries Service. 222, 1–230 (2009).Evans, K. M., Wortley, A. H. & Mann, D. G. An assessment of potential diatom ‘“barcode”’ genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158, 349–364 (2007).CAS 
PubMed 
Article 

Google Scholar 
Hamsher, S. E., Evans, K. M., Mann, D. G., Poulíčková, A. & Saunders, G. W. Barcoding diatoms: Exploring alternatives to COI-5P. Protist 162, 405–422 (2011).CAS 
PubMed 
Article 

Google Scholar 
Bowen, B. W. & Karl, S. A. Population genetics and phylogeography of sea turtles. Mol Ecol. 16, 4886–4907 (2007).CAS 
PubMed 
Article 

Google Scholar 
Shanker, K., Ramadevi, J., Choudhury, B. C., Singh, L. & Aggarwal, R. K. Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Mol. Ecol. 13, 1899–1909 (2004).CAS 
PubMed 
Article 

Google Scholar 
Pinou, T. et al. Standardizing sea turtle epibiont sampling: Outcomes of the epibiont workshop at the 37th International Sea Turtle Symposium. Mar. Turt. Newsl. 157, 22–32 (2019).
Google Scholar 
Ehrhert L., Ogren L. H. Studies in foraging habitats: capturing and handling turtles. In Research and management techniques for the conservation of sea turtles (eds. Eckert, K. L., Bjorndal, K. A., Abreu-Grobois, F. A., Donnelly, M.). IUCN/SSC Marine Turtle Specialist Group. Publication No. 4. (1999).Guillard, R. R. Culture of phytoplankton for feeding marine invertebrates. In Culture of Marine Invertebrate Animals 29–60 (Springer, 1975).Theriot, E. C., Ashworth, M. P., Nakov, T., Ruck, E. & Jansen, R. K. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Mol. Phylogenet. Evol. 89, 28–36 (2015).CAS 
PubMed 
Article 

Google Scholar 
Lobban, C. S., Ashworth, M. P., Calaor, J. J. & Theriot, E. C. Extreme diversity in fine-grained morphology reveals fourteen new species of conopeate Nitzschia (Bacillariophyta: Bacillariales). Phytotaxa. 401, 199–238 (2019).Article 

Google Scholar 
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).CAS 
PubMed 

Google Scholar 
Lanfear, R., Calcott, B., Kainer, D., Mayer, C. & Stamatakis, A. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol. Biol. 14, 1–14 (2014).Article 

Google Scholar 
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 
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).CAS 
PubMed 
Article 

Google Scholar 
Chernomor, O., Von Haeseler, A. & Minh, B. Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65, 997–1008 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Aberer, A. J., Kobert, K. & Stamatakis, A. ExaBayes: Massively parallel bayesian tree inference for the whole-genome Era. Mol. Biol. Evol. 31, 2553–2556 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More

Gregory, R. D. & van Strien, A. Wild bird indicators: Using composite population trends of birds as measures of environmental health. Ornithol. Sci. 9, 3–22 (2010).Article 

Google Scholar 
Cox, D. T. C. & Gaston, K. J. Urban bird feeding: Connecting people with nature. PLoS ONE 11, e0158717 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Anderson, R. M. & May, R. M. Population biology of infectious diseases: Part I. Nature 280, 361–367 (1979).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Keesing, F. et al. Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature 468, 647–652 (2010).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Smith, K. F., Acevedo-Whitehouse, K. & Pedersen, A. B. The role of infectious diseases in biological conservation. Anim. Conserv. 12, 1–12 (2009).Article 

Google Scholar 
Han, B. A., Kramer, A. M. & Drake, J. M. Global patterns of zoonotic disease in mammals. Trends Parasitol. 32, 565–577 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Estrada-Peña, A., Ostfeld, R. S., Peterson, A. T., Poulin, R. & de la Fuente, J. Effects of environmental change on zoonotic disease risk: An ecological primer. Trends Parasitol. 30, 205–214 (2014).PubMed 
Article 

Google Scholar 
Daszak, P., Cunningham, A. A. & Hyatt, A. D. Emerging infectious diseases of wildlife–threats to biodiversity and human health. Science 287(5452), 443–449 (2000).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Pedersen, A. B., Jones, K. E., Nunn, C. L. & Altizer, S. Infectious diseases and extinction risk in wild mammals. Conserv. Biol. 21, 1269–1279 (2007).PubMed 
PubMed Central 
Article 

Google Scholar 
Atkinson, C. T. & Samuel, M. D. Avian malaria Plasmodium relictum in native Hawaiian forest birds: Epizootiology and demographic impacts on àapapane Himatione sanguinea. J. Avian Biol. 41, 357–366 (2010).Article 

Google Scholar 
George, T. L. et al. Persistent impacts of West Nile virus on North American bird populations. Proc. Natl. Acad. Sci. USA. 112, 14290–14294 (2015).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Dhondt, A. A., Tessaglia, D. L. & Slothower, R. L. Epidemic mycoplasmal conjunctivitis in house finches from Eastern North America. J. Wildl. Dis. 34, 265–280 (1998).CAS 
PubMed 
Article 

Google Scholar 
Monterroso, P. et al. Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs. Sci. Rep. 6, 36072 (2016).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cheng, T. L. et al. The scope and severity of white-nose syndrome on hibernating bats in North America. Conserv. Biol. 35, 1586–1597 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Rushton, S. P. et al. Disease threats posed by alien species: The role of a poxvirus in the decline of the native red squirrel in Britain. Epidemiol. Infect. 134, 521–533 (2006).CAS 
PubMed 
Article 

Google Scholar 
Scheele, B. C. et al. Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity. Science 363(6434), 1459–1463 (2019).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Bradley, C. A. & Altizer, S. Urbanization and the ecology of wildlife diseases. Trends Ecol. Evol. 22, 95–102 (2007).PubMed 
Article 

Google Scholar 
Murray, M. H. et al. City sicker? A meta-analysis of wildlife health and urbanization. Front. Ecol. Environ. 17, 575–583 (2019).Article 

Google Scholar 
Giraudeau, M., Mousel, M., Earl, S. & McGraw, K. Parasites in the city: Degree of urbanization predicts poxvirus and coccidian infections in house finches (Haemorhous mexicanus). PLoS ONE 9, e86747 (2014).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Shutt, J. D. & Lees, A. C. Killing with kindness: Does widespread generalised provisioning of wildlife help or hinder biodiversity conservation efforts? Biol. Conserv. 261, 109295 (2021).Article 

Google Scholar 
Van Doren, B. M. et al. Human activity shapes the wintering ecology of a migratory bird. Glob. Chang. Biol. 27, 2715–2727 (2021).PubMed 
Article 
CAS 

Google Scholar 
Plummer, K. E., Risely, K., Toms, M. P. & Siriwardena, G. M. The composition of British bird communities is associated with long-term garden bird feeding. Nat. Commun. 10, 2088 (2019).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Lawson, B. et al. Health hazards to wild birds and risk factors associated with anthropogenic food provisioning. Philos. Trans. R. Soc. B Biol. Sci. 373, 20170091 (2018).Galbraith, J. A., Stanley, M. C., Jones, D. N. & Beggs, J. R. Experimental feeding regime influences urban bird disease dynamics. J. Avian Biol. 48, 700–713 (2017).Article 

Google Scholar 
Siriwardena, G. M. et al. The effect of supplementary winter seed food on breeding populations of farmland birds: Evidence from two large-scale experiments. J. Appl. Ecol. 44, 920–932 (2007).Article 

Google Scholar 
Kubasiewicz, L. M., Bunnefeld, N., Tulloch, A. I. T., Quine, C. P. & Park, K. J. Diversionary feeding: An effective management strategy for conservation conflict? Biodivers. Conserv. 25, 1–22 (2016).Article 

Google Scholar 
Lawson, B. et al. A clonal strain of Trichomonas gallinae is the aetiologic agent of an emerging avian epidemic disease. Infect. Genet. Evol. 11, 1638–1645 (2011).PubMed 
Article 

Google Scholar 
Robinson, R. A. et al. Emerging infectious disease leads to rapid population declines of common British birds. PLoS ONE 5, e12215 (2010).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Forrester, D. J. & Foster, G. W. Trichomonosis. In: Parasitic Diseases of Wild Birds 120–153 (Wiley-Blackwell, 2008).Lawson, B. et al. Evidence of spread of the emerging infectious disease, finch trichomonosis, by migrating birds. EcoHealth 8, 143–153 (2011).PubMed 
Article 

Google Scholar 
Lawson, B. et al. The emergence and spread of finch trichomonosis in the British Isles. Philos. Trans. R. Soc. B Biol. Sci. 367, 2852–2863 (2012).Article 

Google Scholar 
Woodward, I. D. et al. BirdTrends 2020: Trends in numbers, breeding success and survival for UK breeding birds. Research Report 732. BTO, Thetford. (2020).Enoksson, B. Age- and sex-related differences in dominance and foraging behaviour of nuthatches Sitta europaea. Anim. Behav. 36, 231–238 (1988).Article 

Google Scholar 
Tarvin, K. A. & Woolfenden, G. E. Patterns of dominance and aggressive behavior in blue jays at a feeder. Condor 99, 434–444 (1997).Article 

Google Scholar 
Brittingham, M. C. & Temple, S. A. Use of winter feeders by black-capped chickadees. Wildl. Soc. 56, 103–110 (1992).
Google Scholar 
Woodward, I. et al. Population estimates of birds in Great Britain and the United Kingdom. Br. Birds 113, 69–104 (2020).
Google Scholar 
Musgrove, A. J. et al. Population estimates of birds in Great Britain and the United Kingdom. Br. Birds 106, 64–100 (2013).
Google Scholar 
Wernham, C. et al. The Migration Atlas: Movements of the Birds of Britain and Ireland. (T & AD Poyser, 2002).Main, I. G. The partial migration of Fennoscandian Greenfinches Carduelis chloris. Ringing Migr. 20, 167–180 (2000).Article 

Google Scholar 
Lack, P. C. The Atlas of Wintering Birds in Britain and Ireland. (T. & A.D. Poyser, 1986).Robinson, R. A. BirdFacts: profiles of birds occurring in Britain & Ireland. BTO, Thetford (2005). Available at: http://www.bto.org/birdfacts. Accessed: 15 May 2022.Tratalos, J. et al. Bird densities are associated with household densities. Glob. Chang. Biol. 13, 1685–1695 (2007).ADS 
Article 

Google Scholar 
Gregory, R. D. Broad-scale habitat use of sparrows, finches and buntings in Britain. Die Vogelwelt 120, 47–57 (1999).
Google Scholar 
Newton, I. Finches. New Naturalist Series, Volume: 55. (HarperCollins, 1972).Robinson, R. A., Baillie, S. R. & Crick, H. Q. P. Weather-dependent survival: Implications of climate change for passerine population processes. Ibis. 149, 357–364 (2007).Article 

Google Scholar 
Crick, H. Q. P. A bird-habitat coding system for use in Britain and Ireland incorporating aspects of land-management and human activity. Bird Study 39, 1–12 (1992).Article 

Google Scholar 
Davies, Z. G. et al. A national scale inventory of resource provision for biodiversity within domestic gardens. Biol. Conserv. 142, 761–771 (2009).Article 

Google Scholar 
Balmer, D. E. et al. Bird Atlas 2007–11: The breeding and wintering birds of Britain and Ireland. (BTO Books, 2013).Lawson, B. et al. Epidemiology of salmonellosis in garden birds in England and Wales, 1993 to 2003. EcoHealth 7, 294–306 (2010).CAS 
PubMed 
Article 

Google Scholar 
Svensson, L. Identification guide to European passerines, 4th edition. (BTO, 1992).Jenni, L. & Winkler, R. Moult and ageing of European passerines, 2nd edition. (Helm, 2020).Baillie, S. R. The contribution of ringing to the conservation and management of bird populations: A review. Ardea 89, 167–184 (2001).
Google Scholar 
Kéry, M. & Schaub, M. Bayesian Population Analysis using WinBUGS: A hierarchical perspective (Academic Press, 2012).
Google Scholar 
R Core Team. R: A language and environment for statistical computing. (2020).Plummer, M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. in Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003) (eds. Hornik, K., Leisch, F. & Zeileis, A.) (2003).Su, Y.-S. & Yajima, M. R2jags: Using R to Run ‘JAGS’. R package version 0.6–1. (2020).Robinson, R. A., Morrison, C. A. & Baillie, S. R. Integrating demographic data: Towards a framework for monitoring wildlife populations at large spatial scales. Methods Ecol. Evol. 5, 1361–1372 (2014).Article 

Google Scholar 
Newson, S. E., Evans, K. L., Noble, D. G., Greenwood, J. J. D. & Gaston, K. J. Use of distance sampling to improve estimates of national population sizes for common and widespread breeding birds in the UK. J. Appl. Ecol. 45, 1330–1338 (2008).Article 

Google Scholar 
Newson, S. E., Massimino, D., Johnston, A., Baillie, S. R. & Pearce-Higgins, J. W. Should we account for detectability in population trends? Bird Study 60, 384–390 (2013).Article 

Google Scholar 
Crick, H. Q. P., Baillie, S. R. & Leech, D. I. The UK Nest Record Scheme: its value for science and conservation. Bird Study 50, 254–270 (2003).Article 

Google Scholar 
Abadi, F., Gimenez, O., Arlettaz, R. & Schaub, M. An assessment of integrated population models: Bias, accuracy, and violation of the assumption of independence. Ecology 91, 7–14 (2010).PubMed 
Article 

Google Scholar 
Plard, F., Turek, D., Grüebler, M. U. & Schaub, M. IPM2: Toward better understanding and forecasting of population dynamics. Ecol. Monogr. 89, e01364 (2019).Article 

Google Scholar 
Weegman, M. D., Arnold, T. W., Clark, R. G. & Schaub, M. Partial and complete dependency among data sets has minimal consequence on estimates from integrated population models. Ecol. Appl. 31, e02258 (2021).Article 

Google Scholar 
Koons, D. N., Iles, D. T., Schaub, M. & Caswell, H. A life-history perspective on the demographic drivers of structured population dynamics in changing environments. Ecol. Lett. 19, 1023–1031 (2016).PubMed 
Article 

Google Scholar 
Koons, D. N., Arnold, T. W. & Schaub, M. Understanding the demographic drivers of realized population growth rates. Ecol Appl. 27, 2102–2115 (2017).PubMed 
Article 

Google Scholar 
Caswell, H. Matrix population models: Construction, analysis and interpretation. (Sinauer Associates, 2001).Stubben, C. & Milligan, B. Estimating and analyzing demographic models using the popbio package in R. J. Stat. Softw. 22, 1–23 (2007).Article 

Google Scholar 
Stanbury, A. et al. The status of our bird populations: The fifth Birds of Conservation Concern in the United Kingdom, Channel Islands and Isle of Man and second IUCN Red List assessment of extinction risk for Great Britain. Br. Birds 114, 723–747 (2021).
Google Scholar 
Lehikoinen, A., Lehikoinen, E., Valkama, J., Väisänen, R. A. & Isomursu, M. Impacts of trichomonosis epidemics on greenfinch Chloris chloris and chaffinch Fringilla coelebs populations in Finland. Ibis 155, 357–366 (2013).Article 

Google Scholar 
PECBMS. EBCC/BirdLife/RSPB/CSO’ Pan-European Common Bird Monitoring Scheme. (2021). Available at: https://pecbms.info/. (Accessed: 14th July 2022)Keller, V. et al. European Breeding Bird Atlas 2: Distribution, Abundance and Change. (European Bird Census Council and Lynx Edicions, 2020).Rijks, J. M. et al. Trichomonosis in greenfinches (Chloris chloris) in the Netherlands 2009–2017: A concealed threat. Front. Vet. Sci. 6, 425 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Boele, A. et al. Broedvogels in Nederland in 2020. Sovonrapport 2022/05. (Sovon Vogelonderzoek Nederland, Nijmegen., 2022).Jones, D. The Birds at My Table: Why We Feed Wild Birds and Why It Matters. (Cornell University Press, 2018).Pennycott, T. W. et al. Causes of death of wild birds of the family fringillidae in Britain. Vet. Rec. 143, 155–158 (1998).CAS 
PubMed 
Article 

Google Scholar 
Bouwman, K. M. & Hawley, D. M. Sickness behaviour acting as an evolutionary trap? Male house finches preferentially feed near diseased conspecifics. Biol. Lett. 6, 462–465 (2010).PubMed 
PubMed Central 
Article 

Google Scholar 
Lawson, B. et al. Acute necrotising pneumonitis associated with Suttonella ornithocola infection in tits (Paridae). Vet. J. 188, 96–100 (2011).PubMed 
Article 

Google Scholar 
Clewley, G. D., Robinson, R. A. & Clark, J. A. Estimating mortality rates among passerines caught for ringing with mist nets using data from previously ringed birds. Ecol. Evol. 8, 5164–5172 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Francis, M. L. et al. Effects of supplementary feeding on interspecific dominance hierarchies in garden birds. PLoS ONE 13, e0202152 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wojczulanis-Jakubas, K., Kulpińska, M. & Minias, P. Who bullies whom at a garden feeder? Interspecific agonistic interactions of small passerines during a cold winter. J. Ethol. 33, 159–163 (2015).Article 

Google Scholar 
Cramp, S. Handbook of the Birds of Europe, the Middle East and North Africa. Volume VIII: Crows to Finches. (Oxford University Press, 1994).Brook, B. W. & Bradshaw, C. J. A. Strength of evidence for density dependence in abundance time series of 1198 species. Ecology 87, 1445–1451 (2006).PubMed 
Article 

Google Scholar 
Hochachka, W. M. & Dhondt, A. A. Density-dependent decline of host abundance resulting from a new infectious disease. Proc. Natl. Acad. Sci. USA. 97, 5303–5306 (2000).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hochachka, W. M., Dobson, A. P., Hawley, D. M. & Dhondt, A. A. Host population dynamics in the face of an evolving pathogen. J. Anim. Ecol. 90, 1480–1491 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Chi, J. F. et al. The finch epidemic strain of Trichomonas gallinae is predominant in British non-passerines. Parasitology 140, 1234–1245 (2013).PubMed 
Article 

Google Scholar 
Orros, M. E. & Fellowes, M. D. E. Wild bird feeding in an urban area: Intensity, economics and numbers of individuals supported. Acta Ornithol. 50, 43–58 (2015).Article 

Google Scholar 
Dirren, S., Borel, S., Wolfrum, N. & Korner-Nievergelt, F. Trichomonas gallinae infections in the naïve host Montifringilla nivalis subsp nivalis. J. Ornithol. 163, 333–337 (2022).Article 

Google Scholar 
Tulloch, A. I. T., Possingham, H. P., Joseph, L. N., Szabo, J. & Martin, T. G. Realising the full potential of citizen science monitoring programs. Biol. Conserv. 165, 128–138 (2013).Article 

Google Scholar 
Silvertown, J., Buesching, C., Jacobson, S. & Rebelo, T. Citizen science and nature conservation. in Key Topics in Conservation Biology 2 (eds. Macdonald, D. W. & Willis, K. J.) 127–142 (John Wiley & Sons, 2013).Dickinson, J. L., Zuckerberg, B. & Bonter, D. N. Citizen science as an ecological research tool: Challenges and benefits. Annu. Rev. Ecol. Evol. Syst. 41, 149–172 (2010).Article 

Google Scholar 
Baillie, S. R., Wernham, C. V. & Clark, J. A. Development of the British and Irish ringing scheme and its role in conservation biology. Ringing Migr. 19, S5–S19 (1999).Article 

Google Scholar 
Greenwood, J. J. D. Citizens, science and bird conservation. J. Ornithol. 148, S77–S124 (2007).Article 

Google Scholar 
Horns, J. J., Adler, F. R. & Şekercioğlu, Ç. H. Using opportunistic citizen science data to estimate avian population trends. Biol. Conserv. 221, 151–159 (2018).Article 

Google Scholar 
Ryan, R. L., Kaplan, R. & Grese, R. E. Predicting volunteer commitment in environmental stewardship programmes. J. Environ. Plan. Manag. 44, 629–648 (2001).Article 

Google Scholar 
Maund, P. R. et al. What motivates the masses: Understanding why people contribute to conservation citizen science projects. Biol. Conserv. 246, 108587 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Martin, V. Y. & Greig, E. I. Young adults’ motivations to feed wild birds and influences on their potential participation in citizen science: An exploratory study. Biol. Conserv. 235, 295–307 (2019).Article 

Google Scholar 
Cox, D. T. C. & Gaston, K. J. Human–nature interactions and the consequences and drivers of provisioning wildlife. Philos.Trans. R. Soc. B Biol. Sci. 373, 20170092 (2018).Article 

Google Scholar 
Murray, M. H., Becker, D. J., Hall, R. J. & Hernandez, S. M. Wildlife health and supplemental feeding: A review and management recommendations. Biol. Conserv. 204, 163–174 (2016).Article 

Google Scholar 
Rocha, G. & Quillfeldt, P. Effect of supplementary food on age ratios of European turtle doves (Streptopelia turtur L.). Anim. Biodivers. Conserv. 38, 11–21 (2015).Article 

Google Scholar  More

Dubois, S. et al. International consensus principles for ethical wildlife control. Conserv. Biol. 31(4), 753–760 (2017).PubMed 
Article 

Google Scholar 
Frank, B. & Glikman, J. A. Human–wildlife conflicts and the need to include coexistence. In Human–Wildlife Interactions (eds Frank, B. et al.) 1–19 (Cambridge University Press, 2019).
Google Scholar 
Meng, X. J., Lindsay, D. S. & Sriranganathan, N. Wild boars as sources for infectious diseases in livestock and humans. Philos. Trans. R. Soc. B Biol. Sci. 364, 2697–2707 (2009).CAS 
Article 

Google Scholar 
Massei, G., Roy, S. & Bunting, R. Too many hogs? A review of methods to mitigate impact by wild boar and feral hogs. Hum. Wildl. Interact. 5, 79–99 (2011).
Google Scholar 
Carpio, A. J., Apollonio, M. & Acevedo, P. Wild ungulate overabundance in Europe: Contexts, causes, monitoring and management recommendations. Mamm. Rev. 51, 95–108 (2021).Article 

Google Scholar 
Stillfried, M. et al. Secrets of success in a landscape of fear: Urban wild boar adjust risk perception and tolerate disturbance. Front. Ecol. Evol. 5, 157 (2017).Article 

Google Scholar 
Castillo-Contreras, R. et al. Urban wild boars prefer fragmented areas with food resources near natural corridors. Sci. Total Environ. 615, 282–288 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Keuling, O., Strauß, E. & Siebert, U. Regulating wild boar populations is ‘somebody else’s problem’!—Human dimension in wild boar management. Sci. Total Environ. 554–555, 311–319 (2016).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Vajas, P. et al. Many, large and early: Hunting pressure on wild boar relates to simple metrics of hunting effort. Sci. Total Environ. 698, 134251. https://doi.org/10.1016/j.scitotenv.2019.134251 (2020).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Licoppe, A. et al. Wild boar/feral pig in (peri-)urban areas. Managing wild boar in human-dominated landscapes. in International Union of Game Biologists (IUGB)—Congress IUGB 2013, 1–31 (2013).Torres-Blas, I. et al. Assessing methods to live-capture wild boars (Sus scrofa) in urban and peri-urban environments. Vet. Rec. 187, e85. https://doi.org/10.1136/vr.105766 (2020).Article 
PubMed 

Google Scholar 
Adams, C. E. Urban Wildlife Management (CRC Press, 2016).
Google Scholar 
Conejero, C. et al. Past experiences drive citizen perception of wild boar in urban areas. Mamm. Biol. 96, 68–72 (2019).Article 

Google Scholar 
Lewis, J. S., VerCauteren, K. C., Denkhaus, R. M. & Mayer, J. J. Wild pig populations along the urban gradient. In Invasive Wild Pigs in North America (eds VerCauteren, K. C. et al.) 439–463 (CRC Press, 2019).Chapter 

Google Scholar 
Massei, G. et al. Effect of the GnRH vaccine GonaCon on the fertility, physiology and behaviour of wild boar. Wildl. Res. 35, 540–547 (2008).CAS 
Article 

Google Scholar 
Náhlik, A. et al. Wild boar management in Europe: Knowledge and practice. In Ecology, Conservation and Management of Wild Pigs and Peccaries (eds Melletti, M. & Meijaard, E.) 339–353 (Cambridge University Press, 2017).Chapter 

Google Scholar 
Croft, S., Franzetti, B., Gill, R. & Massei, G. Too many wild boar? Modelling fertility control and culling to reduce wild boar numbers in isolated populations. PLoS One 15, e0238429. https://doi.org/10.1371/journal.pone.0238429 (2020).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
González-Crespo, C. et al. Stochastic assessment of management strategies for a Mediterranean peri-urban wild boar population. PLoS One 13, e0202289. https://doi.org/10.1371/journal.pone.0202289 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Schemnitz, S. D., Batcheller, G. R., Lovallo, M. J., White, H. B. & Fall, M. W. Capturing and handling wild animals. In Research and Management Techniques for Wildlife and Habitats (ed. Silvy, N. J.) 232–269 (John Hopkins University Press, 2009).
Google Scholar 
ECGCGRF (European Community, Government of Canada, and Government of the Russian Federation). Agreement on international humane trapping standards. Off. J. Eur. Communities 42, 43–57 (1997).
Google Scholar 
Anonymous. International agreement in the form of an agreed minute between the European Community and the United States of America on humane trapping standards. Off. J. Eur. Communities L219, 26–37 (1998).
Google Scholar 
ISO 10990-4. Methods for testing killing trap systems used on land and underwater. in Animal (Mammal) Traps—Part 4 (International Organization for Standardization, 1999).ISO 10990-5. Methods for testing restraining traps. in Animal (Mammal) Traps—Part 5 (International Organization for Standardization, 1999).Proulx, G., Cattet, M., Serfass, T. L. & Baker, S. E. Updating the AIHTS trapping standards to improve animal welfare and capture efficiency and selectivity. Animals 10, 1–26 (2020).Article 

Google Scholar 
Proulx, G. Mammal Trapping—Wildlife Management, Animal Welfare and International Standards (Alpha Wildlife Publications, 2022).
Google Scholar 
Iossa, G., Soulsbury, C. & Harris, S. Mammal trapping: A review of animal welfare standards of killing and restraining traps. Anim. Welf. 16, 335–352 (2007).CAS 

Google Scholar 
Muñoz-Igualada, J., Shivik, J. A., Domínguez, F. G., Lara, J. & González, L. M. Evaluation of cage-traps and cable restraint devices to capture red foxes in Spain. J. Wildl. Manag. 72, 830–836 (2008).Article 

Google Scholar 
Trap Research and Development Committee. Best Trapping Practices (Fur Institute of Canada, 2018).
Google Scholar 
Virgós, E. et al. A poor international standard for trap selectivity threatens global carnivore and biodiversity conservation. Biodivers. Conserv. 25, 1409–1419 (2016).Article 

Google Scholar 
Barasona, J. A., López-Olvera, J. R., Beltrán-Beck, B., Gortázar, C. & Vicente, J. Trap-effectiveness and response to tiletamine-zolazepam and medetomidine anaesthesia in Eurasian wild boar captured with cage and corral traps. BMC Vet. Res. 9, 107 (2013).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Shury, T. Physical capture and restraint. In Zoo Animal and Wildlife Immobilization and Anesthesia (eds West, G. et al.) 109–124 (Wiley Blackwell, 2015).
Google Scholar 
Webb, S. L., Lewis, J. S., Hewitt, D. G., Hellickson, M. W. & Bryant, F. C. Assessing the helicopter and net gun as a capture technique for white-tailed deer. J. Wildl. Manag. 72, 310–314 (2008).Article 

Google Scholar 
López-Olvera, J. R. et al. Comparative evaluation of effort, capture and handling effects of drive nets to capture roe deer (Capreolus capreolus), Southern chamois (Rupicapra pyrenaica) and Spanish ibex (Capra pyrenaica). Eur. J. Wildl. Res. 55, 193–202 (2009).Article 

Google Scholar 
Breed, D. et al. Conserving wildlife in a changing world: Understanding capture myopathy—A malignant outcome of stress during capture and translocation. Conserv. Physiol. 7, 1–21 (2019).Article 
CAS 

Google Scholar 
Mentaberre, G. et al. Azaperone and sudden death of drive net-captured southern chamois. Eur. J. Wildl. Res. 58, 489–493 (2012).Article 

Google Scholar 
Gaskamp, J. A., Gee, K. L., Campbell, T. A., Silvy, N. J. & Webb, S. L. Effectiveness and efficiency of corral traps, drop nets and suspended traps for capturing wild pigs (Sus scrofa). Animals 11, 1565 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Baker, S. E., Macdonald, D. W. & Ellwood, S. A. Double standards in spring trap welfare. In Proceedings of the Ninth International Conference on Urban Pests (eds Daivies, C. & Pfeiffer, W. H.) 139–145 (Pureprint Group, 2017).
Google Scholar 
López-Olvera, J. R., Castillo-Contreras, R., González-Crespo, C., Conejero, C. & Mentaberre, G. Wild boar is not welcome in the city. Barcelona Metròpolis 103, 22–23 (2017).
Google Scholar 
Conejero, C. et al. Conflicto o habituación: las dos caras de la percepción social del jabalí urbano. in Proceedings of XIV Congreso de la Sociedad Española para la Conservación y Estudio de los Mamíferos (SECEM, 2019).Conferencia Sectorial de Medio Ambiente. Directrices Técnicas para la Captura de Especies Cinegéticas Predadoras: Homologación de Métodos y Acreditación de Usuarios (Ministerio para la Transición Ecológica y el Reto Demográfico de España, 2011).Generalitat de Catalunya—Government of Catalonia. Decret 56/2014 relatiu a l’homologació de mètodes de captura en viu d’espècies cinegètiques depredadores i d’espècies exòtiques invasores depredadores i l’acreditació de les persones que en són usuàries. Diari Oficial de la Generalitat de Catalunya 6609 (2014).Fahlman, Å. et al. Wild boar behaviour during live-trap capture in a corral-style trap: Implications for animal welfare. Acta Vet. Scand. 62, 1–11 (2020).Article 

Google Scholar 
Sharp, T. & Saunders, G. A Model for Assessing the Relative Humaneness of Pest Animal Control Methods (Australian Government—Department of Agriculture, Fisheries and Forestry [New Millennium Print], 2011).
Google Scholar 
Ziegler, L., Fischer, D., Nesseler, A. & Lierz, M. Validation of the live trap ‘Krefelder Fuchsfalle’ in combination with electronic trap sensors based on AIHTS standards. Eur. J. Wildl. Res. 64, 17 (2018).Article 

Google Scholar 
Marco, I. et al. Capture myopathy in little bustards after trapping and marking. J. Wildl. Dis. 42, 889–891 (2006).ADS 
PubMed 
Article 

Google Scholar 
Rideout, C. B. Comparison of techniques for capturing mountain goats. J. Wildl. Manag. 38, 573 (1974).Article 

Google Scholar 
Jedrzejewski, W. & Kamler, J. F. Modified drop-net for capturing ungulates. Wildl. Soc. Bull. 32, 1305–1308 (2004).Article 

Google Scholar 
Gaskamp, J. A. Use of drop-nets for wild pig damage and disease abatement. Master’s thesis, available electronically from https://hdl.handle.net/1969.1/148198 (Texas A&M University, 2012).Lavelle, M. J. et al. When pigs fly: Reducing injury and flight response when capturing wild pigs. Appl. Anim. Behav. Sci. 215, 21–25 (2019).Article 

Google Scholar 
Masilkova, M. et al. Observation of rescue behaviour in wild boar (Sus scrofa). Sci. Rep. 11, 16217 (2021).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Podgórski, T. et al. Spatiotemporal behavioral plasticity of wild boar (Sus scrofa) under contrasting conditions of human pressure: Primeval forest and metropolitan area. J. Mammal. 94, 109–119 (2013).Article 

Google Scholar 
Manfredo, M., Teel, T. & Bright, A. Why are public values toward wildlife changing?. Hum. Dimens. Wildl. 8, 287–306 (2003).Article 

Google Scholar 
Cahill, S., Llimona, F., Cabañeros, L. & Calomardo, F. Characteristics of wild boar (Sus scrofa) habituation to urban areas in the Collserola Natural Park (Barcelona) and comparison with other locations. Anim. Biodivers. Conserv. 35, 221–233 (2012).Article 

Google Scholar  More

Rapacciuolo, G. & Blois, J. L. Understanding ecological change across large spatial, temporal and taxonomic scales: Integrating data and methods in light of theory. Ecography 42, 1247–1266 (2019).
Google Scholar 
Cowles, H. C. The ecological relations of the vegetation on the sand dunes of Lake Michigan. Part I. Geographical relations of the Dune Floras. Bot. Gaz. 27, 95–117 (1899).Article 

Google Scholar 
Gleason, H. A. The individualistic concept of the plant association. Bull. Torrey Bot. Club 53, 7–26 (1926).Article 

Google Scholar 
Denslow, J. S. Patterns of plant species diversity during succession under different disturbance regimes. Oecologia 46, 18–21 (1980).ADS 
PubMed 
Article 

Google Scholar 
Budowski, G. Studies on Forest Succession in Costa Rica und Panama. Ph.D. Thesis, Yale University, New Haven (1961).Opler, P. A., Baker, H. G. & Frankie, G. W. Plant reproductive characteristics during secondary succession in neotropical lowland forest ecosystems. Biotropica 12, 40–46 (1980).Article 

Google Scholar 
Clements, F. E. Plant Succession: An Analysis of Development in Vegetation (Carnegie Institute, Washington, 1916).Book 

Google Scholar 
Grigg, R. W. & Maragos, J. E. Recolonization of hermatypic corals on submerged lava flows in Hawaii. Ecology 55, 387–395 (1974).Article 

Google Scholar 
Tomascik, T., Van Woesik, R. & Mah, A. J. Rapid coral colonization of a recent lava flow following a volcanic eruption, Banda Islands, Indonesia. Coral Reefs 15, 169–175 (1996).ADS 
Article 

Google Scholar 
McClanahan, T. R. Primary succession of coral-reef algae: Differing patterns on fished versus unfished reefs. J. Exp. Mar. Biol. Ecol. 218, 77–102 (1997).Article 

Google Scholar 
Reaka-Kudia, M. L. The global biodiversity of coral reefs: A comparison with rain forests. In Biodiversity II: Understanding and Proteting our Biological Resources (eds Reaka-Kudla, M. et al.) 83–108 (Joseph Henry Press, 1997).
Google Scholar 
Ginsburg, R. N. Geological and biological roles of cavities in coral reefs. In Perspectives on Coral Reefs (ed. Barnes, D. J.) 148–153 (Australian Institute of Marine Science, Manuka, A.C.T., Australia, 1983).Fautin, D. et al. An overview of marine biodiversity in United States waters. PLoS ONE 5, e11914 (2010).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Pearman, J. K., Anlauf, H., Irigoien, X. & Carvalho, S. Please mind the gap—Visual census and cryptic biodiversity assessment at central Red Sea coral reefs. Mar. Environ. Res. 118, 20–30 (2016).CAS 
PubMed 
Article 

Google Scholar 
Kobluk, D. R. & Van Soest, R. W. M. Cavity-dwelling sponges in a southern Caribbean coral reef and their paleontological implications. Bull. Mar. Sci. 44, 1207–1235 (1989).
Google Scholar 
Richter, C. & Wunsch, M. Cavity-dwelling suspension feeders in coral reefs – A new link in reef trophodynamics. Mar. Ecol. Prog. Ser. 188, 105–116 (1999).ADS 
CAS 
Article 

Google Scholar 
Wunsch, M., Al-Moghrabi, S. M. & Kötter, I. Communities of coral reef Cavities in Jordan, Gulf of Aqaba (Red Sea). In Proceedings of 9th International Coral Reef Symposium, Vol. 1 (2000).Kornder, N. A. et al. Implications of 2D versus 3D surveys to measure the abundance and composition of benthic coral reef communities. Coral Reefs 40, 1137–1153 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Richter, C., Wunsch, M., Rasheed, M., Kötter, I. & Badran, M. I. Endoscopic exploration of Red Sea coral reefs reveals dense populations of cavity-dwelling sponges. Nature 413, 726–730 (2001).ADS 
CAS 
PubMed 
Article 

Google Scholar 
De Goeij, J. M. & Van Duyl, F. C. Coral cavities are sinks of dissolved organic carbon (DOC). Limnol. Oceanogr. 52, 2608–2617 (2007).ADS 
Article 

Google Scholar 
Slattery, M., Gochfeld, D. J., Easson, C. G. & O’Donahue, L. R. K. Facilitation of coral reef biodiversity and health by cave sponge communities. Mar. Ecol. Prog. Ser. 476, 71–86 (2013).ADS 
Article 

Google Scholar 
McMurray, S. E., Stubler, A. D., Erwin, P. M., Finelli, C. M. & Pawlik, J. R. A test of the sponge-loop hypothesis for emergent Caribbean reef sponges. Mar. Ecol. Prog. Ser. 588, 1–14 (2018).ADS 
CAS 
Article 

Google Scholar 
De Goeij, J. M., Van Den Berg, H., Van Oostveen, M. M., Epping, E. H. G. & Van Duyl, F. C. Major bulk dissolved organic carbon (DOC) removal by encrusting coral reef cavity sponges. Mar. Ecol. Prog. Ser. 357, 139–151 (2008).ADS 
Article 
CAS 

Google Scholar 
De Goeij, J. M. et al. Surviving in a marine desert: The sponge loop retains resources within coral reefs. Science (80-) 342, 108–110 (2013).ADS 
Article 
CAS 

Google Scholar 
Rix, L. et al. Reef sponges facilitate the transfer of coral-derived organic matter to their associated fauna via the sponge loop. Mar. Ecol. Prog. Ser. 589, 85–96 (2018).ADS 
CAS 
Article 

Google Scholar 
De Goeij, J. M., Lesser, M. P. & Pawlik, J. R. Nutrient fluxes and ecological functions of coral reef sponges in a changing ocean. In Climate Change, Ocean Acidification and Sponges: Impacts Across Multiple Levels of Organization (Springer, 2017). https://doi.org/10.1007/978-3-319-59008-0_8.Choi, D. R. Ecological succession of reef cavity-dwellers (coelobites) in coral rubble. Bull. Mar. Sci. 35, 72–79 (1984).
Google Scholar 
Jackson, J. B. C. Competition on marine hard substrata: The adaptive significance of solitary and colonial strategies. Am. Nat. 111, 743–767 (1977).Article 

Google Scholar 
Kobluk, D. R. Cryptic faunas in reefs: Ecology and geologic importance. Palaios 3, 379–390 (1988).ADS 
Article 

Google Scholar 
Hooper, J. N. A. & Van Soest, R. W. M. Class Demospongiae Sollas, 1885. In Systema Porifera (2002). https://doi.org/10.1007/978-1-4615-0747-5_3.Rützler, K. The role of sponges in the mesoamerican barrier-reef ecosystem, Belize. Adv. Mar. Biol. 61, 211–271 (2012).PubMed 
Article 

Google Scholar 
Wulff, J. Ecological interactions and the distribution, abundance, and diversity of sponges. Adv. Mar. Biol. 61, 273–344 (2012).PubMed 
Article 

Google Scholar 
Riesgo, A. et al. Inferring the ancestral sexuality and reproductive condition in sponges (Porifera). Zool. Scr. 43, 101–117 (2014).Article 

Google Scholar 
Pawlik, J. R., Chanas, B., Toonen, R. J. & Fenical, W. Defenses of Caribbean sponges against predatory reef fish. I. Chemical deterrency. Mar. Ecol. Prog. Ser. 127, 183–194 (1995).ADS 
CAS 
Article 

Google Scholar 
Leong, W. & Pawlik, J. R. Evidence of a resource trade-off between growth and chemical defenses among Caribbean coral reef sponges. Mar. Ecol. Prog. Ser. 406, 71–78 (2010).ADS 
Article 

Google Scholar 
Maldonado, M. & Bergquist, P. R. Phylum porifera. In Atlas of Marine Invertebrates (ed. Young, C.) 21–50 (Academic, 2002).
Google Scholar 
Lanna, E. & Klautau, M. Life history and reproductive dynamics of the cryptogenic calcareous sponge Sycettusa hastifera (Porifera, Calcarea) living in tropical rocky shores. J. Mar. Biol. Assoc. U. K. 98, 505–514 (2018).Article 

Google Scholar 
Lanna, E., Monteiro, L. C. & Klautau, M. Life cycle of Paraleucilla magna Klautau, Monteiro and Borojevic, 2004 (Porifera, Calcarea). In Porifera Research: Biodiversity, Innovation and Sustainability 413–418 (2007).Calazans, V. P. S. B. & Lanna, E. Influence of endogenous and exogenous factors on the reproductive output of a cryptogenic calcareous sponge. Mar. Biodivers. 49, 2837–2850 (2019).Article 

Google Scholar 
Zimmerman, T. L. & Martin, J. W. Artificial reef matrix structures (ARMS): An inexpensive and effective method for collecting coral reef-associated invertebrates. Gulf Caribb. Res. 16, 59–64 (2004).Article 

Google Scholar 
Brainard, R. et al. Autonomous reef monitoring structures (ARMS): A tool for monitoring indices of biodiversity in the Pacific Islands. In 11th Pacific Science Inter-Congress, Papeete, Tahiti (2009).Knowlton, N. et al. Coral reef biodiversity. In Life in the World’s Oceans: Diversity, Distribution, and Abundance 65–74 (2010). https://doi.org/10.1002/9781444325508.ch4.Timmers, M. A., Vicente, J., Webb, M., Jury, C. P. & Toonen, R. J. Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community. Environ. DNA https://doi.org/10.1002/edn3.163 (2020).Article 

Google Scholar 
Vicente, J. et al. Unveiling hidden sponge biodiversity within the Hawaiian reef cryptofauna. Coral Reefs https://doi.org/10.1007/s00338-021-02109-7 (2021).Article 

Google Scholar 
Grottoli, A. G. et al. Increasing comparability among coral bleaching experiments. Ecol. Appl. 31, e02262 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rodgers, K. S., Jokiel, P. L., Brown, E. K., Hau, S. & Sparks, R. Over a decade of change in spatial and temporal dynamics of Hawaiian coral reef communities. Pac. Sci. 69, 1–13 (2015).Article 

Google Scholar 
Franklin, E. C., Jokiel, P. L. & Donahue, M. J. Predictive modeling of coral distribution and abundance in the Hawaiian Islands. Mar. Ecol. Prog. Ser. 481, 121–132 (2013).ADS 
Article 

Google Scholar 
Jury, C. et al. Experimental reef communities persist under future ocean acidification and warming. Res. Sq. (2021).Gorospe, K. D. et al. Local biomass baselines and the recovery potential for Hawaiian coral reef fish communities. Front. Mar. Sci. 5, 162 (2018).Article 

Google Scholar 
Timmers, M. A. et al. Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification. Proc. Natl. Acad. Sci. 118(39), e2103275118 (2021).
Wörheide, G. & Erpenbeck, D. DNA taxonomy of sponges—Progress and perspectives. J. Mar. Biol. Assoc. U. K. 87, 1629–1633 (2007).Article 
CAS 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (2020). https://doi.org/10.1017/CBO9781107415324.004.Oksanen, J. et al. Package vegan. Community Ecology Packaging version 2, 1-295 (2013).Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D. & Team, R. C. nlme: Linear and nonlinear mixed effects models (2020).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 
Lenth, R. V. Least-squares means: The R package. J. Stat. Softw. 69, 1–33 (2016).Article 

Google Scholar 
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).MATH 
Book 

Google Scholar 
Ribeiro, B., Padua, A., Paiva, P. C., Custódio, M. R. & Klautau, M. Exploitation of micro refuges and epibiosis: Survival strategies of a calcareous sponge. J. Mar. Biol. Assoc. U. K. 98, 495–503 (2018).Article 

Google Scholar 
Bahr, K. D., Jokiel, P. L. & Toonen, R. J. The unnatural history of Kāne’ohe bay: Coral reef resilience in the face of centuries of anthropogenic impacts. PeerJ 3, e950 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Byrne, M. Impact of ocean warming and ocean acidification on marine invertebrate life history stages: Vulnerabilities and potential for persistence in a changing ocean. Oceanogr. Mar. Biol. Annu. Rev. 49, 1–42 (2011).
Google Scholar 
Barnes, D. K. A., Ashton, G. V., Morley, S. A. & Peck, L. S. 1 °C warming increases spatial competition frequency and complexity in Antarctic marine macrofauna. Commun. Biol. 4, 1–7 (2021).Article 

Google Scholar 
Maldonado, M., Giraud, K. & Carmona, C. Effects of sediment on the survival of asexually produced sponge recruits. Mar. Biol. 154, 631–641 (2008).CAS 
Article 

Google Scholar 
Eckman, J. E. Hydrodynamic processes affecting benthic recruitment. Limnol. Oceanogr. 28, 241–257 (1983).ADS 
Article 

Google Scholar 
Palardy, J. E. & Witman, J. D. Water flow drives biodiversity by mediating rarity in marine benthic communities. Ecol. Lett. 14, 63–68 (2011).PubMed 
Article 

Google Scholar 
Falter, J. L., Atkinson, M. J. & Merrifield, M. A. Mass-transfer limitation of nutrient uptake by a wave-dominated reef flat community. Limnol. Oceanogr. 49, 1820–1831 (2004).ADS 
CAS 
Article 

Google Scholar 
Sale, P. F. Coexistence of coral reef fishes—A lottery for living space. Environ. Biol. Fish. 3, 85–102 (1978).Article 

Google Scholar 
Karlson, R. H. & Jackson, J. B. C. Competitive networks and community structure: A simulation study. Ecology 62, 670–678 (1981).Article 

Google Scholar 
Hixon, M. A. Predation as a process structuring coral reef fish communities. In The Ecology of Fishes on Coral Reefs (1991). https://doi.org/10.1016/b978-0-08-092551-6.50022-2.Hobson, E. S. Feeding patterns among tropical reef fishes. Am. Sci. 63, 382–392 (1975).ADS 

Google Scholar 
Bailey-Brock, J. H. Fouling community development on an artificial reef in Hawaiian waters. Bull. Mar. Sci. 44, 580–591 (1989).
Google Scholar 
Vicente, J., Toonen, R. J. & Bowen, B. W. Hawaiian green turtles graze on bioeroding sponges at Maunalua Bay, O‘ahu, Hawai‘i, Galaxea. J. Coral Reef Stud. 21, 3–4 (2019).Article 

Google Scholar 
Vicente, J., Osberg, A., Marty, M. J., Rice, K. & Toonen, R. J. Influence of sponge palatability on the feeding preferences of the endemic Hawaiian tiger cowrie for indigenous and introduced sponges. Mar. Ecol. Prog. Ser. 647, 109–122 (2020).ADS 
Article 

Google Scholar 
Klumpp, D., McKinnon, A. & Mundy, C. Motile cryptofauna of a coral reef: Abundance, distribution and trophic potential. Mar. Ecol. Prog. Ser. 45, 95–108 (1988).ADS 
Article 

Google Scholar 
Carpenter, R. C. Invertebrate predators and grazers. In Life and Death of Coral Reefs (1997). https://doi.org/10.1007/978-1-4615-5995-5_9.Glynn, P. W. & Enochs, I. C. Invertebrates and their roles in coral reef ecosystems. In Coral Reefs: An Ecosystem in Transition (2011). https://doi.org/10.1007/978-94-007-0114-4_18.Ďuriš, Z., Horká, I., Juračka, P. J., Petrusek, A. & Sandford, F. These squatters are not innocent: The evidence of parasitism in Sponge-Inhabiting shrimps. PLoS ONE 6, e21987 (2011).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Pawlik, J. R. A sponge-eating worm from Bermuda: Branchiosyllis oculata (Polychaeta, Syllidae). Mar. Ecol. 4, 65–79 (1983).ADS 
Article 

Google Scholar 
Degoeij, J. M. et al. Cell kinetics of the marine sponge Halisarca caerulea reveal rapid cell turnover and shedding. J. Exp. Biol. 212, 3892–3900 (2009).CAS 
Article 

Google Scholar 
Alexander, B. E. et al. Cell turnover and detritus production in marine sponges from tropical and temperate benthic ecosystems. PLoS ONE 9, e109486 (2014).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bart, M. C., Hudspith, M., Rapp, H. T., Verdonschot, P. F. M. & de Goeij, J. M. A deep-sea sponge loop? Sponges transfer dissolved and particulate organic carbon and nitrogen to associated fauna. Front. Mar. Sci. 8, 604879 (2021).Article 

Google Scholar 
Pawlik, J. R. & McMurray, S. E. The emerging ecological and biogeochemical importance of sponges on coral reefs. Annu. Rev. Mar. Sci. 12, 315–337 (2020).ADS 
Article 

Google Scholar 
Brandl, S. J. et al. Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning. Science (80-). 364, 1189–1192 (2019).ADS 
CAS 
Article 

Google Scholar 
Buss, L. W. & Jackson, J. B. C. Competitive networks: Nontransitive competitive relationships in cryptic coral reef environments. Am. Nat. 113, 223–234 (1979).Article 

Google Scholar 
Vicente, J., Ríos, J. A., Zea, S. & Toonen, R. J. Molecular and morphological congruence of three new cryptic Neopetrosia spp in the Caribbean. PeerJ 7, e6371–e6381 (2019).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar  More

Izdebski, A. et al. Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic. Nat. Ecol. Evol. 6, 297–306 (2022).CAS 
Article 

Google Scholar 
Benedictow, O. J. The Complete History of the Black Death (The Boydell Press, 2021).Palermo, L. Mercati del Grano a Roma tra Medioevo e Rinascimento. Il Mercato Distrettuale del Grano in Età Comunale (Istituto Nazionale di Studi Romani, 1990).Cortonesi, A. I cereali nell’Italia del tardo medioevo. Note sugli aspetti qualitativi del consumo. Riv. Stor. Agricol. 37, 3–30 (1997).
Google Scholar 
Nanni, P. in The Crisis of the 14th Century. Teleconnections Between Environmental and Societal Change? (eds Bauch M. & Schenk G. J.) 169–189 (De Gruyter, 2020).Lagerås, P. Environment, Society and the Black Death: An Interdisciplinary Approach to the Late-Medieval Crisis in Sweden (Oxbow Books, 2016).Roosen, J. & Curtis, D. The ‘light touch’ of the Black Death in the southern Netherlands: an urban trick? Econ. Hist. Rev. 72, 32–56 (2019).Article 

Google Scholar 
Preiser-Kapeller, J. Der Lange Sommer und die Kleine Eiszeit: Klima, Pandemien und der Wandel der Alten Welt 500–1500 n. Chr. (Mandelbaum, 2021).Sadori, L. The Lateglacial and Holocene vegetation and climate history of Lago di Mezzano (central Italy). Quat. Sci. Rev. 202, 30–44 (2018).Article 

Google Scholar 
Cortonesi, A. Ruralia. Economie e Paesaggi del Medioevo Italiano (Il Calamo, 1995).Cortonesi, A. L’olivo nell’Italia medievale. Reti Medievali Riv. 6, 1–29 (2005).
Google Scholar 
Mensing, S. A. et al. Historical ecology reveals landscape transformation coincident with cultural development in central Italy since the Roman Period. Sci. Rep. 8, 2138 (2018).Article 

Google Scholar 
Cortonesi, A. in Il Paesaggio Agrario Italiano Medievale: Storia e Didattica, 113–120 (Istituto Alcide Cervi, 2011). More

Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jackson, R. B. et al. The ecology of soil carbon: pools, vulnerabilities, and biotic and abiotic controls. Annu. Rev. Ecol. Evol. Syst. 48, 419–445 (2017).Article 

Google Scholar 
Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).CAS 
PubMed 
Article 

Google Scholar 
Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853–858 (2000).CAS 
PubMed 
Article 

Google Scholar 
IPCC. Climate Change 2021: The Physical Science Basis. (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press, in press).Mora, C. et al. The projected timing of climate departure from recent variability. Nature 502, 183–187 (2013).Wood, T. E. et al. in Ecosystem Consequences of Soil Warming: Microbes, Vegetation, Fauna and Soil Biogeochemistry (ed. Mohan, J.) Ch. 14 (Academic Press, 2019).Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173 (2006).CAS 
PubMed 
Article 

Google Scholar 
van Gestel, N. et al. Predicting soil carbon loss with warming. Nature 554, E4–E5 (2018).PubMed 
Article 
CAS 

Google Scholar 
Melillo, J. M. et al. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 358, 101–104 (2017).CAS 
PubMed 
Article 

Google Scholar 
Romero-Olivares, A. L., Allison, S. D. & Treseder, K. K. Soil microbes and their response to experimental warming over time: a meta-analysis of field studies. Soil Biol. Biochem. 107, 32–40 (2017).CAS 
Article 

Google Scholar 
Anderson-Teixeira, K. J., Wang, M. M. H., McGarvey, J. C. & LeBauer, D. S. Carbon dynamics of mature and regrowth tropical forests derived from a pantropical database (TropForC-db). Glob. Change Biol. 22, 1690–1709 (2016).Article 

Google Scholar 
Nottingham, A. T., Meir, P., Velasquez, E. & Turner, B. L. Soil carbon loss by experimental warming in a tropical forest. Nature 584, 234–237 (2020).CAS 
PubMed 
Article 

Google Scholar 
Kimball, B. A. et al. Infrared heater system for warming tropical forest understory plants and soils. Ecol. Evol. 8, 1932–1944 (2018).DeAngelis, K. M. et al. Long-term forest soil warming alters microbial communities in temperate forest soils. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00104 (2015)Bååth, E. Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation. Glob. Change Biol. 24, 2850–2861 (2018).Article 

Google Scholar 
Wieder, W. R., Bonan, G. B. & Allison, S. D. Global soil carbon projections are improved by modelling microbial processes. Nat. Clim. Change 3, 909–912 (2013).CAS 
Article 

Google Scholar 
Ratkowsky, D. A., Olley, J., Mcmeekin, T. A. & Ball, A. Relationship between temperature and growth-rate of bacterial cultures. J. Bacteriol. 149, 1–5 (1982).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rinnan, R., Rousk, J., Yergeau, E., Kowalchuk, G. A. & Bååth, E. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming. Glob. Change Biol. 15, 2615–2625 (2009).Article 

Google Scholar 
Nottingham, A. T., Bååth, E., Reischke, S., Salinas, N. & Meir, P. Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes. Glob. Change Biol. https://doi.org/10.1111/gcb.14502 (2019).Li, J. Q., Bååth, E., Pei, J. M., Fang, C. M. & Nie, M. Temperature adaptation of soil microbial respiration in alpine, boreal and tropical soils: an application of the square root (Ratkowsky) model. Glob. Change Biol. 27, 1281–1292 (2021).CAS 
Article 

Google Scholar 
Rousk, J., Frey, S. D. & Bååth, E. Temperature adaptation of bacterial communities in experimentally warmed forest soils. Glob. Change Biol. 18, 3252–3258 (2012).Article 

Google Scholar 
Nottingham, A. T. et al. Annual to decadal temperature adaptation of the soil bacterial community after translocation across an elevation gradient in the Andes. Soil Biol. Biochem. 158, 108217 (2021).CAS 
Article 

Google Scholar 
Nottingham, A. T. et al. Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient. Ecol. Lett. 22, 1889–1899 (2019).PubMed 
Article 

Google Scholar 
Donhauser, J., Niklaus, P. A., Rousk, J., Larose, C. & Frey, B. Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils. Soil Biol. Biochem. 148, 107873 (2020).CAS 
Article 

Google Scholar 
Mangan, S. A. et al. Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466, 752–755 (2010).Pold, G., Melillo, J. M. & DeAngelis, K. M. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00480 (2015).Zhou, J. Z. et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat. Commun. 7, 12083 (2016).Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).Wu, L. et al. Reduction of microbial diversity in grassland soil is driven by long-term climate warming. Nat. Microbiol. 7, 1054–1062 (2022).Oliverio, A. M., Bradford, M. A. & Fierer, N. Identifying the microbial taxa that consistently respond to soil warming across time and space. Glob. Change Biol. 23, 2117–2129 (2017).Article 

Google Scholar 
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).CAS 
PubMed 
Article 

Google Scholar 
Spracklen, D. V., Baker, J. C. A., Garcia-Carreras, L. & Marsham, J. H. The effects of tropical vegetation on rainfall. Annu. Rev. Env. Resour. 43, 193–218 (2018).Article 

Google Scholar 
Bradford, M. A. Thermal adaptation of decomposer communities in warming soils. Front. Microbiol. https://doi.org/10.3389/Fmicb.2013.00333 (2013).Pietikäinen, J., Pettersson, M. & Bååth, E. Comparison of temperature effects on soil respiration and bacterial and fungal growth rates. FEMS Microbiol. Ecol. 52, 49–58 (2005).PubMed 
Article 
CAS 

Google Scholar 
Mori, A. S. et al. Biodiversity–productivity relationships are key to nature-based climate solutions. Nat. Clim. Change 11, 543–550 (2021).Article 

Google Scholar 
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).PubMed 
Article 

Google Scholar 
Wagg, C., Bender, S. F., Widmer, F. & van der Heijden, M. G. A. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc. Natl Acad. Sci. USA 111, 5266–5270 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Nottingham, A. T. et al. Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes. Ecology 99, 2455–2466 (2018).PubMed 
Article 

Google Scholar 
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).Article 

Google Scholar 
Brown, J. H. Why are there so many species in the tropics? J. Biogeogr. 41, 8–22 (2014).PubMed 
Article 

Google Scholar 
LaManna, J. A. et al. Plant diversity increases with the strength of negative density dependence at the global scale. Science 356, 1389–1392 (2017).CAS 
PubMed 
Article 

Google Scholar 
Bagchi, R. et al. Pathogens and insect herbivores drive rainforest plant diversity and composition. Nature 506, 85–88 (2014).CAS 
PubMed 
Article 

Google Scholar 
Lapebie, P., Lombard, V., Drula, E., Terrapon, N. & Henrissat, B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat. Commun. https://doi.org/10.1038/s41467-019-10068-5 (2019).Makhalanyane, T. P. et al. Microbial ecology of hot desert edaphic systems. FEMS Microbiol. Rev. 39, 203–221 (2015).CAS 
PubMed 
Article 

Google Scholar 
Aydogan, E. L., Moser, G., Muller, C., Kampfer, P. & Glaeser, S. P. Long-term warming shifts the composition of bacterial communities in the phyllosphere of Galium album in a permanent grassland field-experiment. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.00144 (2018).Hu, D. Y., Zang, Y., Mao, Y. J. & Gao, B. L. Identification of molecular markers that are specific to the class thermoleophilia. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.01185 (2019).Mohan, J. E. et al. Mycorrhizal fungi mediation of terrestrial ecosystem responses to global change: mini-review. Fungal Ecol. 10, 3–19 (2014).Article 

Google Scholar 
Manzoni, S., Taylor, P., Richter, A., Porporato, A. & Agren, G. I. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 196, 79–91 (2012).CAS 
PubMed 
Article 

Google Scholar 
Allison, S. D., Wallenstein, M. D. & Bradford, M. A. Soil-carbon response to warming dependent on microbial physiology. Nat. Geosci. 3, 336–340 (2010).CAS 
Article 

Google Scholar 
Reed, S. C. et al. Soil biogeochemical responses of a tropical forest to warming and hurricane disturbance. Adv. Ecol. Res. 62, 225–252 (2020).Article 

Google Scholar 
Nottingham, A. T., Turner, B. L., Stott, A. W. & Tanner, E. V. J. Nitrogen and phosphorus constrain labile and stable carbon turnover in lowland tropical forest soils. Soil Biol. Biochem. 80, 26–33 (2015).CAS 
Article 

Google Scholar 
Walker, T. W. N. et al. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat. Clim. Change 8, 885–889 (2018).Kemmitt, S. J. et al. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective. Soil Biol. Biochem. 40, 61–73 (2008).CAS 
Article 

Google Scholar 
Nannipieri, P., Trasar-Cepeda, C. & Dick, R. P. Soil enzyme activity: a brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biol. Fert. Soils 54, 11–19 (2018).CAS 
Article 

Google Scholar 
Wallenstein, M., Allison, S., Ernakovich, J., Steinweg, J. M. & Sinsabaugh, R. in Soil Enzymology. Soil Biology Vol. 22 (eds Shukla, G. & Varma, A.) Ch. 13 (Springer, 2011).Zhou, X. Y., Chen, L., Xu, J. M. & Brookes, P. C. Soil biochemical properties and bacteria community in a repeatedly fumigated-incubated soil. Biol. Fert. Soils 56, 619–631 (2020).CAS 
Article 

Google Scholar 
Sanchez-Julia, M. & Turner, B. L. Abiotic contribution to phenol oxidase activity across a manganese gradient in tropical forest soils. Biogeochemistry https://doi.org/10.1007/s10533-021-00764-0 (2021).Razavi, B. S., Liu, S. B. & Kuzyakov, Y. Hot experience for cold-adapted microorganisms: temperature sensitivity of soil enzymes. Soil Biol. Biochem. 105, 236–243 (2017).CAS 
Article 

Google Scholar 
Pinney, M. M. et al. Parallel molecular mechanisms for enzyme temperature adaptation. Science 371, eaay2784 (2021).CAS 
PubMed 
Article 

Google Scholar 
Fanin, N. et al. Soil enzymes in response to climate warming: mechanisms and feedbacks. Funct. Ecol. https://doi.org/10.1111/1365-2435.14027 (2022).Hall, S. J. & Silver, W. L. Iron oxidation stimulates organic matter decomposition in humid tropical forest soils. Glob. Change Biol. 19, 2804–2813 (2013).Article 

Google Scholar 
Freeman, C., Ostle, N. & Kang, H. An enzymic ‘latch’ on a global carbon store. Nature 409, 149 (2001).CAS 
PubMed 
Article 

Google Scholar 
Sarmiento, C. et al. Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proc. Natl Acad. Sci. USA 114, 11458–11463 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Condit, R., Perez, R., Lao, S., Aguilar, S. & Hubbell, S. P. Demographic trends and climate over 35 years in the Barro Colorado 50 ha plot. For. Ecosyst. https://doi.org/10.1186/s40663-017-0103-1 (2017).Woodring, W. P. Geology of Barro Colorado Island. Smithson. Misc. Collect. 135, 1–39 (1958).
Google Scholar 
Sanchez, P. A. & Logan, T. J. Myths and science about the chemistry and fertility of soils in the tropics. SSSA Spec. Publ. 29, 35–46 (1992).CAS 

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

Google Scholar 
Brookes, P. C., Landman, A., Pruden, G. & Jenkinson, D. S. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol. Biochem. 17, 837–842 (1985).CAS 
Article 

Google Scholar 
Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).CAS 
Article 

Google Scholar 
Jenkinson, D. S., Brookes, P. C. & Powlson, D. S. Measuring soil microbial biomass. Soil Biol. Biochem. 36, 5–7 (2004).CAS 
Article 

Google Scholar 
Kouno, K., Tuchiya, Y. & Ando, T. Measurement of soil microbial biomass phosphorus by an anion-exchange membrane method. Soil Biol. Biochem. 27, 1353–1357 (1995).CAS 
Article 

Google Scholar 
Tabatabai, M. A. in Methods of Soil Analysis. Part 2. Microbiological and Biochemical Properties (ed. Page, A.L.) 778–833 (SSSA, 1994).Marx, M. C., Wood, M. & Jarvis, S. C. A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biol. Biochem. 33, 1633–1640 (2001).CAS 
Article 

Google Scholar 
Price, N. & Stevens, L. Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins (Oxford Univ. Press, 1999).Hagerty, S. B., Allison, S. D. & Schimel, J. P. Evaluating soil microbial carbon use efficiency explicitly as a function of cellular processes: implications for measurements and models. Biogeochemistry 140, 269–283 (2018).CAS 
Article 

Google Scholar 
Frey, S. D., Lee, J., Melillo, J. M. & Six, J. The temperature response of soil microbial efficiency and its feedback to climate. Nat. Clim. Change 3, 395–398 (2013).CAS 
Article 

Google Scholar 
Spohn, M. et al. Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland. Soil Biol. Biochem. 97, 168–175 (2016).CAS 
Article 

Google Scholar 
Sinsabaugh, R. L. et al. Stoichiometry of microbial carbon use efficiency in soils. Ecol. Monogr. 86, 172–189 (2016).Article 

Google Scholar 
Geyer, K. M., Dijkstra, P., Sinsabaugh, R. & Frey, S. D. Clarifying the interpretation of carbon use efficiency in soil through methods comparison. Soil Biol. Biochem. 128, 79–88 (2019).CAS 
Article 

Google Scholar 
Bååth, E., Pettersson, M. & Söderberg, K. H. Adaptation of a rapid and economical microcentrifugation method to measure thymidine and leucine incorporation by soil bacteria. Soil Biol. Biochem. 33, 1571–1574 (2001).Article 

Google Scholar 
Bárcenas-Moreno, G., Gomez-Brandon, M., Rousk, J. & Bååth, E. Adaptation of soil microbial communities to temperature: comparison of fungi and bacteria in a laboratory experiment. Glob. Change Biol. 15, 2950–2957 (2009).Article 

Google Scholar 
Smirnova, E., Huzurbazar, S. & Jafari, F. PERFect: PERmutation Filtering test for microbiome data. Biostatistics 20, 615–631 (2019).PubMed 
Article 

Google Scholar 
Alberdi, A. & Gilbert, M. T. P. hilldiv: an R package for the integral analysis of diversity based on Hill numbers. Preprint at bioRxiv https://doi.org/10.1101/545665 (2019).Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169–172 (2011).PubMed 
Article 

Google Scholar 
Oksanen, J. et al. vegan: Community ecology package, R Package version 2 https://cran.r-project.org/web/packages/vegan/ (2018).Dufrene, M. & Legendre, P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).
Google Scholar 
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. https://doi.org/10.1186/gb-2011-12-6-r60 (2011).Roesch, L. F. W. et al. PIME: a package for discovery of novel differences among microbial communities. Mol. Ecol. Resour. 20, 415–428 (2020).CAS 
PubMed 
Article 

Google Scholar 
Roberts, D.W. labdsv: Ordination and multivariate analysis for ecology. R package version 2.0-1 https://cran.r-project.org/web/packages/labdsv/ (2019).Cao, Y. et al. microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics 38, 4027–4029 (2022).Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. Peerj 3, e1319 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Peterson, R. A. & Cavanaugh, J. E. Ordered quantile normalization: a semiparametric transformation built for the cross-validation era. J. Appl. Stat. 47, 2312–2327 (2020).PubMed 
Article 

Google Scholar  More

Ray DK, Mueller ND, West PC, Foley JA. Yield trends are insufficient to double global crop production by 2050. PLoS ONE. 2013;8:1–8.
Google Scholar 
United Nations Department of Economic and Social Affairs. World population prospects: the 2017 revision. 2017. https://www.un.org/development/desa/publications/world-population-prospects-the-2017-revision.html.Pe’er G, Dicks LV, Visconti P, Arlettaz R, Báldi A, Benton TG, et al. EU agricultural reform fails on biodiversity. Science. 2014;344:1090–2.PubMed 

Google Scholar 
Jack CN, Petipas RH, Cheeke TE, Rowland JL, Friesen ML. Microbial inoculants: silver bullet or microbial Jurassic Park? Trends Microbiol. 2020;29:299–308.PubMed 

Google Scholar 
Saad M, Eida A, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. J Exp Bot. 2020;71:3878–901.CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu X, le Roux X, Salles JF. The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges. iScience. 2022;25:103821.CAS 
PubMed 
PubMed Central 

Google Scholar 
Bounaffaa M, Florio A, le Roux X, Jayet PA. Economic and environmental analysis of maize inoculation by plant growth promoting rhizobacteria in the French Rhône-Alpes region. Ecol Econ. 2018;146:334–46.
Google Scholar 
Bashan Y, de-Bashan LE, Prabhu SR, Hernandez JP. Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998-2013). Plant Soil. 2014;378:1–33.CAS 

Google Scholar 
Mallon C, van Elsas J, Salles J. Microbial invasions: the process, patterns, and mechanisms. Trends Microbiol. 2015;23:719–29.CAS 
PubMed 

Google Scholar 
Mawarda PC, le Roux X, van Elsas JD, Salles JF. Deliberate introduction of invisible invaders: a critical appraisal of the impact of microbial inoculants on soil microbial communities. Soil Biol Biochem.2020;148:1–13.
Google Scholar 
Mallon C, Poly F, le Roux X, Marring I, van Elsas J, Salles J. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology. 2015;96:915–26.PubMed 

Google Scholar 
Xing J, Jia X, Wang H, Ma B, Salles JF, Xu J. The legacy of bacterial invasions on soil native communities. Environ Microbiol. 2020;23:1–13.
Google Scholar 
Eisenhauer N, Schulz W, Scheu S, Jousset A. Niche dimensionality links biodiversity and invasibility of microbial communities. Funct Ecol. 2013;27:282–8.
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;43:293–323.
Google Scholar 
Gao Z, Karlsson I, Geisen S, Kowalchuk G, Jousset A. Protists: puppet masters of the rhizosphere microbiome. Trends Plant Sci. 2019;24:165–76.CAS 
PubMed 

Google Scholar 
Sherr BF, Sherr EB, Berman T. Grazing, growth, and ammonium excretion rates of a heterotrophic microflagellate fed with four species of bacteria. Appl Environ Microbiol. 1983;45:1196–201.CAS 
PubMed 
PubMed Central 

Google Scholar 
Koller R, Rodriguez A, Robin C, Scheu S, Bonkowski M. Protozoa enhance foraging efficiency of arbuscular mycorrhizal fungi for mineral nitrogen from organic matter in soil to the benefit of host plants. New Phytol. 2013;199:203–11.CAS 
PubMed 

Google Scholar 
Geisen S, Koller R, Hünninghaus M, Dumack K, Urich T, Bonkowski M. The soil food web revisited: diverse and widespread mycophagous soil protists. Soil Biol Biochem. 2016;94:10–18.CAS 

Google Scholar 
Long JJ, Jahn CE, Sánchez-Hidalgo A, Wheat W, Jackson M, Gonzalez-Juarrero M, et al. Interactions of free-living amoebae with rice bacterial pathogens Xanthomonas oryzae pathovars oryzae and oryzicola. PLoS ONE. 2018;13:e0202941.PubMed 
PubMed Central 

Google Scholar 
Iavicoli A, Boutet E, Buchala A, Métraux JP. Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Mol Plant Microbe Interact. 2003;16:851–8.CAS 
PubMed 

Google Scholar 
Jousset A, Rochat L, Scheu S, Bonkowski M, Keel C. Predator-prey chemical warfare determines the expression of biocontrol genes by rhizosphere-associated pseudomonas fluorescens. Appl Environ Microbiol. 2010;76:5263–8.CAS 
PubMed 
PubMed Central 

Google Scholar 
Berney C, Romac S, Mahé F, Santini S, Siano R, Bass D. Vampires in the oceans: predatory cercozoan amoebae in marine habitats. ISME J. 2013;7:2387–99.CAS 
PubMed 
PubMed Central 

Google Scholar 
Jousset A, Scheu S, Bonkowski M. Secondary metabolite production facilitates establishment of rhizobacteria by reducing both protozoan predation and the competitive effects of indigenous bacteria. Funct Ecol. 2008;22:714–9.
Google Scholar 
Jousset A, Lara E, Wall LG, Valverde C. Secondary metabolites help biocontrol strain Pseudomonas fluorescens CHA0 to escape protozoan grazing. Appl Environ Microbiol. 2006;72:7083–90.CAS 
PubMed 
PubMed Central 

Google Scholar 
Mallon CA, le Roux X, van Doorn GS, Dini-Andreote F, Poly F, Salles JF. The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISME J. 2018;12:728–41.CAS 
PubMed 
PubMed Central 

Google Scholar 
Mawarda PC, Lakke SL, Dirk van Elsas J, Salles JF. Temporal dynamics of the soil bacterial community following Bacillus invasion. iScience. 2022;25:1–17.
Google Scholar 
Yi Y, de Jong A, Spoelder J, Theo J, van Elsas JD, Kuipers OP. Draft genome sequence of Bacillus mycoides M2E15, a strain isolated from the endosphere of potato. Genome Announc. 2016;4:e00031.PubMed 
PubMed Central 

Google Scholar 
Loznik B, Oosterkamp PJ. Fertilizer comprising protozoa and bacteria. World Intelectual Property Organization; 2017. https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2017105238.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;9:1–11.
Google Scholar 
Bargabus RL, Zidack NK, Sherwood JE, Jacobsen BJ. Characterisation of systemic resistance in sugar beet elicited by a non-pathogenic, phyllosphere-colonizing Bacillus mycoides, biological control agent. Physiol Mol Plant Pathol. 2002;61:289–98.CAS 

Google Scholar 
Neher OT, Johnston MR, Zidack NK, Jacobsen BJ. Evaluation of Bacillus mycoides isolate BmJ and B. mojavensis isolate 203-7 for the control of anthracnose of cucurbits caused by Glomerella cingulata var. orbiculare. Biol Control. 2009;48:140–6.
Google Scholar 
Gao Z. Soil protists: from traits to ecological functions. University of Utrecht; 2020. https://dspace.library.uu.nl/handle/1874/400054.Amacker N, Gao Z, Hu J, Jousset ALC, Kowalchuk GA, Geisen S. Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities. FEMS Microbiol Ecol. 2022;98:1–11.
Google Scholar 
Wright DA, Killham K, Glover LA, Prosser JI. Role of pore size location in determining bacterial activity during predation by protozoa in soil. Appl Environ Microbiol. 1995;61:3537–43.CAS 
PubMed 
PubMed Central 

Google Scholar 
Wright D, Killham K, Glover L, Biota JP-SS. The effect of location in soil on protozoal grazing of a genetically modified bacterial inoculum. In: Brussaard L, Kooistra MJ, editors. Soil structure/soil biota interrelationships. Amsterdam: Elsevier; 1993.p.633–40.
Google Scholar 
Thewes S, Soldati T, Eichinger L. Editorial: amoebae as host models to study the interaction with pathogens. Front Cell Infect Microbiol. 2019;9:47.PubMed 
PubMed Central 

Google Scholar 
Kuppardt A, Fester T, Härtig C, Chatzinotas A. Rhizosphere protists change metabolite profiles in Zea mays. Front Microbiol. 2018;9:857.PubMed 
PubMed Central 

Google Scholar 
Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, et al. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat Biotechnol. 2016;34:942–9.CAS 
PubMed 

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 

Google Scholar 
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.CAS 
PubMed 
PubMed Central 

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 

Google Scholar 
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.CAS 
PubMed 
PubMed Central 

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 

Google Scholar 
Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–35.CAS 
PubMed 
PubMed Central 

Google Scholar 
Ritz K. The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology. FEMS Microbiol Ecol. 2007;60:358–62.CAS 
PubMed 

Google Scholar 
Amacker N, Gao Z, Agaras BC, Latz E, Kowalchuk GA, Valverde CF, et al. Biocontrol traits correlate with resistance to predation by protists in soil pseudomonads. Front Microbiol. 2020;11:3164.
Google Scholar 
Glücksman E, Bell T, Griffiths RI, Bass D. Closely related protist strains have different grazing impacts on natural bacterial communities. Environ Microbiol. 2010;12:3105–13.PubMed 

Google Scholar 
Saleem M, Fetzer I, Dormann CF, Harms H, Chatzinotas A. Predator richness increases the effect of prey diversity on prey yield. Nat Commun. 2012;3:1–7.
Google Scholar 
Hünninghaus M, Koller R, Kramer S, Marhan S, Kandeler E, Bonkowski M. Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues. Pedobiologia. 2017;62:1–8.
Google Scholar 
van Elsas J, Chiurazzi M, Mallon C, Elhottova D, Krištůfek V, Salles J. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci USA 2012;109:1159–64.PubMed 
PubMed Central 

Google Scholar 
Horňák K, Corno G. Every coin has a back side: invasion by limnohabitans planktonicus promotes the maintenance of species diversity in bacterial communities. PLoS ONE. 2012;7:e51576.PubMed 
PubMed Central 

Google Scholar 
Gómez P, Paterson S, de Meester L, Liu X, Lenzi L, Sharma MD, et al. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nat Commun. 2016;7:1–8.
Google Scholar 
Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol. 2021;19:726–39.CAS 
PubMed 

Google Scholar 
Xiong W, Li R, Guo S, Karlsson I, Jiao Z, Xun W, et al. Microbial amendments alter protist communities within the soil microbiome. Soil Biol Biochem. 2019;135:379–82.CAS 

Google Scholar 
Schneider FD, Scheu S, Brose U. Body mass constraints on feeding rates determine the consequences of predator loss. Ecol Lett. 2012;15:436–43.PubMed 

Google Scholar 
Brose U, Archambault P, Barnes AD, Bersier L-F, Boy T, Canning-Clode J, et al. Predator traits determine food-web architecture across ecosystems. Nat Ecol Evol. 2019;3:919–27.PubMed 

Google Scholar 
van Elsas JD, Trevors JT, Jansson JK, Nannipieri P, editors. Modern soil microbiology. 3rd ed. Boca Raton: CRC Press; 2019.Berga M, Székely AJ, Langenheder S. Effects of disturbance intensity and frequency on bacterial community composition and function. PLoS ONE. 2012;7:e365969.
Google Scholar 
Wang Z, Chen Z, Kowalchuk GA, Xu Z, Fu X, Kuramae EE. Succession of the resident soil microbial community in response to periodic inoculations. Appl Environ Microbiol. 2021;87:e00046.CAS 
PubMed 
PubMed Central 

Google Scholar  More