Locey KJ, Lennon JT. Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A. 2016;113:5970–5.
Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998;95:6578–83.
Singh JS, Gupta VK. Soil microbial biomass: a key soil driver in management of ecosystem functioning. Sci Total Environ. 2018;634:497–500.
Bardgett RD, van der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, et al. Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol. 2019;17:569–86.
Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007;104:11436–40.
Ettema CH, Wardle DA. Spatial soil ecology. Trends Ecol Evol. 2002;17:177–83.
Terrat S, Horrigue W, Dequietd S, Saby NPA, Lelièvre M, Nowak V, et al. Mapping and predictive variations of soil bacterial richness across France. PLoS ONE. 2017;12:e0186766.
Ladau J, Shi Y, Jing X, He J-S, Chen L, Lin X, et al. Existing climate change will lead to pronounced shifts in the diversity of soil prokaryotes. mSystems. 2018;3:e00167–18.
IPBES. Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science- Policy Platform on Biodiversity and Ecosystem Services. Bonn, Germany: IPBES Secretariat; 2019.
Guisan A, Broennimann O, Buri A, Cianfrani C, D’Amen M, Di Cola V, et al. Climate change impacts on mountain biodiversity. In: Lovejoy TE, Hannah L, editors. Biodiversity and climate change. Yale, USA: Yale University Press; 2019. p. 221–33.
Yashiro E, Pinto-Figueroa E, Buri A, Spangenberg JE, Adatte T, Niculita-Hirzel H, et al. Local environmental factors drive divergent grassland soil bacterial communities in the western Swiss Alps. Appl Environ Microbiol. 2016;82:6303–16.
Karimi B, Terrat S, Dequiedt S, Saby NPA, Horrigue W, Lelièvre M, et al. Biogeography of soil bacteria and archaea across France. Sci Adv. 2018;4:eaat1808.
King AJ, Freeman KR, McCormick KF, Lynch RC, Lozupone C, Knight R, et al. Biogeography and habitat modelling of high-alpine bacteria. Nat Commun. 2010;1:53.
Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A. 2006;103:626–31.
Trumbore SE, Czimczik CI. An uncertain future for soil carbon. Science. 2008;321:1455–6.
Hettelingh JP, Posch M, Slootweg J, Reinds GJ, Spranger T, Tarrason L. Critical loads and dynamic modelling to assess European areas at risk of acidification and eutrophication. In: Brimblecombe P, Hara H, Houle D, Novak M, editors. Acid rain—deposition to recovery. Dordrecht: Springer; 2007. p. 379–84.
IPCC (2014). Climate Change 2014: synthesis report. Contribution of working groups I, II and III to the Fifth assessment report of the Intergovernmental Panel on Climate Change. Core Writing Team, Pachauri RK, Meyer LA, editors. Geneva, Switzerland: IPCC. p. 151.
Hagedorn F, Gavazov K, Alexander JM. Above- and belowground linkages shape responses of mountain vegetation to climate change. Science. 2019;365:1119–23.
Monteith DT, Evans CD. The United Kingdom Acid Waters Monitoring Network: a review of the first 15 years and introduction to the special issue. Environ Pollut. 2005;137:3–13.
Augustin S, Achermann B. Deposition von Luftschadstoffen in der Schweiz: Entwicklung, aktueller Stand und Bewertung. Schweizerische Z fur Forstwes. 2012;163:323–30.
Blaser P, Zysset M, Zimmermann S, Luster J. Soil acidification in southern Switzerland between 1987 and 1997: A case study based on the critical load concept. Environ Sci Technol. 1999;33:2383–9.
McGovern ST, Evans CD, Dennis P, Walmsley CA, Turner A, McDonald MA. Resilience of upland soils to long term environmental changes. Geoderma. 2013;197-198:36–42.
Kirk GJD, Bellamy PH, Lark RM. Changes in soil pH across England and Wales in response to decreased acid deposition. Glob Change Biol. 2010;16:3111–9.
Kosonen Z, Schnyder E, Hiltbrunner E, Thimonier A, Schmitt M, Seitler E, et al. Current atmospheric nitrogen deposition still exceeds critical loads for sensitive, semi-natural ecosystems in Switzerland. Atmos Environ. 2019;211:214–25.
Tipping E, Davies JAC, Henrys PA, Kirk GJD, Lilly A, Dragosits U, et al. Long-term increases in soil carbon due to ecosystem fertilization by atmospheric nitrogen deposition demonstrated by regional-scale modelling and observations. Sci Rep. 2017;7:1890.
Bond-Lamberty B, Bailey VL, Chen M, Gough CM, Vargas R. Globally rising soil heterotrophic respiration over recent decades. Nature. 2018;560:80–83.
Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, et al. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat Clim Change. 2018;8:885–9.
Kirschbaum MUF. The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biol Biochem. 1995;27:753–60.
Streit K, Hagedorn F, Hiltbrunner D, Portmann M, Saurer M, Buchmann N, et al. Soil warming alters microbial substrate use in alpine soils. Glob Change Biol. 2014;20:1327–38.
Lettens S, Van Orshoven J, Van Wesemael B, Muys B, Perrin D. Soil organic carbon changes in landscape units of Belgium between 1960 and 2000 with reference to 1990. Glob Change Biol. 2005;11:2128–40.
Yang Y, Fang J, Smith P, Tang Y, Chen A, Ji C, et al. Changes in topsoil carbon stock in the Tibetan grasslands between the 1980s and 2004. Glob Change Biol. 2009;15:2723–9.
Yang Y, Li P, Ding J, Zhao X, Ma W, Ji C, et al. Increased topsoil carbon stock across China’s forests. Glob Change Biol. 2014;20:2687–96.
Smith P. Soils and climate change. Curr Opin Environ Sustain. 2012;4:539–44.
Davidson EA, Janssens IA. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature. 2006;440:165–73.
Glenn AR, Dilworth MJ. Soil acidity and the microbial population: survival and growth of bacteria in low pH. In: Wright RJ, Baligar VC, Murrmann RP, editors. Developments in plant and soil sciences. Dordrecht: Springer; 1991. p. 567–79.
Xue P-P, Carrillo Y, Pino V, Minasny B, McBratney AB. Soil properties drive microbial community structure in a large scale transect in South Eastern Australia. Sci Rep. 2018;8:11725.
Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW. Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol. 2010;76:999–1007.
Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013;342:621–4.
Evans SE, Wallenstein MD. Climate change alters ecological strategies of soil bacteria. Ecol Lett. 2014;17:155–64.
Zhang X, Zhang G, Chen Q, Han X. Soil bacterial communities respond to climate changes in a temperate steppe. PLoS ONE. 2013;8:e78616.
Guisan A, Thuiller W, Zimmermann NE. Habitat suitability and distribution models: with applications in R. Cambridge, UK: Cambridge University Press; 2017.
D’Amen M, Rahbek C, Zimmermann NE, Guisan A. Spatial predictions at the community level: from current approaches to future frameworks. Biol Rev Camb Philos Soc. 2017;92:169–87.
Guisan A, Rahbek C. SESAM—a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages. J Biogeogr. 2011;38:1433–44.
Dubuis A, Pottier J, Rion V, Pellissier L, Theurillat J-P, Guisan A. Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches. Divers Distrib. 2011;17:1122–31.
Randin CF, Dirnböck T, Dullinger S, Zimmermann NE, Zappa M, Guisan A. Are niche-based species distribution models transferable in space? J Biogeogr. 2006;33:1689–703.
Buri A, Grand S, Yashiro E, Adatte T, Spangenberg JE, Pinto‐Figueroa E, et al. What are the most crucial soil variables for predicting the distribution of mountain plant species? A comprehensive study in the Swiss Alps. J Biogeogr. 2020;47:1143–53.
Bouët M. Climat et météorologie de la Suisse romande. Lausanne: Payot edn; 1985.
Zingg B. Modélisation de la réserve hydrique des sols dans les Alpes vaudoises méridionales. Master thesis. Lausanne, Switzerland: University of Lausanne; 2015.
Swisstopo. Geological map of Switzerland. 2019.
Hirzel A, Guisan A. Which is the optimal sampling strategy for habitat suitability modelling. Ecol Model. 2002;157:331–41.
Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Østerås M, et al. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods. 2009;79:266–71.
Yashiro E, Pinto-Figueroa E, Buri A, Spangenberg JE, Adatte T, Niculita-Hirzel H, et al. Meta-scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities. Sci Rep. 2018;8:5758.
Edgar RC. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics. 2018;34:2371–5.
Myers EW, Miller W. Optimal alignments in linear space. Bioinformatics. 1988;4:11–17.
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.
Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, et al. A global atlas of the dominant bacteria found in soil. Science. 2018;359:320–5.
McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288–97.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
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.
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.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108:4516–22.
Dubuis A, Giovanettina S, Pellissier L, Pottier J, Vittoz P, Guisan A. Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables. J Veg Sci. 2013;24:593–606.
Zubler EM, Fischer AM, Liniger MA, Croci-Maspoli M, Scherrer SC, Appenzeller C. Localized climate change scenarios of mean temperature and precipitation over Switzerland. Clim Change. 2014;125:237–52.
Buri A. Above- and belowground biogeography: spatial modelling of a hidden system. PhD thesis. Lausanne: University of Lausanne; 2019.
Guisan A, Theurillat J-P. Assessing alpine plant vulnerability to climate change: a modeling perspective. Integr Assess. 2000;1:307–20.
Wood SN. Generalized additive models: an introduction with R. Boca Raton, USA: Chapman and Hall/CRC; 2017.
Greenwell B, Boehmke B, Cunningham J, Developers G. gbm: Generalized boosted regression models, 2.1.5. edn. 2019.
Ver Hoef JM, Boveng PL. Quasi-Poisson vs. negative binomial regression: how should we model overdispersed count data? Ecology. 2007;88:2766–72.
Hartig F. DHARMa: residual diagnostics for hierarchical (Multi-Level/Mixed) regression models. R package, 0.2.4 edn. 2019.
Friedman JH. Greedy function approximation: a gradient boosting machine. Ann Stat. 2001;29:1189–232.
Scherrer D, D’Amen M, Fernandes RF, Mateo RG, Guisan A. How to best threshold and validate stacked species assemblages? Community optimisation might hold the answer. Methods Ecol Evol. 2018;9:2155–66.
Evans JD. Straightforward statistics for the behavioral sciences. Pacific Grove, USA: Thomson Brooks/Cole Publishing Co; 1996.
Elith J, Ferrier S, Huettmann F, Leathwick J. The evaluation strip: a new and robust method for plotting predicted responses from species distribution models. Ecol Model. 2005;186:280–9.
Bradie J, Leung B. A quantitative synthesis of the importance of variables used in MaxEnt species distribution models. J Biogeogr. 2017;44:1344–61.
Pacifici M, Foden WB, Visconti P, Watson JEM, Butchart SHM, Kovacs KM, et al. Assessing species vulnerability to climate change. Nat Clim Change. 2015;5:215.
Fierer N, Schimel JP, Holden PA. Influence of drying–rewetting frequency on soil bacterial community structure. Micro Ecol. 2003;45:63–71.
Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340.
Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol. 2009;75:5111–20.
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.
Lennon JT, Aanderud ZT, Lehmkuhl BK, Schoolmaster DR Jr. Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology. 2012;93:1867–79.
Wiens JJ, Ackerly DD, Allen AP, Anacker BL, Buckley LB, Cornell HV, et al. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol Lett. 2010;13:1310–24.
Pearman PB, Guisan A, Broennimann O, Randin CF. Niche dynamics in space and time. Trends Ecol Evol. 2008;23:149–58.
Bååth E, Anderson TH. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem. 2003;35:955–63.
Nottingham AT, Baath 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. 2019;25:827–38.
Li L, Xu M, Eyakub Ali M, Zhang W, Duan Y, Li D. Factors affecting soil microbial biomass and functional diversity with the application of organic amendments in three contrasting cropland soils during a field experiment. PLoS ONE. 2018;13:e0203812.
Eilers KG, Debenport S, Anderson S, Fierer N. Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem. 2012;50:58–65.
Galloway JN. Acid deposition: perspectives in time and space. Water Air Soil Pollut. 1995;85:15–24.
Tian D, Niu S. A global analysis of soil acidification caused by nitrogen addition. Environ Res Lett. 2015;10:024019.
Falkengren-Grerup U, Brink D-Jt, Brunet J. Land use effects on soil N, P, C and pH persist over 40–80 years of forest growth on agricultural soils. For Ecol Manage. 2006;225:74–81.
Saby NPA, Arrouays D, Antoni V, Lemercier B, Follain S, Walter C, et al. Changes in soil organic carbon in a mountainous French region, 1990–2004. Soil Use Manage. 2008;24:254–62.
Cianfrani C, Buri A, Verrecchia E, Guisan A. Generalizing soil properties in geographic space: approaches used and ways forward. PLoS ONE. 2018;13:e0208823.
Ren B, Hu Y, Chen B, Zhang Y, Thiele J, Shi R, et al. Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China. Sci Rep. 2018;8:5619.
Lembrechts JJ, Nijs I, Lenoir J. Incorporating microclimate into species distribution models. Ecography. 2019;42:1267–79.
Schink B. Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek. 2002;81:257–61.
Crowther TW, Thomas SM, Maynard DS, Baldrian P, Covey K, Frey SD, et al. Biotic interactions mediate soil microbial feedbacks to climate change. Proc Natl Acad Sci U S A. 2015;112:7033–8.
Schröder B. Challenges of species distribution modeling belowground. J Plant Nutr Soil Sci. 2008;171:325–37.
Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A. 2012;109:21390–5.
Araújo MB, Anderson RP, Márcia Barbosa A, Beale CM, Dormann CF, Early R, et al. Standards for distribution models in biodiversity assessments. Sci Adv. 2019;5:eaat4858.
Pinto-Figueroa EA, Seddon E, Yashiro E, Buri A, Niculita-Hirzel H, van der Meer JR, et al. Archaeorhizomycetes spatial distribution in soils along wide elevational and environmental gradients reveal co-abundance patterns with other fungal saprobes and potential weathering capacities. Front Microbiol. 2019;10:656.
Smith AB, Godsoe W, Rodriguez-Sanchez F, Wang HH, Warren D. Niche estimation above and below the species level. Trends Ecol Evol. 2019;34:260–73.
Hadly EA, Spaeth PA, Li C. Niche conservatism above the species level. Proc Natl Acad Sci U S A. 2009;106 Suppl 2:19707–14.
Peterson AT. Ecological niche conservatism: a time-structured review of evidence. J Biogeogr. 2011;38:817–27.
Carini P, Marsden PJ, Leff JW, Morgan EE, Strickland MS, Fierer N, et al. is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol. 2016;2:16242.
Gardner W, Mulvey EP, Shaw EC. Regression analyses of counts and rates: Poisson, overdispersed Poisson, and negative binomial models. Psychol Bull. 1995;118:392–404.
Guisan A, Lehmann A, Ferrier S, Austin M, Overton JMC, Aspinall R, et al. Making better biogeographical predictions of species’ distributions. J Appl Ecol. 2006;43:386–92.
Elith J, Graham CH. Do they? How do they? WHY do they differ? On finding reasons for differing performances of species distribution models. Ecography. 2009;32:66–77.
Sites JW, Marshall JC. Delimiting species: a Renaissance issue in systematic biology. Trends Ecol Evol. 2003;18:462–70.
Ward DM. A macrobiological perspective on microbial species. Microbe. 2006;1:269.
Ward DM, Cohan FM, Bhaya D, Heidelberg JF, Kühl M, Grossman A. Genomics, environmental genomics and the issue of microbial species. Heredity. 2008;100:207–19.
Vandermeer J. Niche theory. Annu Rev Ecol Syst. 1972;3:107–32.
Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM, et al. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci U S A. 2008;105:2504–9.
Song H-K, Shi Y, Yang T, Chu H, He J-S, Kim H, et al. Environmental filtering of bacterial functional diversity along an aridity gradient. Sci Rep. 2019;9:866.
Parmesan C, Yohe G. A globally coherent fingerprint of climate change impacts across natural systems. Nature. 2003;421:37–42.
Lenoir J, Svenning J-C. Climate-related range shifts—a global multidimensional synthesis and new research directions. Ecography. 2015;38:15–28.
Hoffmann AA, Sgrò CM. Climate change and evolutionary adaptation. Nature. 2011;470:479–85.
Source: Ecology - nature.com
