Brewer TE, Aronson EL, Arogyaswamy K, Billings SA, Botthoff JK, Campbell AN, et al. Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons. mBio. 2019;10:e01318–19.
Google Scholar
Brubaker SC, Jones AJ, Lewis DT, Frank K. Soil properties associated with landscape position. Soil Sci Soc Am J. 1993;57:235–9.
Richter DD, Markewitz D. How deep is soil? BioScience. 1995;45:600–9.
Rumpel C, Kögel-Knabner I. Deep soil organic matter—a key but poorly understood component of terrestrial C cycle. Plant Soil. 2010;338:143–58.
Dove NC, Arogyaswamy K, Billings SA, Botthoff JK, Carey CJ, Cisco C, et al. Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity. Environ Res Lett. 2020;15:1040a1.
Google Scholar
Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, et al. Stoichiometry of soil enzyme activity at global scale. Ecol Lett. 2008;11:1252–64.
Google Scholar
Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, et al. Global diversity and geography of soil fungi. Science. 2014;346:6213.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–63.
Google Scholar
Jobbágy EG, Jackson RB. The vertical distribution of soil organic carbon and its relation to climate and vegetation. Ecol Appl. 2000;10:423–36.
Chapin FS, Matson PA, Vitousek P. Principles of terrestrial ecosystem ecology. New York: Springer Science & Business Media; 2011.
Bárcenas‐Moreno G, Gómez‐Brandón M, Rousk J, Bååth E. Adaptation of soil microbial communities to temperature: comparison of fungi and bacteria in a laboratory experiment. Glob Change Biol. 2009;15:2950–7.
Wallenstein M, Allison SD, Ernakovich J, Steinweg JM, Sinsabaugh R. Controls on the temperature sensitivity of soil enzymes: a key driver of in situ enzyme activity rates. In: Shukla G, Varma A, editors. Soil enzymology. Berlin, Heidelberg: Springer; 2011. p. 245–58.
German DP, Marcelo KRB, Stone MM, Allison SD. The Michaelis–Menten kinetics of soil extracellular enzymes in response to temperature: a cross-latitudinal study. Glob Change Biol. 2012;18:1468–79.
Oliverio AM, Bradford MA, Fierer N. Identifying the microbial taxa that consistently respond to soil warming across time and space. Glob Change Biol. 2017;23:2117–29.
Jenny H. Factors of soil formation. New York: McGraw-Hill; 1941.
Parton WJ, Scurlock JMO, Ojima DS, Schimel DS, Hall DO. Impact of climate change on grassland production and soil carbon worldwide. Glob Change Biol. 1995;1:13–22.
Jenny H. The soil resource: origin and behavior. Berlin: Springer Science & Business Media; 1980.
Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. PNAS. 2006;103:626–31.
Google Scholar
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.
Google Scholar
Slessarev EW, Lin Y, Bingham NL, Johnson JE, Dai Y, Schimel JP, et al. Water balance creates a threshold in soil pH at the global scale. Nature. 2016;540:567–9.
Google Scholar
Brovkin V. Climate-vegetation interaction. J Phys IV France. 2002;12:57–72.
Aerts R. Climate, leaf litter chemistry and leaf litter decomposition in terrestrial ecosystems: a triangular relationship. Oikos. 1997;79:439–49.
Djukic I, Kepfer-Rojas S, Schmidt IK, Larsen KS, Beier C, Berg B, et al. Early stage litter decomposition across biomes. Sci Total Environ. 2018;628–9:1369–94.
Shiozawa S, Campbell GS. Soil thermal conductivity. Remote Sens Rev. 1990;5:301–10.
Verhoef A, Fernández-Gálvez J, Diaz-Espejo A, Main BE, El-Bishti M. The diurnal course of soil moisture as measured by various dielectric sensors: effects of soil temperature and the implications for evaporation estimates. J Hydrol. 2006;321:147–62.
Dove NC, Torn MS, Hart SC, Taş N. Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. Nat Commun. 2021;12:2089.
Google Scholar
Bai W, Wang G, Xi J, Liu Y, Yin P. Short-term responses of ecosystem respiration to warming and nitrogen addition in an alpine swamp meadow. Eur J Soil Biol. 2019;92:16–23.
Google Scholar
Yost JL, Hartemink AE. How deep is the soil studied—an analysis of four soil science journals. Plant Soil. 2020;425:5–18.
Hicks Pries CE, Castanha C, Porras RC, Torn MS. The whole-soil carbon flux in response to warming. Science. 2017;355:1420–3.
Google Scholar
Jones DL, Magthab EA, Gleeson DB, Hill PW, Sánchez-Rodríguez AR, Roberts P, et al. Microbial competition for nitrogen and carbon is as intense in the subsoil as in the topsoil. Soil Biol Biochem. 2018;117:72–82.
Google Scholar
Ofiti NOE, Zosso CU, Soong JL, Solly EF, Torn MS, Wiesenberg GLB, et al. Warming promotes loss of subsoil carbon through accelerated degradation of plant-derived organic matter. Soil Biol Biochem. 2021;156:108185.
Google Scholar
Soong JL, Castanha C, Pries CEH, Ofiti N, Porras RC, Riley WJ, et al. Five years of whole-soil warming led to loss of subsoil carbon stocks and increased CO2 efflux. Sci Adv. 2021;7:eabd1343.
Google Scholar
Nottingham AT, Fierer N, Turner BL, Whitaker J, Ostle NJ, McNamara NP, et al. Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes. Ecology. 2018;99:2455–66.
Google Scholar
O‘Geen A (Toby), Safeeq M, Wagenbrenner J, Stacy E, Hartsough P, Devine S., et al. Southern Sierra Critical Zone Observatory and Kings River Experimental Watersheds: a synthesis of measurements, new insights, and future directions. Vadose Zone J. 2018;17:180081.
Frisbie JA. Soil organic carbon storage and aggregate stability in an arid mountain range, White Mountains, CA. UC Riverside Master’s Thesis. 2014. https://escholarship.org/uc/item/4rn6j9rq.
Marchand DE. Soil contamination in the White Mountains, Eastern California. GSA Bull. 1970;81:2497–506.
Aciego SM, Riebe CS, Hart SC, Blakowski MA, Carey CJ, Aarons SM, et al. Dust outpaces bedrock in nutrient supply to montane forest ecosystems. Nat Commun. 2017;8:14800.
Google Scholar
Dove NC, Safford HD, Bohlman GN, Estes BL, Hart SC. High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests. Ecol Appl. 2020;30:e02072.
Google Scholar
USDA-NRCS. Soil taxonomy: a basic system of soil classification for making and interpreting soil surveys. U.S. Department of Agriculture Handbook 436. 2nd edition. Washington D.C.: Natural Resources Conservation Service; 1999.
Lajtha K, Driscoll CT, Jarrell WM, Elliot ET. Phosphorus characterization and total element analysis. In: Robertson GP, Coleman DC, Bledsoe CS, Sollins P, editors. Standard soil methods for long-term ecological research. New York: Oxford University Press; 1999. p. 115–42.
Harris D, Horwáth WR, vanKessel C. Acid fumigation of soils to remove carbonates prior to total organic carbon or CARBON-13 isotopic analysis. Soil Sci Soc Am J. 2001;65:1853–6.
Google Scholar
Thomas GW, Soil pH and soil acidity. In: Sparks DL, Page AL, Helmke PA, Loeppert RH, Soltanpour PN, Tabatabai MA, et al., editors. Methods of soil analysis, part 3: chemical methods. Madison, WI, USA: Soil Science Society of America, American Society of Agronomy; 1996, p. 475–90.
Vance ED, Brookes PC, Jenkinson DS. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem. 1987;19:703–7.
Google Scholar
Hart SC, Firestone MK. Forest floor-mineral soil interactions in the internal nitrogen cycle of an old-growth forest. Biogeochemistry. 1991;12:103–27.
Google Scholar
Haubensak KA, Hart SC, Stark JM. Influences of chloroform exposure time and soil water content on C and N release in forest soils. Soil Biol Biochem. 2002;34:1549–62.
Google Scholar
Stenberg B, Johansson M, Pell M, Sjödahl-Svensson K, Stenström J, Torstensson L. Microbial biomass and activities in soil as affected by frozen and cold storage. Soil Biol Biochem. 1998;30:393–402.
Google Scholar
Bell CW, Fricks BE, Rocca JD, Steinweg JM, McMahon SK, Wallenstein MD. High-throughput fluorometric measurement of potential soil extracellular enzyme activities. J Vis Exp. 2013;81:e50961.
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.
Google Scholar
Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, et al. New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol. 2012;82:666–77.
Google Scholar
Smith DP, Peay KG. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE. 2014;9:e90234.
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.
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 2019;37:852–7.
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–D596.
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.
Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, et al. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist. 2010;186:281–5.
Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 2016;20:241–8.
R Development Core Team. R: a language and environment for statistical computing. 2008. Vienna, Australia: R Foundation for Statistical Computing. http://www.R-project.org.
Cribari-Neto F, Zeileis A. Beta regression in R. J Statl Softw. 2010;34:1–24.
Fox J, Weisberg S. An {R} companion to applied regression, Second. 2011. Thousand Oaks, CA: Sage.
Bates D, Maechler M, Bolker B, Walker S. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Google Scholar
Oksanen J, Blanchet FG, Kindt R, Legendre P, Simpson GL, Minchin PR, et al. vegan: community Ecology Package. 2013 http://CRAN.R-project.org/package=vegan.
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.
Anderson MJ, Ellingsen KE, McArdle BH. Multivariate dispersion as a measure of beta diversity. Ecol Lett. 2006;9:683–93.
Google Scholar
Legendre P, Cáceres MD. Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecol Lett. 2013;16:951–63.
Google Scholar
Legendre P, Anderson MJ. Distance-based redundancy analysis: Testing multispecies responses in multifactorial ecological experiments. Ecol Monogr. 1999;69:1–24.
Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11:3514.
Google Scholar
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.
Google Scholar
Kanzaki Y, Takemoto K. Diversity of dominant soil bacteria increases with warming velocity at the global scale. Diversity. 2021;13:120.
Russell NJ, Harrisson P, Johnston IA, Jaenicke R, Zuber M, Franks F, et al. Cold adaptation of microorganisms. Philos Trans R Soc Lond B Biol Sci. 1990;326:595–611.
Google Scholar
Chanal A, Chapon V, Benzerara K, Barakat M, Christen R, Achouak W, et al. The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ Microbiol. 2006;8:514–25.
Google Scholar
Jobbágy EG, Jackson RB. The distribution of soil nutrients with depth: global patterns and the imprint of plants. Biogeochemistry. 2001;53:51–77.
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.
Google Scholar
Offre P, Spang A, Schleper C. Archaea in biogeochemical cycles. Ann Rev Microbiol. 2013;67:437–57.
Google Scholar
Stegen JC, Bottos EM, Jansson JK. A unified conceptual framework for prediction and control of microbiomes. Curr Opin in Microbiol. 2018;44:20–27.
Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, et al. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiol Ecol. 2014;89:281–92.
Google Scholar
DeAngelis KM, Pold G, Topçuoğlu BD, van Diepen LTA, Varney RM, Blanchard JL, et al. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol. 2015;6:104.
Google Scholar
Hayden HL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, et al. Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO2 and warming in an Australian native grassland soil. Environ Microbiol. 2012;14:3081–96.
Google Scholar
Johnston ER, Hatt JK, He Z, Wu L, Guo X, Luo Y, et al. Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. PNAS. 2019;116:15096–105.
Google Scholar
Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE. 2013;8:e57923.
Google Scholar
Sarkar JM, Leonowicz A, Bollag J-M. Immobilization of enzymes on clays and soils. Soil Biol Biochem. 1989;21:223–30.
Google Scholar
Burns RG, DeForest JL, Marxsen J, Sinsabaugh RL, Stromberger ME, Wallenstein MD, et al. Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biol Biochem. 2013;58:216–34.
Google Scholar
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.
Google Scholar
Kellogg CA, Griffin DW. Aerobiology and the global transport of desert dust. Trends Ecol Evol. 2006;21:638–44.
Google Scholar
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12.
Google Scholar
Du X, Deng Y, Li S, Escalas A, Feng K, He Q, et al. Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process. Mol Ecol. 2021;30:1072–85.
Google Scholar
Fanning DS, Fanning MCB. Soil morphology, genesis and classification. New York: John Wiley & Sons; 1989.
IPCC. Climate Change 2014: synthesis report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. 2014. Geneva, Switzerland: IPCC.
Bradford MA, Davies CA, Frey SD, Maddox TR, Melillo JM, Mohan JE, et al. Thermal adaptation of soil microbial respiration to elevated temperature. Ecol Lett. 2008;11:1316–27.
Google Scholar
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