1. Brewer, T. E. et al. Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. mBio 10, e01318-19 (2019).
2. Brubaker, S. C., Jones, A. J., Lewis, D. T. & Frank, K. Soil Properties Associated with Landscape Position. Soil Science Society of America Journal 57, 235–239 (1993).
3. Richter, D. D. & Markewitz, D. How Deep Is Soil? BioScience 45, 600–609 (1995).
4. Rumpel, C. & Kögel-Knabner, I. Deep soil organic matter—a key but poorly understood component of terrestrial C cycle. Plant Soil 338, 143–158 (2010).
5. Dove, N. C. et al. Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity. Environ. Res. Lett. 15, 1040a1 (2020).
6. Sinsabaugh, R. L. et al. Stoichiometry of soil enzyme activity at global scale. Ecology Letters 11, 1252–1264 (2008).
7. Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, (2014).
8. Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature advance online publication, (2017).
9. Chapin, F. S., Matson, P. A. & Vitousek, P. Principles of Terrestrial Ecosystem Ecology. (Springer Science & Business Media, 2011).
10. 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. Global Change Biology 15, 2950–2957 (2009).
11. Wallenstein, M., Allison, S. D., Ernakovich, J., Steinweg, J. M. & Sinsabaugh, R. Controls on the Temperature Sensitivity of Soil Enzymes: A Key Driver of In Situ Enzyme Activity Rates. in Soil Enzymology (eds. Shukla, G. & Varma, A.) 245–258 (Springer, 2011). doi:10.1007/978-3-642-14225-3_13.
12. German, D. P., Marcelo, K. R. B., Stone, M. M. & Allison, S. D. The Michaelis–Menten kinetics of soil extracellular enzymes in response to temperature: a cross-latitudinal study. Glob Change Biol 18, 1468–1479 (2012).
13. Oliverio, A. M., Bradford, M. A. & Fierer, N. Identifying the microbial taxa that consistently respond to soil warming across time and space. Global Change Biology 23, 2117–2129 (2017).
14. Jenny, H. Factors of soil formation. (1941).
15. Parton, W. J., Scurlock, J. M. O., Ojima, D. S., Schimel, D. S. & Hall, D. O. Impact of climate change on grassland production and soil carbon worldwide. Global Change Biology 1, 13–22 (1995).
16. Jenny, H. The Soil Resource: Origin and Behavior. (Springer Science & Business Media, 1980).
17. Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. PNAS 103, 626–631 (2006).
18. Lauber, C. L., 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. 75, 5111–5120 (2009).
19. Slessarev, E. W. et al. Water balance creates a threshold in soil pH at the global scale. Nature 540, 567–569 (2016).
20. Brovkin, V. Climate-vegetation interaction. J. Phys. IV France 12, 57–72 (2002).
21. Aerts, R. Climate, Leaf Litter Chemistry and Leaf Litter Decomposition in Terrestrial Ecosystems: A Triangular Relationship. Oikos 79, 439–449 (1997).
22. Djukic, I. et al. Early stage litter decomposition across biomes. Science of The Total Environment 628–629, 1369–1394 (2018).
23. Shiozawa, S. & Campbell, G. S. Soil thermal conductivity. Remote Sensing Reviews 5, 301–310 (1990).
24. Verhoef, A., Fernández-Gálvez, J., Diaz-Espejo, A., Main, B. E. & 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. Journal of Hydrology 321, 147–162 (2006).
25. Dove, N. C., Torn, M. S., Hart, S. C. & Taş, N. Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. Nature Communications 12, 2089 (2021).
26. 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. European Journal of Soil Biology 92, 16–23 (2019).
27. Yost, J. L. & Hartemink, A. E. How deep is the soil studied – an analysis of four soil science journals. Plant Soil (2020) doi:10.1007/s11104-020-04550-z.
28. Jobbágy, E. G. & Jackson, R. B. The vertical distribution of soil organic carbon and its relation to climate and vegetation. Ecological Applications 10, 423–436 (2000).
29. Hicks Pries, C. E., Castanha, C., Porras, R. C. & Torn, M. S. The whole-soil carbon flux in response to warming. Science 355, 1420–1423 (2017).
30. Jones, D. L. et al. Microbial competition for nitrogen and carbon is as intense in the subsoil as in the topsoil. Soil Biology and Biochemistry 117, 72–82 (2018).
31. Ofiti, N. O. E. et al. Warming promotes loss of subsoil carbon through accelerated degradation of plant-derived organic matter. Soil Biology and Biochemistry 156, 108185 (2021).
32. Soong, J. L. et al. Five years of whole-soil warming led to loss of subsoil carbon stocks and increased CO2 efflux. Science Advances 7, eabd1343 (2021).
33. 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).
34. O’Geen, A. (Toby) et al. Southern Sierra Critical Zone Observatory and Kings River Experimental Watersheds: A Synthesis of Measurements, New Insights, and Future Directions. Vadose Zone Journal 17, 180081 (2018).
35. Frisbie, J. A. Soil Organic Carbon Storage and Aggregate Stability in an Arid Mountain Range, White Mountains, CA. (UC Riverside, 2014).
36. Marchand, D. E. Soil Contamination in the White Mountains, Eastern California. GSA Bulletin 81, 2497–2506 (1970).
37. Aciego, S. M. et al. Dust outpaces bedrock in nutrient supply to montane forest ecosystems. Nature Communications 8, 14800 (2017).
38. Dove, N. C., Safford, H. D., Bohlman, G. N., Estes, B. L. & Hart, S. C. High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests. Ecological Applications 30, e02072 (2020).
39. Lajtha, K., Driscoll, C. T., Jarrell, W. M. & Elliot, E. T. Phosphorus Characterization and Total Element Analysis. in Standard Soil Methods for Long-Term Ecological Research (eds. Robertson, G. P., Coleman, D. C., Bledsoe, C. S. & Sollins, P.) 115–142 (Oxford University Press, 1999).
40. Harris, D., Horwáth, W. R. & Kessel, C. van. Acid fumigation of soils to remove carbonates prior to total organic carbon or CARBON-13 isotopic analysis. Soil Science Society of America Journal 65, 1853–1856 (2001).
41. Thomas, G. W. Soil pH and soil acidity. in Methods of Soil Analysis, Part 3: Chemical Methods (eds. Sparks, D. L. et al.) 475- (Soil Science Society of America, American Society of Agronomy, 1996).
42. Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry 19, 703–707 (1987).
43. Hart, S. C. & Firestone, M. K. Forest floor-mineral soil interactions in the internal nitrogen cycle of an old-growth forest. Biogeochemistry 12, 103–127 (1991).
44. Haubensak, K. A., Hart, S. C. & Stark, J. M. Influences of chloroform exposure time and soil water content on C and N release in forest soils. Soil Biology and Biochemistry 34, 1549–1562 (2002).
45. Stenberg, B. et al. Microbial biomass and activities in soil as affected by frozen and cold storage. Soil Biology and Biochemistry 30, 393–402 (1998).
46. Bell, C. W. et al. High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities. Journal of Visualized Experiments (2013) doi:10.3791/50961.
47. Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental Microbiology 18, 1403–1414 (2016).
48. Ihrmark, K. et al. New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol 82, 666–677 (2012).
49. Smith, D. P. & Peay, K. G. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE 9, e90234 (2014).
50. R Development Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2008).
51. Cribari-Neto, F. & Zeileis, A. Beta Regression in R. Journal of Statistical Software 34, 1–24 (2010).
52. Fox, J. & Weisberg, S. An {R} Companion to Applied Regression. (Sage, 2011).
53. Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software 67, 1–48 (2015).
54. McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLOS ONE 8, e61217 (2013).
55. Oksanen, J. et al. vegan: Community Ecology Package. (2013).
56. Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecology 26, 32–46 (2001).
57. Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecology Letters 9, 683–693 (2006).
58. Legendre, P. & Cáceres, M. D. Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters 16, 951–963 (2013).
59. Legendre, P. & Anderson, M. J. Distance-Based Redundancy Analysis: Testing Multispecies Responses in Multifactorial Ecological Experiments. Ecological Monographs 69, 1–24 (1999).
60. Lin, H. & Peddada, S. D. Analysis of compositions of microbiomes with bias correction. Nature Communications 11, 3514 (2020).
61. Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).
62. Kanzaki, Y. & Takemoto, K. Diversity of Dominant Soil Bacteria Increases with Warming Velocity at The Global Scale. Diversity 13, 120 (2021).
63. Russell, N. J. et al. Cold adaptation of microorganisms. Philosophical Transactions of the Royal Society of London. B, Biological Sciences 326, 595–611 (1990).
64. Chanal, A. et al. The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environmental Microbiology 8, 514–525 (2006).
65. Jobbágy, E. G. & Jackson, R. B. The distribution of soil nutrients with depth: Global patterns and the imprint of plants. Biogeochemistry 53, 51–77 (2001).
66. Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an Ecological Classification of Soil Bacteria. Ecology 88, 1354–1364 (2007).
67. Offre, P., Spang, A. & Schleper, C. Archaea in Biogeochemical Cycles. Annual Review of Microbiology 67, 437–457 (2013).
68. Xiong, J. et al. Characterizing changes in soil bacterial community structure in response to short-term warming. FEMS Microbiol Ecol 89, 281–292 (2014).
69. DeAngelis, K. M. et al. Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol 6, (2015).
70. Hayden, H. L. 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. Environmental Microbiology 14, 3081–3096 (2012).
71. Johnston, E. R. et al. Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. PNAS 116, 15096–15105 (2019).
72. Sarkar, J. M., Leonowicz, A. & Bollag, J.-M. Immobilization of enzymes on clays and soils. Soil Biology and Biochemistry 21, 223–230 (1989).
73. Burns, R. G. et al. Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biology and Biochemistry 58, 216–234 (2013).
74. Eilers, K. G., 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 Biology and Biochemistry 50, 58–65 (2012).
75. Kellogg, C. A. & Griffin, D. W. Aerobiology and the global transport of desert dust. Trends in Ecology & Evolution 21, 638–644 (2006).
76. Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4, 102–112 (2006).
77. Du, X. et al. Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process. Molecular Ecology 30, 1072–1085 (2021).
78. Fanning, D. S. & Fanning, M. C. B. Soil morphology, genesis and classification. Soil morphology, genesis and classification. (1989).
79. 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. 1–151 (2014).
80. Bradford, M. A. et al. Thermal adaptation of soil microbial respiration to elevated temperature. Ecology Letters 11, 1316–1327 (2008).