FAO, ITPS. Status of the World’s Soil Resources – Main report. Food and Agriculture Organization of the United Nations and Intergovernmental Technical Panel on Soils, 2015. Rome, Italy. https://www.fao.org/3/a-i5199e.pdf.
UN (United Nations). Sustainable Development Goals [online]. 2015. https://www.un.org/sustainabledevelopment/sustainabledevelopment-goals/.
FAO. 2019. Soil erosion: the greatest challenge for sustainable soil management. Rome: Food and Agriculture Organization of the United Nations; 2019. p. 104.
Pimentel D, Harvey C, Resosudarmo P, Sinclair K, Kurz D, McNair M, et al. Environmental and economic costs of soil erosion and conservation benefits. Science. 1995;267:1117–23.
Borrelli P, Robinson DA, Fleischer LR, Lugato E, Ballabio C, Alewell C, et al. An assessment of the global impact of 21st century land use change on soil erosion. Nat Commun. 2017;8:1–13.
UN (United Nations). World Soil Day [online]. 2019. https://www.un.org/en/observances/world-soil-day.
Van Oost K, Bakker MM. Soil productivity and erosion. In: Wall DH, Bardgett RD, Behan-Pelletier V, Herrick JE, Jones H, Ritz K, et al. (eds.). Soil ecology and ecosystem services. Oxford, UK: Oxford University Press; 2012. 301–14.
Gregorich EG, Greer KJ, Anderson DW, Liang BC. Carbon distribution and losses: erosion and deposition effects. Soil Res. 1998;47:291–302.
Lal R, Pimentel D. Soil erosion: a carbon sink or source? Science. 2008;319:1040–2.
Mendonça R, Müller RA, Clow D, Verpoorter C, Raymond P, Tranvik LJ, et al. Organic carbon burial in global lakes and reservoirs. Nat Commun. 2017;8:1694.
Quinton JN, Govers G, Van Oost K, Bardgett RD. The impact of agricultural soil erosion on biogeochemical cycling. Nat Geosci. 2010;3:311–4.
Smith RW, Bianchi TS, Allison M, Savage C, Galy V. High rates of organic carbon burial in fjord sediments globally. Nat Geosci. 2015;8:450–U46.
Van Oost K, Quine TA, Govers G, De Gryze S, Six J, Harden JW, et al. The impact of agricultural soil erosion on the global carbon cycle. Science. 2007;318:626–9.
Maestre FT, Quero JL, Gotelli NJ, Escudero A, Ochoa V, Delgado-Baquerizo M, et al. Plant species richness and ecosystem multifunctionality in global drylands. Science. 2012;335:214–8.
Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun. 2016;7:10541.
Fanin N, Gundale MJ, Farrell M, Ciobanu M, Baldock JA, Nilsson MC, et al. Consistent effects of biodiversity loss on multifunctionality across contrasting ecosystems. Nat Ecol Evol. 2018;2:269–78.
Garland G, Banerjee S, Edlinger A, Oliveira EM, Herzog C, Wittwer R, et al. A closer look at the functions behind ecosystem multifunctionality: a review. J Ecol. 2020, https://doi.org/10.1111/1365-2745.13511.
Bardgett RD, Van Der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15:579–90.
Wall H, Nielsen UN, Six J. Soil biodiversity and human health. Nature. 2015;528:69–76.
Saleem M, Hu J, Jousset A. More than the sum of its parts: microbiome biodiversity as a driver of plant growth and soil health. Annu Rev Ecol Evol Syst. 2019;50:145–68.
Crowther TW, Van Den Hoogen J, Wan J, Mayes MA, Keiser AD, Mo L, et al. The global soil community and its influence on biogeochemistry. Science. 2019;365:eaav0550.
de Vries FT, Griffiths RI, Bailey M, Craig H, Girlanda M, Gweon HS, et al. Soil bacterial networks are less stable under drought than fungal networks. Nat Commun. 2018;9:3033.
Zhou J, Deng Y, Luo F, He Z, Yang Y. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. MBio. 2011;2:e00122–11.
Bragazza L, Parisod J, Buttler A, Bardgett RD. Biogeochemical plant–soil microbe feedback in response to climate warming in peatlands. Nat Clim Change. 2013;3:273–7.
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 USA. 2015;112:7033–8.
Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, et al. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci USA. 2015;112:15684–9.
Guo X, Feng J, Shi Z, Zhou X, Yuan M, Tao X, et al. Climate warming leads to divergent succession of grassland microbial communities. Nat Clim Change. 2018;8:813–8.
Li Z, Tian D, Wang B, Wang J, Wang S, Chen H, et al. Microbes drive global soil nitrogen mineralization and availability. Glob Change Biol. 2019;25:1078–88.
Wieder WR, Bonan GB, Allison SD. Global soil carbon projections are improved by modelling microbial processes. Nat Clim Change. 2013;3:909–12.
Chen Q, Dong J, Zhu D, Hu H, Delgado-Baquerizo M, Ma Y, et al. Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils. Soil Biol Biochem. 2020;141:107686.
Delgado-Baquerizo M, Reich PB, Trivedi C, Eldridge DJ, Abades S, Alfaro FD, et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol. 2020;4:210–20.
Wagg C, Schlaeppi K, Banerjee S, Kuramae EE, Van Der Heijden MGA. Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun. 2019;10:4841.
Van der Heijden MGA, Bardgett RD, Van Straalen NM. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett. 2008;11:296–310.
Barberán A, Bates ST, Casamayor EO, Fierer N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012;6:343–51.
Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 2019;13:1722–36.
Freilich MA, Wieters E, Broitman BR, Marquet PA, Navarrete SA. Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities? Ecology. 2018;99:690–9.
Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459:193–9.
Banerjee S, Schlaeppi K, Van Der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.
Herren CM, McMahon KD. Keystone taxa predict compositional change in microbial communities. Environ Microbiol. 2018;20:2207–17.
Ochoa-Hueso R, Collins SL, Delgado-Baquerizo M, Hamonts K, Pockman WT, Sinsabaugh RL, et al. Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents. Glob Change Biol. 2018;24:2818–27.
Mabuhay JA, Nakagoshi N, Isagi Y. Influence of erosion on soil microbial biomass, abundance and community diversity. Land Degrad Dev. 2004;15:183–95.
Li Z, Xiao H, Tang Z, Huang J, Nie X, Huang B, et al. Microbial responses to erosion-induced soil physico-chemical property changes in the hilly red soil region of southern China. Eur J Soil Biol. 2015;71:37–44.
Hou S, Xin M, Wang LL, Jiang H, Li N, Wang Z. The effects of erosion on the microbial populations and enzyme activity in black soil of northeastern China. Acta Ecologica Sin. 2014;34:295–301.
Zhang Y, Wu Y, Liu B, Zheng Q, Yin J. Characteristics and factors controlling the development of ephemeral gullies in cultivated catchments of black soil region, Northeast China. Soil Res. 2007;96:28–41.
Li H, Zhu H, Qiu L, Wei X, Liu B, Shao M. Response of soil OC, N and P to land-use change and erosion in the black soil region of the Northeast China. Agr Ecosyst Environ. 2020;302:107081.
Zheng F. Effect of vegetation changes on soil erosion on the Loess Plateau. Pedosphere 2006;16:420–7.
Page A, Miller R, Keeney D. Methods of Soil Analysis, Part 2. Chemical and Microbiological Properties. Madison, Wisconsin, American Society of Agronomy, Inc., Soil Science Society of America, Inc, 1982.
Brookes P, Landman A, Pruden G, Jenkinson D. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem. 1985;17:837–42.
Lefcheck JS, Byrnes JEK, Isbell F, Gamfeldt L, Griffin JN, Eisenhauer N, et al. Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats. Nat Commun. 2015;6:6936.
Maestre FT, Castillo-Monroy AP, Bowker MA, Ochoa-Hueso R. Species richness effects on ecosystem multifunctionality depend on evenness, composition and spatial pattern. J Ecol. 2012;100:317–30.
Wang Z, Zhang Q, Staley C, Gao H, Ishii S, Wei X, et al. Impact of long-term grazing exclusion on soil microbial community composition and nutrient availability. Biol Fertil Soils. 2019;55:121–34.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Mueller RC, Paula FS, Mirza BS, Rodrigues JLM, Nuesslein K, Bohannan BJM. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. ISME J. 2014;8:1548–50.
Al-Ghalith GA, Hillmann B, Ang K, Shields-Cutler R, Knights D. SHI7 is a self-learning pipeline for multipurpose short-read DNA quality control. mSystems. 2018;3:e00202–17.
Al-Ghalith GA, Montassier E, Ward HN, Knights D. NINJA-OPS: fast accurate marker gene alignment using concatenated ribosomes. PLoS Comput Biol. 2016;12:e1004658.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
Bray JR, Curtis JT. An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957;27:326–49.
Anderson MJ, Willis TJ. Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology. 2003;84:511–25.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, et al. Vegan: community ecology package. R package version 2.3-1. 2015, http://CRAN.R-project.org/package=vegan.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinforma. 2008;9:559.
Luo F, Zhong J, Yang Y, Scheuermann RH, Zhou J. Application of random matrix theory to biological networks. Phys Lett A. 2006;357:420–3.
Benjamini Y, Krieger AM, Yekutieli D. Adaptive linear step-up procedures that control the false discovery rate. Biometrika. 2006;93:491–507.
Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. Complex Syst. 2006;1695:1–9.
Ma B, Wang HZ, Dsouza M, Lou J, He Y, Dai ZM, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.
Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol. 2014;5:219.
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. ICWSM Conf. 2009;8:361–2.
Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–7.
Qiu L, Zhu H, Liu J, Yao Y, Wang X, Rong G, et al. Soil erosion significantly reduces organic carbon and nitrogen mineralization in a simulated experiment. Agr Ecosyst Environ. 2021;307:107232.
Crits-Christoph A, Robinson CK, Barnum T, Fricke WF, Davila AF, Jedynak B, et al. Colonization patterns of soil microbial communities in the Atacama Desert. Microbiome. 2013;1:28.
Tiemann LK, Billings SA. Changes in variability of soil moisture alter microbial community C and N resource use. Soil Biol Biochem. 2011;43:1837–47.
Banerjee S, Misra A, Sar A, Pal S, Chaudhury S, Dam B. Poor nutrient availability in opencast coalmine influences microbial community composition and diversity in exposed and underground soil profiles. Appl Soil Ecol. 2020;152:103544.
Abu-Hamdeh NH, Reeder RC. Soil thermal conductivity: effects of density, moisture, salt concentration, and organic matter. Soil Sci Soc Am J. 2000;64:1285–90.
Bajracharya RM, Lal R, Kimble JM. Diurnal and seasonal CO2-C flux from soil as related to erosion phases in central Ohio. Soil Sci Soc Am J. 2000;64:286–93.
Liang Y, Lal R, Guo S, Liu R, Hu Y. Impacts of simulated erosion and soil amendments on greenhouse gas fluxes and maize yield in Miamian soil of central Ohio. Sci Rep. 2018;8:520.
Van Der Voort M, Kempenaar M, Van Driel M, Raaijmakers JM, Mendes R. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecol Lett. 2016;19:375–82.
García-Palacios P, Vandegehuchte ML, Shaw EA, Dam M, Post KH, Ramirez KS, et al. Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective. Glob Change Biol. 2015;21:1590–1600.
Karimi B, Terrat S, Dequiedt S, Saby NPA, Horriguel W, Lelievre M, et al. Biogeography of soil bacteria and archaea across France. Sci Adv. 2018;4:eaat1808.
Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microb. 2006;72:1719–28.
Spain AM, Krumholz LR, Elshahed MS. Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J. 2009;3:992–1000.
Zhang C, Liu G, Xue S, Wang G. Soil bacterial community dynamics reflect changes in plant community and soil properties during the secondary succession of abandoned farmland in the Loess Plateau. Soil Biol Biochem. 2016;97:40–49.
Wolińska A, Kuzniar A, Zielenkiewicz U, Izak D, Szafranek-Nakonieczna A, Banach A, et al. Bacteroidetes as a sensitive biological indicator of agricultural soil usage revealed by a culture-independent approach. Appl Soil Ecol. 2017;119:128–37.
DeBruyn LM, Nixon LT, Fawaz MN, Johnson AM, Radosevich M. Global biogeography and quantitative seasonal dynamics of gemmatimonadetes in soil. Appl Environ Microb. 2011;77:6295–6300.
Bouskill NJ, Lim HC, Borglin S, Salve R, Wood TE, Silver WL, et al. Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J. 2013;7:384–94.
Naylor D, DeGraaf S, Purdom E, Coleman-Derr D. Drought and host selection influence bacterial community dynamics in the grass root microbiome. ISME J. 2017;11:2691–704.
Santos-Medellin C, Edwards J, Liechty Z, Nguyen B, Sundaresan V. Drought stress results in a compartment-specific restructuring of the rice root-associated microbiomes. mBio. 2017;8:e00764–17.
Chowdhury TR, Lee JY, Bottos EM, Brislawn CJ, White RA, Bramer LM, et al. Metaphenomic responses of a native prairie soil microbiome to moisture perturbations. mSystems. 2019;4:e00061–19.
Mickan BS, Abbott LK, Solaiman ZM, Mathes F, Siddique KHM, Jenkins SN. Soil disturbance and water stress interact to influence arbuscular mycorrhizal fungi, rhizosphere bacteria and potential for N and C cycling in an agricultural soil. Biol Fert Soils. 2019;55:53–66.
Van Horn DJ, Okie JG, Buelow HN, Gooseff MN, Barrett JE, Takacs-Vesbach CD. Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microb. 2014;80:3034–43.
Kielak A, Pijl AS, Van Veen JA, Kowalchuk GA. Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J. 2009;3:378–82.
Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 2012;6:1007–17.
Wolińska A, Kuzniar A, Zielenkiewicz U, Banach A, Blaszczyk M. Indicators of arable soils fatigue Bacterial – families and genera: a metagenomic approach. Ecol Indic. 2018;93:490–500.
Yang F, Niu KC, Collins CG, Yan XB, Ji YG, Ling N. Grazing practices affect the soil microbial community composition in a Tibetan alpine meadow. Land Degrad Dev. 2019;30:49–59.
Vitousek PM, Menge DNL, Reed SC, Cleveland CC. Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems. Philos Trans R Soc B Biol Sci. 2013;368:1621.
Fan KK, Delgado-Baquerizo M, Guo XS, Wang DZ, Wu YY, Zhu M, et al. Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome. 2019;7:143.
Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, et al. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol. 2020;5:314–30.
Banerjee S, Kirkby CA, Schmutter D, Bissett A, Kirkegaard JA, Richardson AE. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol Biochem. 2016;97:188–98.
Guo J, Ling N, Chen Z, Xue C, Li L, Liu L, et al. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. N Phytol. 2020;226:232–43.
Qi G, Ma G, Chen S, Lin C, Zhao X. Microbial network and soil properties are changed in bacterial wilt-susceptible soil. Appl Environ Microb. 2019;85:e00162–19.
Xue L, Ren H, Brodribb TJ, Wang J, Yao X, Li S. Long term effects of management practice intensification on soil microbial community structure and co-occurrence network in a non-timber plantation. For Ecol Manag. 2020;459:117805.
Ling N, Zhu C, Xue C, Chen H, Duan YH, Peng C. Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis. Soil Biol Biochem 2016;99:137–49.
Deng Y, Jiang YH, Yang YF, He ZL, Luo F, Zhou JZ. Molecular ecological network analyses. BMC Bioinforma. 2012;13:113.
Bai YX, She WW, Miao L, Qin SG, Zhang YQ. Soil microbial interactions modulate the effect of Artemisia ordosica on herbaceous species in a desert ecosystem, northern China. Soil Biol Biochem. 2020;150:108013.
Szoboszlay M, Dohrmann AB, Poeplau C, Don A, Tebbe CC. Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe. FEMS Microbiol Ecol. 2017;93:fix146.
Marcos MS, Bertiller MB, Olivera NL. Microbial community composition and network analyses in arid soils of the Patagonian Monte under grazing disturbance reveal an important response of the community to soil particle size. Appl Soil Ecol. 2019;138:223–32.
Hamamura N, Olson SH, Ward DM, Inskeep WP. Microbial population dynamics associated with crude-oil biodegradation in diverse soils. Appl Environ Microb. 2006;72:6316–24.
Acosta‐Martínez V, Cotton J, Gardner T, Moore‐Kucera J, Zak J, Wester D, et al. Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling. Appl Soil Ecol. 2014;84:69–82.
Peng M, Jia H, Wang Q. The effect of land use on bacterial communities in Saline-Alkali soil. Curr Microbiol. 2017;74:325–33.
Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, et al. Soil microbiome responses to the short-term effects of Amazonian deforestation. Mol Ecol. 2015;24:2433–48.
Byers AK, Condron L, Donavan T, O’Callaghan M, Patuawa T, Waipara N, et al. Soil microbial diversity in adjacent forest systems—contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest. FEMS Microbiol Ecol. 2020;96:fiaa047.
Schmidt MWI, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens IA, et al. Trumbore, Persistence of soil organic matter as an ecosystem property. Nature. 2011;478:49–56.
Lehmann J, Kleber M. The contentious nature of soil organic matter. Nature. 2015;528:60–68.
Buzzard V, Michaletz ST, Deng Y, He Z, Ning D, Shen L, et al. Continental scale structuring of forest and soil diversity via functional traits. Nat Ecol Evol. 2019;3:1298–308.
Wei X, Shao M, Gale W, Li L. Global pattern of soil carbon losses due to the conversion of forests to agricultural land. Sci Rep. 2014;4:4062.
Delgado‐Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, et al. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology. 2018;99:583–96.
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.
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.
Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun. 2016;7:12083.
Allison SD, Martiny JBH, et al. Resistance resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA. 2008;105:11512–9.
Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, et al. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J. 2014;8:226–44.
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