Guerra, C. A. et al. Tracking, targeting, and conserving soil biodiversity. Science 371, 239–241 (2021).
Google Scholar
Orgiazzi, A. et al. Global Soil Biodiversity Atlas (European Commission, Publications Office of the European Union, 2016).
Tecon, R. & Or, D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol. Rev. 41, 599–623 (2017).
Google Scholar
Williamson, K. E., Fuhrmann, J. J., Wommack, K. E. & Radosevich, M. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu. Rev. Virol. 4, 201–219 (2017). This Review provides a comprehensive overview of methods and technologies used to study soil viruses alongside a guide of metrics describing soil viruses across diverse soil ecosystems.
Google Scholar
Stefan, G., Cornelia, B., Jörg, R. & Michael, B. Soil water availability strongly alters the community composition of soil protists. Pedobiologia 57, 205–213 (2014).
Leake, J. et al. Networks of power and influence: the role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning. Can. J. Bot. 82, 1016–1045 (2004).
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018). This study compiled metagenomic and metabarcoding data from 189 sites to demonstrate global patterns in the structure and function of soil microbial communities as well as the widespread prevalence of bacterial–fungal antagonism as an important structuring force of microbial communities.
Google Scholar
He, L. et al. Global biogeography of fungal and bacterial biomass carbon in topsoil. Soil Biol. Biochem. 151, 108024 (2020).
Google Scholar
Bach, E. M., Williams, R. J., Hargreaves, S. K., Yang, F. & Hofmockel, K. S. Greatest soil microbial diversity found in micro-habitats. Soil Biol. Biochem. 118, 217–226 (2018).
Google Scholar
Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).
Google Scholar
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Google Scholar
Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).
Google Scholar
Crowther, T. W. et al. The global soil community and its influence on biogeochemistry. Science 365, eaav0550 (2019).
Google Scholar
Liang, C., Amelung, W., Lehmann, J. & Kästner, M. Quantitative assessment of microbial necromass contribution to soil organic matter. Glob. Change Biol. 25, 3578–3590 (2019). This article estimates that more than 50% of SOM may be derived from microbial necromass in grassland and agricultural ecosystems based on extrapolations from amino sugar biomarker data.
Angst, G., Mueller, K. E., Nierop, K. G. J. & Simpson, M. J. Plant- or microbial-derived? A review on the molecular composition of stabilized soil organic matter. Soil Biol. Biochem. 156, 108189 (2021).
Google Scholar
Ludwig, M. et al. Microbial contribution to SOM quantity and quality in density fractions of temperate arable soils. Soil Biol. Biochem. 81, 311–322 (2015). This study uses lipid biomarkers to estimate that at least 50% of SOM may be derived from microbial necromass.
Google Scholar
Simpson, A. J., Simpson, M. J., Smith, E. & Kelleher, B. P. Microbially derived inputs to soil organic matter: are current estimates too low? Environ. Sci. Technol. 41, 8070–8076 (2007).
Google Scholar
Blazewicz, S. J. et al. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J. 14, 1520–1532 (2020). This study used quantitative stable isotope probing to calculate growth and mortality rates of bacteria following the rewetting of a dry Mediterranean soil, and demonstrated that bacterial growth was density independent whereas bacterial mortality was density dependent.
Google Scholar
Vieira, S. et al. Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME J. 14, 463–475 (2020).
Google Scholar
Nuccio, E. E. et al. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME J. 14, 999–1014 (2020).
Google Scholar
Shi, S. et al. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6, e00746 (2015).
Google Scholar
Bastian, F., Bouziri, L., Nicolardot, B. & Ranjard, L. Impact of wheat straw decomposition on successional patterns of soil microbial community structure. Soil Biol. Biochem. 41, 262–275 (2009).
Google Scholar
Whitman, T. et al. Microbial community assembly differs across minerals in a rhizosphere microcosm. Environ. Microbiol. 20, 4444–4460 (2018).
Google Scholar
Maynard, D. S., Crowther, T. W. & Bradford, M. A. Fungal interactions reduce carbon use efficiency. Ecol. Lett. 20, 1034–1042 (2017). This study demonstrated that antagonistic interactions between wood-decay fungi can reduce CUE of the fungal community.
Google Scholar
Crowther, T. W. et al. Environmental stress response limits microbial necromass contributions to soil organic carbon. Soil Biol. Biochem. 85, 153–161 (2015).
Google Scholar
Hu, Y., Zheng, Q., Noll, L., Zhang, S. & Wanek, W. Direct measurement of the in situ decomposition of microbial-derived soil organic matter. Soil Biol. Biochem. 141, 107660 (2020).
Google Scholar
Fernandez, C. W., Langley, J. A., Chapman, S., McCormack, M. L. & Koide, R. T. The decomposition of ectomycorrhizal fungal necromass. Soil Biol. Biochem. 93, 38–49 (2016). This review article summarizes how the stoichiometry, morphology and chemistry of microbial necromass affects its decomposition rate in soil.
Google Scholar
Buckeridge, K. M. et al. Sticky dead microbes: rapid abiotic retention of microbial necromass in soil. Soil Biol. Biochem. 149, 107929 (2020).
Google Scholar
Creamer, C. A. et al. Mineralogy dictates the initial mechanism of microbial necromass association. Geochim. Cosmochim. Acta 260, 161–176 (2019). This study used Raman microspectroscopy and 13C-labelled necromass to demonstrate that different mineral types retained microbial necromass through different mechanisms and with different strengths.
Google Scholar
Schurig, C. et al. Microbial cell-envelope fragments and the formation of soil organic matter: a case study from a glacier forefield. Biogeochemistry 113, 595–612 (2013).
Google Scholar
Kopittke, P. M. et al. Nitrogen-rich microbial products provide new organo-mineral associations for the stabilization of soil organic matter. Glob. Change Biol. 24, 1762–1770 (2018).
Miltner, A., Bombach, P., Schmidt-Brücken, B. & Kästner, M. SOM genesis: microbial biomass as a significant source. Biogeochemistry 111, 41–55 (2012).
Google Scholar
Kleber, M. et al. Dynamic interactions at the mineral–organic matter interface. Nat. Rev. Earth Environ. 2, 402–421 (2021).
Blagodatskaya, E. & Kuzyakov, Y. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol. Biochem. 67, 192–211 (2013).
Google Scholar
Or, D., Smets, B. F., Wraith, J. M., Dechesne, A. & Friedman, S. P. Physical constraints affecting bacterial habitats and activity in unsaturated porous media–a review. Adv. Water Resour. 30, 1505–1527 (2007).
Kuzyakov, Y. & Blagodatskaya, E. Microbial hotspots and hot moments in soil: concept & review. Soil Biol. Biochem. 83, 184–199 (2015).
Google Scholar
Finzi, A. C. et al. Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles. Glob. Change Biol. 21, 2082–2094 (2015).
Yuan, M. M. et al. Fungal-bacterial cooccurrence patterns differ between arbuscular mycorrhizal fungi and nonmycorrhizal fungi across soil niches. mBio 12, e03509-20 (2015).
Zhang, L. & Lueders, T. Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. FEMS Microbiol. Ecol. 93, fix103 (2017).
Sokol, N. W. & Bradford, M. A. Microbial formation of stable soil carbon is more efficient from belowground than aboveground input. Nat. Geosci. 12, 46–53 (2019).
Google Scholar
Kallenbach, C. M., Frey, S. D. & Grandy, A. S. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat. Commun. 7, 13630 (2016). This study used artificial soils to provide empirical evidence that SOM can be entirely microbially derived, and also demonstrated a positive relationship between CUE and SOM formation.
Google Scholar
Wood, J. L., Tang, C. & Franks, A. E. Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology. Front. Microbiol. 9, 121 (2018).
Google Scholar
Violle, C. et al. Let the concept of trait be functional! Oikos 116, 882–892 (2007).
Madin, J. S. et al. A synthesis of bacterial and archaeal phenotypic trait data. Sci. Data 7, 170 (2020).
Google Scholar
Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).
Google Scholar
Brown, C. T., Olm, M. R., Thomas, B. C. & Banfield, J. F. Measurement of bacterial replication rates in microbial communities. Nat. Biotechnol. 34, 1256–1263 (2016). This study developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates.
Google Scholar
Nayfach, S. & Pollard, K. S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 16, 51 (2015).
Google Scholar
Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl Acad. Sci. USA 112, 10967–10972 (2015).
Google Scholar
Vieira-Silva, S. & Rocha, E. P. C. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 6, e1000808 (2010).
Google Scholar
Hasby, F. A., Barbi, F., Manzoni, S. & Lindahl, B. D. Transcriptomic markers of fungal growth, respiration and carbon-use efficiency. FEMS Microbiol. Lett. 368, fnab100 (2021).
Google Scholar
Maillard, F., Schilling, J., Andrews, E., Schreiner, K. M. & Kennedy, P. Functional convergence in the decomposition of fungal necromass in soil and wood. FEMS Microbiol. Ecol. 96, fiz209 (2020).
Google Scholar
Clemmensen, K. E. et al. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. N. Phytol. 205, 1525–1536 (2015).
Google Scholar
Olivelli, M. S. et al. Unraveling mechanisms behind biomass–clay interactions using comprehensive multiphase nuclear magnetic resonance (NMR) Spectroscopy. ACS Earth Space Chem. 4, 2061–2072 (2020).
Google Scholar
Achtenhagen, J., Goebel, M.-O., Miltner, A., Woche, S. K. & Kästner, M. Bacterial impact on the wetting properties of soil minerals. Biogeochemistry 122, 269–280 (2015).
Google Scholar
Lehmann, J. et al. Persistence of soil organic carbon caused by functional complexity. Nat. Geosci. 13, 529–534 (2020).
Google Scholar
Ahmed, E. & Holmström, S. J. M. Microbe–mineral interactions: The impact of surface attachment on mineral weathering and element selectivity by microorganisms. Chem. Geol. 403, 13–23 (2015).
Google Scholar
Chenu, C. Clay- or sand-polysaccharide associations as models for the interface between micro-organisms and soil: water related properties and microstructure. Geoderma 56, 143–156 (1993).
Google Scholar
Sher, Y. et al. Microbial extracellular polysaccharide production and aggregate stability controlled by switchgrass (Panicum virgatum) root biomass and soil water potential. Soil Biol. Biochem. 143, 107742 (2020).
Google Scholar
Lybrand, R. A. et al. A coupled microscopy approach to assess the nano-landscape of weathering. Sci. Rep. 9, 5377 (2019).
Google Scholar
Prommer, J. et al. Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity. Glob. Change Biol. 26, 669–681 (2020).
Cotrufo, M. F., Wallenstein, M. D., Boot, C. M., Denef, K. & Paul, E. The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Glob. Change Biol. 19, 988–995 (2013).
Liang, C., Schimel, J. P. & Jastrow, J. D. The importance of anabolism in microbial control over soil carbon storage. Nat. Microbiol. 2, 17105 (2017).
Google Scholar
Geyer, K. M., Kyker-Snowman, E., Grandy, A. S. & Frey, S. D. Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter. Biogeochemistry 127, 173–188 (2016).
Google Scholar
Kallenbach, C. M., Grandy, A. S., Frey, S. D. & Diefendorf, A. F. Microbial physiology and necromass regulate agricultural soil carbon accumulation. Soil Biol. Biochem. 91, 279–290 (2015).
Google Scholar
Buckeridge, K. M. et al. Environmental and microbial controls on microbial necromass recycling, an important precursor for soil carbon stabilization. Commun. Earth Env. 1, 36 (2020).
Saifuddin, M., Bhatnagar, J. M., Segrè, D. & Finzi, A. C. Microbial carbon use efficiency predicted from genome-scale metabolic models. Nat. Commun. 10, 3568 (2019).
Google Scholar
Schimel, J., Balser, T. C. & Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386–1394 (2007).
Google Scholar
Mason‐Jones, K., Banfield, C. C. & Dippold, M. A. Compound-specific 13C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria. Rapid Commun. Mass. Spectrom. 33, 795–802 (2019).
Google Scholar
Bååth, E. The use of neutral lipid fatty acids to indicate the physiological conditions of soil fungi. Microb. Ecol. 45, 373–383 (2003).
Google Scholar
Slessarev, E. W. et al. Cellular and extracellular C contributions to respiration after wetting dry soil. Biogeochemistry 147, 307–324 (2020).
Google Scholar
Slessarev, E. W. & Schimel, J. P. Partitioning sources of CO2 emission after soil wetting using high-resolution observations and minimal models. Soil Biol. Biochem. 143, 107753 (2020).
Google Scholar
Lennon, J. T. & Jones, S. E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 9, 119–130 (2011).
Google Scholar
Brangarí, A. C., Manzoni, S. & Rousk, J. A soil microbial model to analyze decoupled microbial growth and respiration during soil drying and rewetting. Soil Biol. Biochem. 148, 107871 (2020).
Zha, J. & Zhuang, Q. Microbial dormancy and its impacts on northern temperate and boreal terrestrial ecosystem carbon budget. Biogeosciences 17, 4591–4610 (2020).
Google Scholar
Anderson, T.-H. Microbial eco-physiological indicators to asses soil quality. Agric. Ecosyst. Environ. 98, 285–293 (2003).
Geyer, K., Schnecker, J., Grandy, A. S., Richter, A. & Frey, S. Assessing microbial residues in soil as a potential carbon sink and moderator of carbon use efficiency. Biogeochemistry 151, 237–249 (2020).
Google Scholar
Sepehrnia, N. et al. Transport, retention, and release of Escherichia coli and Rhodococcus erythropolis through dry natural soils as affected by water repellency. Sci. Total Environ. 694, 133666 (2019).
Google Scholar
Boeddinghaus, R. S. et al. The mineralosphere — interactive zone of microbial colonization and carbon use in grassland soils. Biol. Fertil. Soils 57, 587–601 (2021).
Google Scholar
Vieira, S. et al. Bacterial colonization of minerals in grassland soils is selective and highly dynamic. Environ. Microbiol. 22, 917–933 (2020).
Google Scholar
Ma, T. et al. Divergent accumulation of microbial necromass and plant lignin components in grassland soils. Nat. Commun. 9, 3480 (2018).
Google Scholar
Blazewicz, S. J., Schwartz, E. & Firestone, M. K. Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil. Ecology 95, 1162–1172 (2014).
Google Scholar
Ceja-Navarro, J. A. et al. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome 9, 96 (2021).
Google Scholar
Starr, E. P., Nuccio, E. E., Pett-Ridge, J., Banfield, J. F. & Firestone, M. K. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc. Natl Acad. Sci. USA 116, 25900–25908 (2019). This comprehensive study of RNA viruses detectable in a grassland soil showed how these viruses are shaped by the presence of plant roots and litter.
Google Scholar
Shi, S. et al. The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages. Ecol. Lett. 19, 926–936 (2016).
Google Scholar
Yan, Y., Kuramae, E. E., de Hollander, M., Klinkhamer, P. G. L. & van Veen, J. A. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME J. 11, 56–66 (2017).
Google Scholar
Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470 (2018).
Google Scholar
Pett-Ridge, J. et al. in Rhizosphere Biology: Interactions Between Microbes and Plants (eds Gupta, V. V. S. R. & Sharma, A. K.) 51–73 (Springer, 2021).
Poll, C., Marhan, S., Ingwersen, J. & Kandeler, E. Dynamics of litter carbon turnover and microbial abundance in a rye detritusphere. Soil Biol. Biochem. 40, 1306–1321 (2008).
Google Scholar
Buchkowski, R. W., Bradford, M. A., Grandy, A. S., Schmitz, O. J. & Wieder, W. R. Applying population and community ecology theory to advance understanding of belowground biogeochemistry. Ecol. Lett. 20, 231–245 (2017).
Google Scholar
Erktan, A., Or, D. & Scheu, S. The physical structure of soil: determinant and consequence of trophic interactions. Soil Biol. Biochem. 148, 107876 (2020).
Google Scholar
Roesch, L. F. W. et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283–290 (2007).
Google Scholar
Carson, J. K. et al. Low pore connectivity increases bacterial diversity in soil. Appl. Environ. Microbiol. 76, 3936–3942 (2010).
Google Scholar
Raynaud, X. & Nunan, N. Spatial ecology of bacteria at the microscale in soil. PLoS ONE 9, e87217 (2014).
Google Scholar
Ekelund, F., Rønn, R. & Christensen, S. Distribution with depth of protozoa, bacteria and fungi in soil profiles from three Danish forest sites. Soil Biol. Biochem. 33, 475–481 (2001).
Google Scholar
Sharrar, A. M. et al. Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type. mBio 11, e00416-20 (2020).
Google Scholar
Georgiou, K., Abramoff, R. Z., Harte, J., Riley, W. J. & Torn, M. S. Microbial community-level regulation explains soil carbon responses to long-term litter manipulations. Nat. Commun. 8, 1223 (2017). This modelling study demonstrated that including a density-dependent microbial mortality term can reduce the oscillatory behaviour of soil carbon models.
Google Scholar
Thakur, M. P. & Geisen, S. Trophic regulations of the soil microbiome. Trends Microbiol. 27, 771–780 (2019).
Google Scholar
Fanin, N. et al. The ratio of Gram-positive to Gram-negative bacterial PLFA markers as an indicator of carbon availability in organic soils. Soil Biol. Biochem. 128, 111–114 (2019).
Google Scholar
Wang, W. et al. Predatory Myxococcales are widely distributed in and closely correlated with the bacterial community structure of agricultural land. Appl. Soil Ecol. 146, 103365 (2020).
Hungate, B. A. et al. The functional significance of bacterial predators. mBio 12, e00466-21 (2021).
Google Scholar
Jover, L. F., Effler, T. C., Buchan, A., Wilhelm, S. W. & Weitz, J. S. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat. Rev. Microbiol. 12, 519–528 (2014).
Google Scholar
Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018). This study identified novel viral genomes from metagenomes and linked many of these viruses in silico to bacterial hosts and carbon metabolisms across the spatial gradient of permafrost thaw.
Google Scholar
Ren, D., Madsen, J. S., Sørensen, S. J. & Burmølle, M. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation. ISME J. 9, 81–89 (2015).
Google Scholar
Lee, K. W. K. et al. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 8, 894–907 (2014).
Google Scholar
Witzgall, K. et al. Particulate organic matter as a functional soil component for persistent soil organic carbon. Nat. Commun. 12, 4115 (2021).
Google Scholar
Frey, S. D. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annu. Rev. Ecol. Evol. Syst. 50, 237–259 (2019).
Drigo, B. et al. Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. Proc. Natl Acad. Sci. USA 107, 10938–10942 (2010).
Google Scholar
Kaiser, C. et al. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation. N. Phytol. 205, 1537–1551 (2015).
Google Scholar
Shah, F. et al. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. N. Phytol. 209, 1705–1719 (2016).
Google Scholar
Tisserant, E. et al. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc. Natl Acad. Sci. USA 110, 20117–20122 (2013).
Google Scholar
Hestrin, R., Hammer, E. C., Mueller, C. W. & Lehmann, J. Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition. Commun. Biol. 2, 233 (2019).
Google Scholar
Averill, C., Turner, B. L. & Finzi, A. C. Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505, 543–545 (2014).
Google Scholar
Averill, C. & Hawkes, C. V. Ectomycorrhizal fungi slow soil carbon cycling. Ecol. Lett. 19, 937–947 (2016).
Google Scholar
Craig, M. E. et al. Tree mycorrhizal type predicts within-site variability in the storage and distribution of soil organic matter. Glob. Change Biol. 24, 3317–3330 (2018).
See, C. R. et al. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. Glob. Change Biol. https://doi.org/10.1111/gcb.16073 (2022).
Google Scholar
Adamczyk, B., Sietiö, O.-M., Biasi, C. & Heinonsalo, J. Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils. N. Phytol. 223, 16–21 (2019).
Vidal, A. et al. Visualizing the transfer of organic matter from decaying plant residues to soil mineral surfaces controlled by microorganisms. Soil Biol. Biochem. 160, 108347 (2021).
Google Scholar
Kallenbach, C. M., Wallenstein, M. D., Schipanksi, M. E. & Grandy, A. S. Managing agroecosystems for soil microbial carbon use efficiency: ecological unknowns, potential outcomes, and a path forward. Front. Microbiol. 10, 1146 (2019).
Google Scholar
Blagodatskaya, E., Blagodatsky, S., Anderson, T.-H. & Kuzyakov, Y. microbial growth and carbon use efficiency in the rhizosphere and root-free soil. PLoS ONE 9, e93282 (2014).
Google Scholar
Domeignoz-Horta, L. A. et al. Microbial diversity drives carbon use efficiency in a model soil. Nat. Commun. 11, 3684 (2020).
Google Scholar
Fernandez, C. W. & Kennedy, P. G. Revisiting the ‘Gadgil effect’: do interguild fungal interactions control carbon cycling in forest soils? N. Phytol. 209, 1382–1394 (2016).
Google Scholar
Nicolas, A. M. et al. Soil candidate phyla radiation bacteria encode components of aerobic metabolism and co-occur with nanoarchaea in the rare biosphere of rhizosphere grassland communities. mSystems 6, e0120520 (2021).
Google Scholar
Starr, E. P. et al. Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. Microbiome 6, 122 (2018).
Google Scholar
Pace, M. L. Bacterial mortality and the fate of bacterial production. Hydrobiologia 159, 41–49 (1988).
Cram, J. A., Parada, A. E. & Fuhrman, J. A. Dilution reveals how viral lysis and grazing shape microbial communities. Limnol. Oceanogr. 61, 889–905 (2016).
Ankrah, N. Y. D. et al. Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. ISME J. 8, 1089–1100 (2014). This study demonstrated that in a marine environment, the mechanism of death (that is, phage infection) altered the biochemistry of microbial necromass relative to uninfected cells.
Google Scholar
Lindeman, R. L. The trophic-dynamic aspect of ecology. Ecology 23, 399–417 (1942).
Clarholm, M. Interactions of bacteria, protozoa and plants leading to mineralization of soil nitrogen. Soil Biol. Biochem. 17, 181–187 (1985).
Google Scholar
Pasternak, Z. et al. In and out: an analysis of epibiotic vs periplasmic bacterial predators. ISME J. 8, 625–635 (2014).
Google Scholar
Lee, X., Wu, H.-J., Sigler, J., Oishi, C. & Siccama, T. Rapid and transient response of soil respiration to rain. Glob. Change Biol. 10, 1017–1026 (2004).
Schimel, J. P. Life in dry soils: effects of drought on soil microbial communities and processes. Annu. Rev. Ecol. Evol. Syst. 49, 409–432 (2018).
Granato, E. T., Meiller-Legrand, T. A. & Foster, K. R. The evolution and ecology of bacterial warfare. Curr. Biol. 29, R521–R537 (2019).
Google Scholar
Bradford, M. A. et al. Managing uncertainty in soil carbon feedbacks to climate change. Nat. Clim. Change 6, 751–758 (2016).
Sierra, C. A. & Müller, M. A general mathematical framework for representing soil organic matter dynamics. Ecol. Monogr. 85, 505–524 (2015).
Wang, G. et al. Microbial dormancy improves development and experimental validation of ecosystem model. ISME J. 9, 226–237 (2015).
Google Scholar
Wieder, W., Grandy, S., Kallenbach, M. & Bonan, B. Integrating microbial physiology and physio-chemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model. Biogeosciences 11, 3899–3917 (2014).
Allison, S. D. A trait-based approach for modelling microbial litter decomposition. Ecol. Lett. 15, 1058–1070 (2012). This paper described one of the first trait-based modelling approaches to link microbial community composition with physiological and enzymatic traits to predict litter decomposition in soil.
Google Scholar
Kaiser, C., Franklin, O., Dieckmann, U. & Richter, A. Microbial community dynamics alleviate stoichiometric constraints during litter decay. Ecol. Lett. 17, 680–690 (2014).
Google Scholar
Ebrahimi, A. & Or, D. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles – upscaling an aggregate biophysical model. Glob. Change Biol. 22, 3141–3156 (2016). This paper presented a demonstration of how to upscale results from a mechanistic model of microbial activity in soil aggregates to scales of practical interest for hydrological and climate models.
Lajoie, G. & Kembel, S. W. Making the most of trait-based approaches for microbial ecology. Trends Microbiol. 27, 814–823 (2019). This opinion article discussed trait-based approaches in microbial ecology with a focus on utilization of large-scale datasets for improved ecological understanding.
Google Scholar
Wang, G., Post, W. M. & Mayes, M. A. Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses. Ecol. Appl. 23, 255–272 (2013).
Google Scholar
Moorhead, D. L. & Sinsabaugh, R. L. A theoretical model of litter decay and microbial interaction. Ecol. Monogr. 76, 151–174 (2006).
Kooijman, S. A. L. M., Muller, E. B. & Stouthamer, A. H. Microbial growth dynamics on the basis of individual budgets. Antonie Van Leeuwenhoek 60, 159–174 (1991).
Google Scholar
Evans, S., Dieckmann, U., Franklin, O. & Kaiser, C. Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model. Soil Biol. Biochem. 93, 28–37 (2016).
Google Scholar
Allison, S. D. Modeling adaptation of carbon use efficiency in microbial communities. Front. Microbiol. 5, 571 (2014).
Google Scholar
Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).
Google Scholar
Tang, J. & Riley, W. J. Weaker soil carbon–climate feedbacks resulting from microbial and abiotic interactions. Nat. Clim. Change 5, 56–60 (2015).
Google Scholar
Zhang, Y. et al. Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically-defined MEMS 2.0 model. Biogeosciences 18, 3147–3171 (2021).
Google Scholar
Blankinship, J. C. et al. Improving understanding of soil organic matter dynamics by triangulating theories, measurements, and models. Biogeochemistry 140, 1–13 (2018).
Google Scholar
Ebrahimi, A. N. & Or, D. Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks. Water Resour. Res. 50, 7406–7429 (2014).
Tang, J. & Riley, W. J. A theory of effective microbial substrate affinity parameters in variably saturated soils and an example application to aerobic soil heterotrophic respiration. J. Geophys. Res. Biogeosci. 124, 918–940 (2019).
Manzoni, S., Schaeffer, S. M., Katul, G., Porporato, A. & Schimel, J. P. A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils. Soil Biol. Biochem. 73, 69–83 (2014).
Google Scholar
Brangarí, A. C., Fernàndez-Garcia, D., Sanchez-Vila, X. & Manzoni, S. Ecological and soil hydraulic implications of microbial responses to stress – a modeling analysis. Adv. Water Resour. 116, 178–194 (2018).
Alster, C. J., Weller, Z. D. & von Fischer, J. C. A meta-analysis of temperature sensitivity as a microbial trait. Glob. Change Biol. 24, 4211–4224 (2018).
Wang, G., Li, W., Wang, K. & Huang, W. Uncertainty quantification of the soil moisture response functions for microbial dormancy and resuscitation. Soil Biol. Biochem. 160, 108337 (2021).
Google Scholar
Sierra, C. A., Trumbore, S. E., Davidson, E. A., Vicca, S. & Janssens, I. Sensitivity of decomposition rates of soil organic matter with respect to simultaneous changes in temperature and moisture. J. Adv. Model. Earth Syst. 7, 335–356 (2015).
Nunan, N., Schmidt, H. & Raynaud, X. The ecology of heterogeneity: soil bacterial communities and C dynamics. Philos. Trans. R. Soc. B Biol. Sci. 375, 20190249 (2020).
Google Scholar
Kaiser, C., Franklin, O., Richter, A. & Dieckmann, U. Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils. Nat. Commun. 6, 8960 (2015).
Google Scholar
Craig, M. E., Mayes, M. A., Sulman, B. N. & Walker, A. P. Biological mechanisms may contribute to soil carbon saturation patterns. Glob. Change Biol. 27, 2633–2644 (2021).
Fan, X. et al. Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool. ISME J. 15, 2248–2263 (2021).
Google Scholar
Sulman, B. N. et al. Multiple models and experiments underscore large uncertainty in soil carbon dynamics. Biogeochemistry 141, 109–123 (2018). This paper addressed key uncertainties in the representation of microbial degradation and mineral stabilization in five microbially explicit soil carbon models.
Google Scholar
Marschmann, G. L., Pagel, H., Kügler, P. & Streck, T. Equifinality, sloppiness, and emergent structures of mechanistic soil biogeochemical models. Environ. Model. Softw. 122, 104518 (2019).
Martiny, J. B. H., Jones, S. E., Lennon, J. T. & Martiny, A. C. Microbiomes in light of traits: a phylogenetic perspective. Science 350, aac9323 (2015).
Google Scholar
Malik, A. A., Thomson, B. C., Whiteley, A. S., Bailey, M. & Griffiths, R. I. Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics. mBio 8, e00799-17 (2017).
Google Scholar
Westoby, M. et al. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol. Lett. 24, 1487–1504 (2021).
Google Scholar
Jung, M.-Y. et al. Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283 (2022).
Google Scholar
Kempes, C. P., Wang, L., Amend, J. P., Doyle, J. & Hoehler, T. Evolutionary tradeoffs in cellular composition across diverse bacteria. ISME J. 10, 2145–2157 (2016).
Google Scholar
Dethlefsen, L. & Schmidt, T. M. Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol. 189, 3237–3245 (2007).
Google Scholar
Andersen, K. H. et al. Characteristic sizes of life in the oceans, from bacteria to whales. Annu. Rev. Mar. Sci. 8, 217–241 (2016).
Google Scholar
Malik, A. A. et al. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J. 14, 1–9 (2020).
Google Scholar
Weissman, J. L., Hou, S. & Fuhrman, J. A. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proc. Natl Acad. Sci. USA 118, e2016810118 (2021).
Google Scholar
Li, G., Rabe, K. S., Nielsen, J. & Engqvist, M. K. M. Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima. ACS Synth. Biol. 8, 1411–1420 (2019).
Google Scholar
Hungate, B. A. et al. Quantitative microbial ecology through stable isotope probing. Appl. Environ. Microbiol. 81, 7570–7581 (2015).
Google Scholar
Couradeau, E. et al. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat. Commun. 10, 2770 (2019).
Google Scholar
Starr, E. P. et al. Stable-isotope-informed, genome-resolved metagenomics uncovers potential cross-kingdom interactions in rhizosphere soil. mSphere 6, e0008521 (2021).
Google Scholar
Rousk, J. & Bååth, E. Fungal and bacterial growth in soil with plant materials of different C/N ratios. FEMS Microbiol. Ecol. 62, 258–267 (2007).
Google Scholar
Koechli, C., Campbell, A. N., Pepe-Ranney, C. & Buckley, D. H. Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing. Soil Biol. Biochem. 130, 150–158 (2019).
Google Scholar
Wilhelm, R. C., Singh, R., Eltis, L. D. & Mohn, W. W. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J. 13, 413–429 (2019).
Google Scholar
Neurath, R. A. et al. Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially derived residues. Environ. Sci. Technol. 55, 13345–13355 (2021).
Google Scholar
Luo, Y. et al. Rice rhizodeposition promotes the build-up of organic carbon in soil via fungal necromass. Soil Biol. Biochem. 160, 108345 (2021).
Google Scholar
Carini, P. et al. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat. Microbiol. 2, 16242 (2016).
Google Scholar
Sharma, K., Palatinszky, M., Nikolov, G., Berry, D. & Shank, E. A. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. eLife 9, e56275 (2020).
Google Scholar
Arellano-Caicedo, C., Ohlsson, P., Bengtsson, M., Beech, J. P. & Hammer, E. C. Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation. Commun. Biol. 4, 1226 (2021).
Google Scholar
Jansson, J. K. & Hofmockel, K. S. Soil microbiomes and climate change. Nat. Rev. Microbiol. 18, 35–46 (2020).
Google Scholar
García-Palacios, P. et al. Evidence for large microbial-mediated losses of soil carbon under anthropogenic warming. Nat. Rev. Earth Env. 2, 507–517 (2021).
Schulz, F. et al. Hidden diversity of soil giant viruses. Nat. Commun. 9, 4881 (2018).
Google Scholar
Trubl, G. et al. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 7, e7265 (2019).
Google Scholar
Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).
Google Scholar
Sommers, P., Chatterjee, A., Varsani, A. & Trubl, G. Integrating viral metagenomics into an ecological framework. Annu. Rev. Virol. 8, 133–158 (2021).
Google Scholar
Pratama, A. A. & van Elsas, J. D. The ‘neglected’ soil virome–potential role and impact. Trends Microbiol. 26, 649–662 (2018).
Google Scholar
Ghosh, D. et al. Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA. Appl. Environ. Microbiol. 74, 495–502 (2008).
Google Scholar
Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).
Google Scholar
Howard-Varona, C. et al. Phage-specific metabolic reprogramming of virocells. ISME J. 14, 881–895 (2020).
Google Scholar
Howard-Varona, C. et al. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. ISME J. 12, 1605–1618 (2018).
Google Scholar
Van Goethem, M. Characteristics of wetting-induced bacteriophage blooms in biological soil crust. mBio 10, e02287-19 (2019).
Google Scholar
Trubl, G. et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9, 208 (2021).
Google Scholar
Lee, S. et al. Methane-derived carbon flows into host–virus networks at different trophic levels in soil. Proc. Natl Acad. Sci. USA 118, e2105124118 (2021). This study used stable isotope probing metagenomics to connect, in situ, active virus–host infections with the biogeochemical process of methane oxidation in soil.
Google Scholar
Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B. L. & Sullivan, M. B. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. ISME J. 11, 7–14 (2017).
Google Scholar
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