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Life and death in the soil microbiome: how ecological processes influence biogeochemistry

  • Guerra, C. A. et al. Tracking, targeting, and conserving soil biodiversity. Science 371, 239–241 (2021).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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.

    CAS 
    PubMed 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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.

    CAS 
    PubMed 

    Google Scholar 

  • He, L. et al. Global biogeography of fungal and bacterial biomass carbon in topsoil. Soil Biol. Biochem. 151, 108024 (2020).

    CAS 

    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).

    CAS 

    Google Scholar 

  • Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).

    PubMed 

    Google Scholar 

  • Crowther, T. W. et al. The global soil community and its influence on biogeochemistry. Science 365, eaav0550 (2019).

    CAS 
    PubMed 

    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.

    Google Scholar 

  • 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).

    CAS 

    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.

    CAS 

    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).

    CAS 
    PubMed 

    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.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Vieira, S. et al. Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME J. 14, 463–475 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nuccio, E. E. et al. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME J. 14, 999–1014 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shi, S. et al. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6, e00746 (2015).

    PubMed 
    PubMed Central 

    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).

    CAS 

    Google Scholar 

  • Whitman, T. et al. Microbial community assembly differs across minerals in a rhizosphere microcosm. Environ. Microbiol. 20, 4444–4460 (2018).

    CAS 
    PubMed 

    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.

    PubMed 

    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).

    CAS 

    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).

    CAS 

    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.

    CAS 

    Google Scholar 

  • Buckeridge, K. M. et al. Sticky dead microbes: rapid abiotic retention of microbial necromass in soil. Soil Biol. Biochem. 149, 107929 (2020).

    CAS 

    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.

    CAS 

    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).

    CAS 

    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).

    Google Scholar 

  • Miltner, A., Bombach, P., Schmidt-Brücken, B. & Kästner, M. SOM genesis: microbial biomass as a significant source. Biogeochemistry 111, 41–55 (2012).

    CAS 

    Google Scholar 

  • Kleber, M. et al. Dynamic interactions at the mineral–organic matter interface. Nat. Rev. Earth Environ. 2, 402–421 (2021).

    Google Scholar 

  • Blagodatskaya, E. & Kuzyakov, Y. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol. Biochem. 67, 192–211 (2013).

    CAS 

    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).

    Google Scholar 

  • Kuzyakov, Y. & Blagodatskaya, E. Microbial hotspots and hot moments in soil: concept & review. Soil Biol. Biochem. 83, 184–199 (2015).

    CAS 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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).

    CAS 

    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.

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Violle, C. et al. Let the concept of trait be functional! Oikos 116, 882–892 (2007).

    Google Scholar 

  • Madin, J. S. et al. A synthesis of bacterial and archaeal phenotypic trait data. Sci. Data 7, 170 (2020).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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.

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    CAS 

    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).

    CAS 

    Google Scholar 

  • Lehmann, J. et al. Persistence of soil organic carbon caused by functional complexity. Nat. Geosci. 13, 529–534 (2020).

    CAS 

    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).

    CAS 

    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).

    CAS 

    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).

    CAS 

    Google Scholar 

  • Lybrand, R. A. et al. A coupled microscopy approach to assess the nano-landscape of weathering. Sci. Rep. 9, 5377 (2019).

    PubMed 
    PubMed Central 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • Liang, C., Schimel, J. P. & Jastrow, J. D. The importance of anabolism in microbial control over soil carbon storage. Nat. Microbiol. 2, 17105 (2017).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    CAS 

    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).

    Google Scholar 

  • 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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Schimel, J., Balser, T. C. & Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386–1394 (2007).

    PubMed 

    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).

    PubMed 

    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).

    PubMed 

    Google Scholar 

  • Slessarev, E. W. et al. Cellular and extracellular C contributions to respiration after wetting dry soil. Biogeochemistry 147, 307–324 (2020).

    CAS 

    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).

    CAS 

    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).

    CAS 
    PubMed 

    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).

    Google Scholar 

  • Zha, J. & Zhuang, Q. Microbial dormancy and its impacts on northern temperate and boreal terrestrial ecosystem carbon budget. Biogeosciences 17, 4591–4610 (2020).

    CAS 

    Google Scholar 

  • Anderson, T.-H. Microbial eco-physiological indicators to asses soil quality. Agric. Ecosyst. Environ. 98, 285–293 (2003).

    Google Scholar 

  • 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).

    CAS 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    Google Scholar 

  • Vieira, S. et al. Bacterial colonization of minerals in grassland soils is selective and highly dynamic. Environ. Microbiol. 22, 917–933 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Ma, T. et al. Divergent accumulation of microbial necromass and plant lignin components in grassland soils. Nat. Commun. 9, 3480 (2018).

    PubMed 
    PubMed Central 

    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).

    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shi, S. et al. The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages. Ecol. Lett. 19, 926–936 (2016).

    PubMed 

    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).

    PubMed 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    PubMed 

    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).

    CAS 

    Google Scholar 

  • Roesch, L. F. W. et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283–290 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • Carson, J. K. et al. Low pore connectivity increases bacterial diversity in soil. Appl. Environ. Microbiol. 76, 3936–3942 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Raynaud, X. & Nunan, N. Spatial ecology of bacteria at the microscale in soil. PLoS ONE 9, e87217 (2014).

    PubMed 
    PubMed Central 

    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).

    CAS 

    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).

    PubMed 
    PubMed Central 

    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.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Thakur, M. P. & Geisen, S. Trophic regulations of the soil microbiome. Trends Microbiol. 27, 771–780 (2019).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    Google Scholar 

  • Hungate, B. A. et al. The functional significance of bacterial predators. mBio 12, e00466-21 (2021).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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.

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Witzgall, K. et al. Particulate organic matter as a functional soil component for persistent soil organic carbon. Nat. Commun. 12, 4115 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Frey, S. D. Mycorrhizal fungi as mediators of soil organic matter dynamics. Annu. Rev. Ecol. Evol. Syst. 50, 237–259 (2019).

    Google Scholar 

  • 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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 

    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).

    CAS 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Averill, C. & Hawkes, C. V. Ectomycorrhizal fungi slow soil carbon cycling. Ecol. Lett. 19, 937–947 (2016).

    PubMed 

    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).

    Google Scholar 

  • 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).

    Article 

    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).

    Google Scholar 

  • 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).

    CAS 

    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).

    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Domeignoz-Horta, L. A. et al. Microbial diversity drives carbon use efficiency in a model soil. Nat. Commun. 11, 3684 (2020).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 

    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).

    PubMed 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Pace, M. L. Bacterial mortality and the fate of bacterial production. Hydrobiologia 159, 41–49 (1988).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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.

    CAS 
    PubMed 

    Google Scholar 

  • Lindeman, R. L. The trophic-dynamic aspect of ecology. Ecology 23, 399–417 (1942).

    Google Scholar 

  • Clarholm, M. Interactions of bacteria, protozoa and plants leading to mineralization of soil nitrogen. Soil Biol. Biochem. 17, 181–187 (1985).

    CAS 

    Google Scholar 

  • Pasternak, Z. et al. In and out: an analysis of epibiotic vs periplasmic bacterial predators. ISME J. 8, 625–635 (2014).

    CAS 
    PubMed 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • Granato, E. T., Meiller-Legrand, T. A. & Foster, K. R. The evolution and ecology of bacterial warfare. Curr. Biol. 29, R521–R537 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Bradford, M. A. et al. Managing uncertainty in soil carbon feedbacks to climate change. Nat. Clim. Change 6, 751–758 (2016).

    Google Scholar 

  • Sierra, C. A. & Müller, M. A general mathematical framework for representing soil organic matter dynamics. Ecol. Monogr. 85, 505–524 (2015).

    Google Scholar 

  • Wang, G. et al. Microbial dormancy improves development and experimental validation of ecosystem model. ISME J. 9, 226–237 (2015).

    CAS 
    PubMed 

    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).

    Google Scholar 

  • 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.

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    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.

    Google Scholar 

  • 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.

    CAS 
    PubMed 

    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).

    PubMed 

    Google Scholar 

  • Moorhead, D. L. & Sinsabaugh, R. L. A theoretical model of litter decay and microbial interaction. Ecol. Monogr. 76, 151–174 (2006).

    Google Scholar 

  • 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).

    CAS 
    PubMed 

    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).

    CAS 

    Google Scholar 

  • Allison, S. D. Modeling adaptation of carbon use efficiency in microbial communities. Front. Microbiol. 5, 571 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).

    PubMed 

    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).

    CAS 

    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).

    CAS 

    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).

    CAS 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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).

    CAS 

    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).

    Google Scholar 

  • 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).

    Google Scholar 

  • 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).

    CAS 

    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).

    Google Scholar 

  • 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).

    CAS 

    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).

    CAS 
    PubMed 

    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).

    Google Scholar 

  • 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).

    CAS 
    PubMed 

    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.

    CAS 

    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).

    Google Scholar 

  • 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).

    PubMed 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Westoby, M. et al. Trait dimensions in bacteria and archaea compared to vascular plants. Ecol. Lett. 24, 1487–1504 (2021).

    PubMed 

    Google Scholar 

  • Jung, M.-Y. et al. Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities. ISME J. 16, 272–283 (2022).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Hungate, B. A. et al. Quantitative microbial ecology through stable isotope probing. Appl. Environ. Microbiol. 81, 7570–7581 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Couradeau, E. et al. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat. Commun. 10, 2770 (2019).

    PubMed 
    PubMed Central 

    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).

    PubMed 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    Google Scholar 

  • Carini, P. et al. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat. Microbiol. 2, 16242 (2016).

    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Jansson, J. K. & Hofmockel, K. S. Soil microbiomes and climate change. Nat. Rev. Microbiol. 18, 35–46 (2020).

    CAS 
    PubMed 

    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).

    Google Scholar 

  • Schulz, F. et al. Hidden diversity of soil giant viruses. Nat. Commun. 9, 4881 (2018).

    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Sommers, P., Chatterjee, A., Varsani, A. & Trubl, G. Integrating viral metagenomics into an ecological framework. Annu. Rev. Virol. 8, 133–158 (2021).

    PubMed 

    Google Scholar 

  • Pratama, A. A. & van Elsas, J. D. The ‘neglected’ soil virome–potential role and impact. Trends Microbiol. 26, 649–662 (2018).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Howard-Varona, C. et al. Phage-specific metabolic reprogramming of virocells. ISME J. 14, 881–895 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Howard-Varona, C. et al. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. ISME J. 12, 1605–1618 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Van Goethem, M. Characteristics of wetting-induced bacteriophage blooms in biological soil crust. mBio 10, e02287-19 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Trubl, G. et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9, 208 (2021).

    CAS 
    PubMed 
    PubMed Central 

    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.

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 

    Google Scholar 


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