The interplay between microbial communities and soil properties

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018). This study is a global survey of the soil bacteria and fungi revealing the importance of both environmental filtering and niche differentiation in determining the soil microbial composition.

Article  CAS  PubMed  Google Scholar 

Keiluweit, M., Wanzek, T., Kleber, M., Nico, P. & Fendorf, S. Anaerobic microsites have an unaccounted role in soil carbon stabilization. Nat. Commun. 8, 1771 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Schuur, Ea. G. et al. Climate change and the permafrost carbon feedback. Nature 520, 171–179 (2015).

Article  CAS  PubMed  Google Scholar 

Schimel, J. & Schaeffer, S. Microbial control over carbon cycling in soil. Front. Microbiol. 3, 348 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fowler, D. et al. The global nitrogen cycle in the twenty-first century. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20130164 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Barker, W. W. & Banfield, J. F. Biologically versus inorganically mediated weathering reactions: relationships between minerals and extracellular microbial polymers in lithobiontic communities. Chem. Geol. 132, 55–69 (1996).

Article  CAS  Google Scholar 

Doetterl, S. et al. Links among warming, carbon and microbial dynamics mediated by soil mineral weathering. Nat. Geosci. 11, 589–593 (2018).

Article  CAS  Google Scholar 

Napieralski, S. A. et al. Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock. Proc. Natl Acad. Sci. USA 116, 26394–26401 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finlay, R. D. et al. Reviews and syntheses: biological weathering and its consequences at different spatial levels — from nanoscale to global scale. Biogeosciences 17, 1507–1533 (2020).

Article  CAS  Google Scholar 

Sokol, N. W. et al. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat. Rev. Microbiol. 20, 415–430 (2022).

Article  CAS  PubMed  Google Scholar 

Moreau, D., Bardgett, R. D., Finlay, R. D., Jones, D. L. & Philippot, L. A plant perspective on nitrogen cycling in the rhizosphere. Funct. Ecol. 33, 540–552 (2019).

Article  Google Scholar 

Schimel, J. P. & Bennett, J. Nitrogen mineralization: challenges of a changing paradigm. Ecology 85, 591–602 (2004).

Article  Google Scholar 

Geisseler, D., Horwath, W. R., Joergensen, R. G. & Ludwig, B. Pathways of nitrogen utilization by soil microorganisms — a review. Soil Biol. Biochem. 42, 2058–2067 (2010).

Article  CAS  Google Scholar 

Husson, O. Redox potential (Eh) and pH as drivers of soil/plant/microorganism systems: a transdisciplinary overview pointing to integrative opportunities for agronomy. Plant Soil 362, 389–417 (2013).

Article  CAS  Google Scholar 

Bolan, N. S. & Hedley, M. J. Role of carbon, nitrogen, and sulfur cycles in soil acidification. in Handbook of Soil Acidity (CRC Press, 2003).

Sánchez-Cañete, E. P., Barron-Gafford, G. A. & Chorover, J. A considerable fraction of soil-respired CO2 is not emitted directly to the atmosphere. Sci. Rep. 8, 13518 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Mergelov, N. et al. Alteration of rocks by endolithic organisms is one of the pathways for the beginning of soils on Earth. Sci. Rep. 8, 3367 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Gadd, G. M. et al. Oxalate production by fungi: significance in geomycology, biodeterioration and bioremediation. Fungal Biol. Rev. 28, 36–55 (2014).

Article  Google Scholar 

Jones, D. L., Dennis, P. G., Owen, A. G. & van Hees, P. A. W. Organic acid behavior in soils — misconceptions and knowledge gaps. Plant Soil 248, 31–41 (2003).

Article  CAS  Google Scholar 

Hervé, V., Junier, T., Bindschedler, S., Verrecchia, E. & Junier, P. Diversity and ecology of oxalotrophic bacteria. World J. Microbiol. Biotechnol. 32, 28 (2016).

Article  PubMed  Google Scholar 

Syed, S., Buddolla, V. & Lian, B. Oxalate carbonate pathway — conversion and fixation of soil carbon — a potential scenario for sustainability. Front. Plant Sci. 11, 591297 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Norton, J. & Ouyang, Y. Controls and adaptive management of nitrification in agricultural soils. Front. Microbiol. 10, 1931 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Huet, S. et al. Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions. Microbiome 11, 42 (2023). This work experimentally demonstrated that depletion of bacterial ammonia oxidizers through community manipulation reduces soil pH.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fernandes, T. R., Segorbe, D., Prusky, D. & Di Pietro, A. How alkalinization drives fungal pathogenicity. PLoS Pathog. 13, e1006621 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Palmieri, D., Vitale, S., Lima, G., Di Pietro, A. & Turrà, D. A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization. Nat. Commun. 11, 5264 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vylkova, S. Environmental pH modulation by pathogenic fungi as a strategy to conquer the host. PLoS Pathog. 13, e1006149 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Howarth, R. W., Stewart, J. W. B. & Ivanov, M. V. Sulphur Cycling on the Continents: Wetlands, Terrestrial Ecosystems and Associated Water Bodies (John Wiley & Sons, Ltd, 1992).

Koch, T. & Dahl, C. A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds. ISME J. 12, 2479–2491 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, Z., Haneklaus, S., Ram Singh, B. & Schnug, E. Effect of repeated applications of elemental sulfur on microbial population, sulfate concentration, and pH in soils. Commun. Soil Sci. Plant Anal. 39, 124–140 (2007).

Article  Google Scholar 

Linder, T. Assimilation of alternative sulfur sources in fungi. World J. Microbiol. Biotechnol. 34, 51 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Kappler, A. et al. An evolving view on biogeochemical cycling of iron. Nat. Rev. Microbiol. 19, 360–374 (2021). This study is a comprehensive review of abiotic and biotic processes involved in oxidation of Fe(II) and reduction of Fe(III).

Article  CAS  PubMed  Google Scholar 

Vaksmaa, A. et al. Stratification of diversity and activity of methanogenic and methanotrophic microorganisms in a nitrogen-fertilized Italian paddy soil. Front. Microbiol. 8, 2127 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Gabriel, G. V. M. et al. Methane emission suppression in flooded soil from Amazonia. Chemosphere 250, 126263 (2020).

Article  CAS  PubMed  Google Scholar 

Borch, T. et al. Biogeochemical redox processes and their impact on contaminant dynamics. Environ. Sci. Technol. 44, 15–23 (2010).

Article  CAS  PubMed  Google Scholar 

Byrne, J. M. et al. Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria. Science 347, 1473–1476 (2015).

Article  CAS  PubMed  Google Scholar 

Johnstone, T. C. & Nolan, E. M. Beyond iron: non-classical biological functions of bacterial siderophores. Dalton Trans. 44, 6320–6339 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schalk, I. J., Hannauer, M. & Braud, A. New roles for bacterial siderophores in metal transport and tolerance. Environ. Microbiol. 13, 2844–2854 (2011).

Article  CAS  PubMed  Google Scholar 

Gadd, G. M. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156, 609–643 (2010). 2010.

Article  CAS  PubMed  Google Scholar 

Samuels, T. et al. in Biogeochemical Cycles 59–79 (American Geophysical Union (AGU), 2020).

Jongmans, A. G. et al. Rock-eating fungi. Nature 389, 682–683 (1997).

Article 

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