Microorganisms drive carbon transformation in soils, the largest active terrestrial carbon reservoir, and they shape both soil carbon loss and persistence, the dynamic process by which organic molecules are retained over long timescales. The diverse microorganisms that comprise soil microbiomes execute a myriad of biogeochemical functions. At large scales, decomposition of organic matter is one of the most important ecological functions of soil microbiomes because it closes the loops of many terrestrial biogeochemical cycles, including carbon, which begin with fixation and photosynthesis to bring elements in mineral form into organic forms in the biosphere. In this chapter, the author focuses primarily on catabolic heterotrophic respiration, which results in soil organic matter decomposition and carbon mineralization. The microbial decomposition of organic matter and its conversion to CO2 and other metabolites is a biogeochemical function shared among a wide range of phylogenic groups (e.g. the orange ring in Fig. 1). Because such a wide phylogenetic range of soil microbiomes participates in carbon cycling in soil, the diversity of organisms is sometimes of secondary importance compared to the total number, mass or volume of microbes, and their rates of activity. For this reason, soil microbiologists and biogeochemists refer to the soil microbiomes as ‘soil microbial biomass’ when speaking from the functional biogeochemical context. The term ‘soil microbial biomass’ was first coined by David Jenkinson in a 1966 paper in the then Journal of Soil Science (later to become the European Journal of Soil Science) titled ‘Studies on the decomposition of plant materials in soil. II. Partial sterilization of soil and the soil microbial biomass’ (Jenkinson, 1966). Even then, before the -omics revolution, the focus of soil microbiology was the identification of organisms responsible for specific soil processes. The concept of quantifying properties of the soil microbial population as a whole was unusual. However, the methods developed by Jenkinson, Powlson, Brookes, Vance, and others proved revolutionary (Tate, 2017). The lens created by the soil microbial biomass approach linked soil microbiology to biogeochemistry and illustrated the varied roles of soil microbiomes in organic matter decomposition and formation in soils.

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Advances in understanding the role of soil microbiomes in carbon cycling in soil

  • Alain F. Plante,
  • Jennifer Pett-Ridge,
  • Lawrence Livermore

摘要

Microorganisms drive carbon transformation in soils, the largest active terrestrial carbon reservoir, and they shape both soil carbon loss and persistence, the dynamic process by which organic molecules are retained over long timescales. The diverse microorganisms that comprise soil microbiomes execute a myriad of biogeochemical functions. At large scales, decomposition of organic matter is one of the most important ecological functions of soil microbiomes because it closes the loops of many terrestrial biogeochemical cycles, including carbon, which begin with fixation and photosynthesis to bring elements in mineral form into organic forms in the biosphere. In this chapter, the author focuses primarily on catabolic heterotrophic respiration, which results in soil organic matter decomposition and carbon mineralization. The microbial decomposition of organic matter and its conversion to CO2 and other metabolites is a biogeochemical function shared among a wide range of phylogenic groups (e.g. the orange ring in Fig. 1). Because such a wide phylogenetic range of soil microbiomes participates in carbon cycling in soil, the diversity of organisms is sometimes of secondary importance compared to the total number, mass or volume of microbes, and their rates of activity. For this reason, soil microbiologists and biogeochemists refer to the soil microbiomes as ‘soil microbial biomass’ when speaking from the functional biogeochemical context. The term ‘soil microbial biomass’ was first coined by David Jenkinson in a 1966 paper in the then Journal of Soil Science (later to become the European Journal of Soil Science) titled ‘Studies on the decomposition of plant materials in soil. II. Partial sterilization of soil and the soil microbial biomass’ (Jenkinson, 1966). Even then, before the -omics revolution, the focus of soil microbiology was the identification of organisms responsible for specific soil processes. The concept of quantifying properties of the soil microbial population as a whole was unusual. However, the methods developed by Jenkinson, Powlson, Brookes, Vance, and others proved revolutionary (Tate, 2017). The lens created by the soil microbial biomass approach linked soil microbiology to biogeochemistry and illustrated the varied roles of soil microbiomes in organic matter decomposition and formation in soils.