“Omics” Technologies for the Study of Soil Carbon Stabilization: A Review

Abstract

Evidence-based decisions governing sustainable agricultural land management practices require a mechanistic understanding of soil organic matter (SOM) transformations and stabilization of carbon in soil. Large amounts of carbon from organic fertilizers, root exudates, and crop residues are input into agricultural soils. Microbes then catalyze soil biogeochemical processes including carbon extracellular transformation, mineralization, and assimilation of resources that are later returned to the soil as metabolites and necromass. A systems biology approach for a holistic study of the transformation of carbon inputs into stable SOM requires the use of soil “omics” platforms (metagenomics, metatranscriptomics, metaproteomics, and metabolomics). Linking the data derived from these various platforms will enhance our knowledge of structure and function of the microbial communities involved in soil carbon cycling and stabilization. In this review, we discuss the application, potential, and suitability of different “omics” approaches (independently and in combination) for elucidating processes involved in the transformation of stable carbon in soil. We highlight biases associated with these approaches including limitations of the methods, experimental design, and soil sampling, as well as those associated with data analysis and interpretation.

Linking Soil Structure, Hydraulic Properties, and Organic Carbon Dynamics: A Holistic Framework to Study the Impact of Climate Change and Land Management

“…These models relate microbial growth to intrinsic microbial traits (e.g., maximum substrate uptake rate, mortality rate) and metabolism (e.g., maintenance respiration, C use efficiency), to environmental conditions in the soil (such as moisture, temperature, and availability of C and nutrients), as well as the production of extracellular enzymes to depolymerize high molecular weight C compounds. Integrating such models and emerging omics data on microbial community composition and activity (Overy et al., 2021; Prosser, 2015) into our proposed modeling framework might pave the way for a more holistic understanding of environmental changes and land use impacts on the soil system, in terms of structure (i.e., physical properties, heterogeneity), biological activity (i.e., microbial community composition, traits, C cycling), and their interaction (Bonetti et al., 2021; Fatichi et al., 2020; Hartmann & Six, 2023; Kallenbach et al., 2019; Sullivan et al., 2022).…”

Rapid niche shifts in bacteria following conditioning in novel soil environments

“…We expected to see changes in carbon resource use in the derived populations, as we expected they would have access to a wider range of resources in the biotically cleared conditioning soils. It is difficult to assess the complete suite of carbon resources metabolized by soil microbes without the use of transcriptomic or metabolomic methods (Overy et al, 2021), so we instead used a suite of 31 common environmental carbon resources from a standardized metabolic assay. While this method cannot reveal alterations in carbon resource use breadth, it does reveal variation in the use of specific carbon resources between bacterial populations (Gómez & Buckling, 2013).…”

Can molecular genetic techniques improve our understanding of the role the microbial biomass plays in soil aggregation?

“…This can then be related to species diversity and/or soil functioning (Geisen et al, 2019). However, the diversity and complexity of the soil microbial biomass makes characterising the relationship between aggregation and microbial biomass incredibly complex (Garoutte et al, 2016; Jansson & Hofmockel, 2018; Kuzyakov & Blagodatskaya, 2015; Overy et al, 2021; Thiele‐Bruhn et al, 2020), and only a limited amount of work has been conducted to date (for a selected summary, see Table 1).…”