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.
Highlights
AND BACKGROUNDSoil organic matter (SOM) underpins the health and productivity of soil
Growth and metabolism of soil microbial communities involve the transcription of genes into ribonucleic acids (RNA); molecules that are physically involved with protein assembly in the cell or carry specific template information for protein translation [messenger RNA]
Mitchell et al (2015) used untargeted nuclear magnetic resonance (NMR) paired with a targeted analysis of phospholipid fatty acids (PLFAs) to link the effects of biochar amendment to impacts on the soil microbial community and the water extractable organic matter” (WEOM) fraction of soil organic matter (SOM)
Summary
Soil organic matter (SOM) underpins the health and productivity of soil. Representing the largest carbon (C) pool in terrestrial ecosystems, SOM plays a pivotal role in the global C cycle and climate regulation. The turnover rate of this cycle affects many ecosystem processes and properties: soil biodiversity—by delivery of solar energy; plant growth—by providing soil nutrients; water quality—by release of soluble nitrogen and phosphorus; climate change—by exchange of CO2 and other greenhouse gases; and soil resilience—by effects on SOM stocks (Handa et al, 2014). Biological, physical, and chemical transformation processes convert plant root exudates and intact residues into derivative products that form complex and intimate associations with soil minerals (Lehmann and Kleber, 2015) These transformative processes of SOM are determined by interdependent factors that include: compound chemistry, spatial arrangement and interaction with mineral surfaces, temperature and moisture conditions, soil acidity and redox state, and the proximity, biomass, and community composition of microbial degraders (Schmidt et al, 2011; Lehmann and Kleber, 2015). We highlight potential methodological biases associated with these approaches, from limitations of the methods to experimental design and soil sampling to data analysis and interpretation
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