Microbial energy and matter transformation in agricultural soils

Abstract

a b s t r a c tLow bioavailability of organic carbon (C) and energy are key constraints to microbial biomass and activity. Microbial biomass, biodiversity and activity are all involved in regulating soil ecosystem services such as plant productivity, nutrient cycling and greenhouse gas emissions. A number of agricultural practices, of which tillage and fertiliser application are two examples, can increase the availability of soil organic C (SOC). Such practices often lead to reductions in soil aggregation and increases in SOC loss and greenhouse gas emissions. This review focuses on how the bioavailability of SOC and energy influence the ecology and functioning of microorganisms in agricultural soils. Firstly we consider how management practices affect the bioavailability of SOC and energy at the ecosystem level. Secondly we consider the interaction between SOC bioavailability and ecological principles that shape microbial community composition and function in agricultural systems. Lastly, we discuss and compare several examples of physiological differences that underlie how microbial species respond to C availability and management practices. We present evidence whereby management practices that increase the bioavailability of SOC alter community structure and function to favour microbial species likely to be associated with increased rates of SOC loss compared to natural ecosystems. We argue that efforts to restore stabilised, sequestered SOC stocks and improve ecosystem services in agricultural systems should be directed toward the manipulation of the microbial community composition and function to favour species associated with reduced rates of SOC loss. We conclude with several suggestions regarding where improvements in multi-disciplinary approaches concerning soil microbiology can be made to improve the sustainability of agricultural systems.

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

“…Long-term maize monoculture system significantly (p < 0.001) reduced the humus content, which correlates with decreased bacterial diversity, as found in the work of Zhao et al [28]. Higher concentrations of humus could increase the amount of essential absorbable nutrients for plant growth [29] and enhance the number of soil microorganisms [30]. Liu et al [31] found that increasing the crop rotation of legumes could release nutrients more quickly, leading to higher nitrogen (N) and potassium (K) content in plants and lower available phosphorus (P) content in soil.…”

Structural and functional microbial community response to short-term impact of switching between tillage and no-tillage at soil aggregate level

“…The changes on soil agricultural management, such as tillage systems or fertilization rates, alter the structure of different phylum and classes of soil microorganisms (Carbonetto et al, 2014;Finn et al, 2017;Trivedi et al, 2015). Also, soil bacterial abundances present a variation within different aggregate size fractions (Blaud et al, 2014;Trivedi et al, 2017).…”

“…Therefore, β-Proteobacteria was highest in microaggregates ( avinic et al, 2012), on the contrary, α-Proteobacteria was highest in macroaggregates (Trivedi et al, 2015) both aggregates from clay soils. Shifts in the microbial community composition have important implications for soil functioning since different phylum would produce and contribute to different soil enzymes which are involved in the dynamics of nutrients in soil (Finn et al, 2017). Enzymes activities (EAs) also showed a heterogeneous distribution in micro-environments (Bustos & Perez-Mateos, 2000).…”

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

“…Specific traits for stress tolerance depend on the kind of abiotic stress experienced by microbial communities. Regardless of the form of stress imposed, certain global patterns in phenotypic expression are common, including σ factors or molecular chaperons aimed to minimise or mitigate biomolecular damage (Table 1, Finn et al, 2016;Hecker and Völker, 2001;Malik et al, 2017;Wood et al, 2018). In cases such as high acidity or salinity, microbes employ various strategies to maintain cellular integrity and osmotic balance through changes in the structure and composition of cell envelopes (Wood, 2015).…”

“…Stress tolerance traits in the form of σ factors, molecular chaperons or specific physiological adaptations can be extracted from widely used omics tools (Finn et al, 2016;Malik et al, 2018). Some low molecular weight metabolites synthesised in response to environmental stimuli can be quantified using mass spectrometry tools like LC-MS and FT-ICRMS (Table 1, Tfaily et al, 2015;Swenson et al, 2018;Bouskill et al, 2016).…”