Agricultural Pollution: Effects on Soil Microbiome and Ecosystem Functioning

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Background

Agricultural intensification, a necessity to meet the food demand of the growing population is often characterized by increased use of production inputs such as fertilizer, pesticide, livestock manure, use of plastic-mulch (plasticulture), and high yielding crop varieties. Some of these inputs generate direct environmental externalities, such as (i) run-off from pesticide and fertilizer that end in contamination or degradation of the agro-systems and surrounding environments, (ii) soil acidification and degradation resulted from excess nitrogen deposition, (iii) leaching of antibiotics from livestock manures and development of antibiotic resistance, (iv) leaching of heavy metals/metalloid from soil amendments (e.g., phosphorous-containing fertilizer, calcium silicate fertilizer, and organic manure), and (v) microplastic and phthalate (potential carcinogen) contamination from plasticulture. The agricultural pollutions raised due to the intensification of agricultural practices may result in consequences for its ecosystem health, including unsustainable degradation of soils, loss of soil fertility and biodiversity, and contamination of the food chain.

Owing to their high degree of metabolic flexibility, soil microorganisms have varying responses to agricultural inputs as disturbances. Disturbances, in ecological theory, are defined as a force, agent, or process that causes a perturbation in a system. Two quantifiable metrics that are used to characterize responses to disturbances are resistance and resilience. Resistance is the ability for a system to withstand a disturbance, and resilience is the ability of a system to maintain stability during or after a disturbance. Related to defining the impacts of disturbance on resistance and resilience is the definition of an ecosystem’s stability, or what are normal patterns in the system. In agricultural soils, existing stable states are influenced by disturbances and can also be affected by the soil type, management history, and the surrounding environment. Disturbances can further influence soil functions and processes. For example, in response to agricultural pollutants, the composition and/or functions of soil microbial communities may change to have the inherent properties of resistance (display a high degree of tolerance to disturbances and community composition stays largely the same) or resilience (composition changes but returns to its initial state) to the agricultural pollutants. Even after changes in composition, communities may continue to support ecosystem processes, in which different taxa carry out the same process due to functional redundancy, such that the process is maintained even after some taxa are lost. These behaviors of microbes help maintain specific microbial populations in a contaminated environment.

We currently lack in depth knowledge of the microbial responses to agricultural pollutions and do not understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems therein. New developments of omic tools (metagenomics, metaproteomics, metatranscriptomics, metametabolomics) are increasingly contributing to the understanding of microbial network complexity and their expression profiles in response to pollution in cropping systems.

This Research Topic will showcase novel experimental concepts such as process-oriented omics-approaches to better understand the resistance, resilience, assemblage, and functional redundancy of soil microbiome and the mechanisms and processes underlying plant-microbe interactions in response to pollutants raised due to agricultural intensification.

The following article types are particularly welcomed: Original Research, Reviews, Mini reviews, and Opinions. Manuscripts should address a clear hypothesis. Genome Announcement, Data Report, and Case Report will not be considered. Potential topics include, but are not limited to:
(i) Resistance, resilience, and ecosystem functioning of soil microbiome in response to agricultural pollutions
(ii) Agricultural management impacts on soil microbiome reducing agricultural pollutions
(iii) Bioremediation of soils polluted by agricultural intensification
(iv) the mechanisms and processes underlying plant-microbe interactions in response to pollutions in agro-ecosystems.

Keywords: Omics, antibiotic resistance, microplastic and phthalate, pesticide contamination, heavy metals/metalloid contamination, excess nitrogen load

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