Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

Abstract

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

Keywords: abiotic stress; genomics; metabolomics; microbes; multi-omics; plant–microbe interactions.

FIGURE 1

Diverse abiotic stresses and the strategic defense mechanisms adopted by the plants. Though the consequences of heat, drought, salinity and chilling are different, the biochemical responses seem more or less similar. High light intensity and heavy metal toxicity also generate similar impact but submergence/flood situation leads to degenerative responses in plants where aerenchyma are developed to cope with anaerobiosis. It is therefore, clear that adaptive strategies of plants against variety of abiotic stresses are analogous in nature. It may provide an important key for mounting strategic tolerance to combined abiotic stresses in crop plants.

FIGURE 2

Cellular level components, multi-omics approaches to address different levels and the strategies that help identify the outcome of the impact of abiotic stresses or impact of microbial-interactions.

FIGURE 3

Meta-omics approaches to exploit yet-unexplored environmental population of microbial communities that have major impact on plant roots and support plants against stresses. Metatranscriptomics and metaproteomics are relatively new approaches to characterize functional attributes of microbial communities that have not yet been cultured. The approach could generate a deeper snapshot of major metabolic pathways and interactions and dominance of functional microbial communities in the rhizosphere of crop plants facing multiple environmental stresses. (^∗Enrichment techniques in metagenomics. In order to trace out less abundant genes from the environment, these techniques are usually employed. In induced enrichment approach, the physico-chemical factors such as nutrients, temperature, acidity/alkalinity, xenobiotic compounds, etc. (Eyers et al., 2004; Bertrand et al., 2005) are used to enrich the respective populations in situ. These factors are either directly implemented in the microbial habitat itself or used in simulated in situ laboratory conditions. The natural sample enrichment is mainly dependent on executing fine criteria while proceeding for sampling of an environment. The naturally predominating bio-geo-physico-chemical situations need to be considered, as they are the key factors for selective natural enrichment of genes, e.g., sites contaminated with xenobiotic compounds and habitats with extreme environments can be expected to yield the genes participating in the metabolism of xenobiotic compounds and the genes participating in environmental stress tolerance respectively. The enrichment of nucleic acids from natural environment is principally carried out for the samples containing insufficient quantities of nucleic acids. It involves techniques such as affinity capture, differential expression analysis, stable isotope probing, e.g., addition of ¹³C labeled carbon source in the habitat. For the samples with low density of biomass, whole genome amplification technique is recommended to yield relatively larger quantity of nucleic acids (Abulencia et al., 2006; Binga et al., 2008). These approaches may work better with the samples collected from highly saline/sodic/drought affected, barren soils, where it is virtually difficult to cultivate the crop. The stress-genes of the little microbial community thriving in such harsh environments may provide novel guidelines for stress alleviation strategies in the crop).