Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Abstract

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health

“…(3) shows the schematic representation of procedures used in microbiome analysis. A number of tools available to analyze the metagenomic data are presented in Table 2, and discussed in detail in a review published by the authors [4].…”

“…NGS, along with other molecular techniques has greatly expanded and deepened the extent of microbiome research by uncovering novel ways to understand the microbial world, disease etiology and a number of other scientific studies [1,14], A rapid increase in microbiome rese-arch entails analyzing an adequate number of samples directly from the environmental sites using appropriate sequencing technology that helps in resolving the rare species or to perceive subtle variations within the collected microbial samples. Recently, a number of review papers have been published, where the authors have stressed either on plant or human microbiome [1,4], however, in the present review the authors have discussed the microbiome studies at the interface of plants and humans by establishing a linkage between the two. This review primarily focused on the advances and challenges in microbiome research at the interface of plants and humans, the role of microbiome at different compartments of the body's ecosystems along with their correlation to health and diseases.…”

“…However, the availability of high throughput sequencing technologies has enabled the scientific community to taxonomically and functionally characterize this unseen majority of microbes up to a much greater extent [12]. Analyzing these microbiomes by employing the Next-Generation Sequencing (NGS) capabilities has helped researchers to reveal the vast majority of microbial diversity associated with plants, animals and humans [4,13]. NGS, along with other molecular techniques has greatly expanded and deepened the extent of microbiome research by uncovering novel ways to understand the microbial world, disease etiology and a number of other scientific studies [1,14], A rapid increase in microbiome rese-arch entails analyzing an adequate number of samples directly from the environmental sites using appropriate sequencing technology that helps in resolving the rare species or to perceive subtle variations within the collected microbial samples.…”

Taxonomic and Functional Annotation of Termite Degraded Butea monosperma (Lam.) Kuntze (Flame of the Forest)

“…There are various approaches to study the microbiota of the termite degraded Butea such as culture-independent and culture-depended. The culture dependent molecular approaches can trace very less amount of bacterial diversity [27,28] whilst the culture independent methods still have some limitations such as they are time consuming, costly, low coverage and insufficient to reflect the true bacterial diversity, however recent advances in molecular approach of high throughput next-generation sequencing technology have provided large scale analysis with unprecedented depths and coverage [29,30]. Nowadays, the use of NGS technology has made it possible to study the descriptive metagenomics.…”

Fungal Population Dynamics Associated with Active-phase of Hydrocarbon Degradation in Oil-polluted Soil

“…These results to loss of biodiversity mostly observed as destruction to ecosystem, flora and fauna performance and therefore have been a crucial issue for environmental scientists throughout the last decades [7][8][9][10][11][12]. Both the environment and humans are exposed to danger by this hydrocarbon pollution [13]. There is increasing need to remedy the adverse effects of anthropogenic activities in this area.…”