‘Omics’ Tools in Soil Microbiology: The State of the Art

Biswas, Rimi; Sarkar, Angana

doi:10.1007/978-981-10-6178-3_3

Cited by 27 publications

(16 citation statements)

References 98 publications

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“…Thus, modern culture-independent molecular techniques represent a feasible approach to unrevealing the diversity and functional dynamics of microbial population in contaminated environments. Moreover, the advanced innovation in molecular tools and techniques provides new insights and changes the traditional research trend in the field of bioremediation (Malik et al, 2008 ; Shah et al, 2011 ; Devarapalli and Kumavnath, 2015 ; Mahmoud, 2016 ; Biswas and Sarkar, 2018 ; Shakya et al, 2019 ). Omics technologies are the result of advanced molecular techniques, which involved direct characterization of genome structure of microorganisms, devoid of their culture sample (Segata et al, 2013 ; Biswas and Sarkar, 2018 ; Jaiswal et al, 2019 ; Yu K. et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, the advanced innovation in molecular tools and techniques provides new insights and changes the traditional research trend in the field of bioremediation (Malik et al, 2008 ; Shah et al, 2011 ; Devarapalli and Kumavnath, 2015 ; Mahmoud, 2016 ; Biswas and Sarkar, 2018 ; Shakya et al, 2019 ). Omics technologies are the result of advanced molecular techniques, which involved direct characterization of genome structure of microorganisms, devoid of their culture sample (Segata et al, 2013 ; Biswas and Sarkar, 2018 ; Jaiswal et al, 2019 ; Yu K. et al, 2019 ). Therefore, the applications of modern molecular techniques like metagenomic, transcriptomic, proteomic generates relevant information on genes and proteins expression levels in whole microbial communities under contaminated environments attempted to unravel the mechanism of microbial degradation and successful execution of bioremediation (Keller and Hettich, 2009 ; Yang, 2013 ; Malla et al, 2018 ; Bharagava et al, 2019 ; Marco and Abram, 2019 ; Rodriguez et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Mishra

Lin

Pang

et al. 2021

Front. Bioeng. Biotechnol.

181

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Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Mishra

Lin

Pang

et al. 2021

Front. Bioeng. Biotechnol.

181

View full text Add to dashboard Cite

show abstract

“…Traditionally, direct and indirect counting of cells have been the most common methods for the enumeration of bacteria. Although these methods are inexpensive, culturing high levels of bacterial and fungal species with these techniques is limited (Biswas and Sarkar 2018). The development of multi-"omics" technologies has provided very powerful tools for the analysis of complex ecosystems.…”

Section: Methods For the Characterisation Of Microbial Communitiesmentioning

confidence: 99%

“…Other rapidly emerging technologies that use mass spectrometry for studying the microbiome include metabolomics and metaproteomics. Through metabolomics, comprehensive coverage of a large number of small-molecule metabolites in microbial communities can be profiled under a given set of conditions (Wang et al 2020) while metaproteomics focuses on identifying and quantifying proteins expressed by the microbial community (Biswas and Sarkar 2018;Shulaev 2016). Metabolomics has already been applied in many biological studies involving environmental interactions, functional genomics, and gene discovery, although not yet in aquaponics.…”

Section: Methods For the Characterisation Of Microbial Communitiesmentioning

confidence: 99%

The complex microbiome in aquaponics: significance of the bacterial ecosystem

et al. 2021

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Purpose Aquaponics is a technology that has minimal impact on the environment and which is often promoted as a solution for sustainable food production. Developing aquaponics sustainably requires a thorough understanding of the biological components of the system. Recent reports on the bacterial populations of aquaponics systems using new DNA sequencing technologies are revealing a complex and diverse microbial ecosystem. The purpose of this review is to present information on microbial composition and various factors affecting bacterial activity in aquaponics systems. Approaches for establishing a bacterial ecosystem during the setup of an aquaponics system, and microbiological safety of aquaponics products are also highlighted. Methods This review was developed by evaluating and synthesising current literature of peer-reviewed publications related to aquaponics and microbial communities. Based on the results from credible academic journals, publications were categorised into five groups: methods used to characterise microbiomes, biofiltration microorganisms, bacterial diversity, biofilter establishment, and safety of aquaponics products. Results The microbial ecosystem is essential for biological filtration of water through the mineralisation of nutrients required for plant growth in an integrated system. The aquaponics microbiome is complex, and bacterial composition varies between the different compartments of these systems. Establishing these bacterial ecosystems is essential for optimal functioning of aquaponics. At the phylum level, Proteobacteria and Bacteroidetes are dominant in aquaponics systems. Despite bacteria being fundamental to aquaponics, there are currently no reports of human pathogens in aquaponics products. Conclusion Knowledge of the composition of bacterial populations in aquaponics systems will enhance understanding of relationships and functions within the microbiome. This in turn will allow for the establishment of sustainable and healthy aquaponics systems for food production.

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“…This appeal is now becoming an extension of all life sciences research (Tekle et al, 2018). Metaproteomics is the protein study derived from environmental samples (Biswas and Sarkar, 2018; Bhatt, 2018). Recent reports highlighted metaproteomics approach to observe the bacterial adaptation tactics in various contaminated sites, i.e., heavy metals, oil, xenobiotics, POPs, and other pollutants (Covino et al, 2016; Gianfreda and Rao, 2017; Das and Osborne, 2018).…”

Section: Keys Of Systems Biologymentioning

confidence: 99%

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

2019

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Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

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‘Omics’ Tools in Soil Microbiology: The State of the Art

Cited by 27 publications

References 98 publications

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

The complex microbiome in aquaponics: significance of the bacterial ecosystem

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

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