Applications of Metagenomics in Microbial Bioremediation of Pollutants

Bharagava, Ram Naresh; Purchase, Diane; Saxena, Gaurav; Mulla, Sikandar I.

doi:10.1016/b978-0-12-814849-5.00026-5

Cited by 110 publications

(33 citation statements)

References 123 publications

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“…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 ). These methods are comparatively efficient, quicker, and accurate, which overcome the limitations of conventional molecular techniques.…”

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.

195

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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%

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

Mishra

Lin

Pang

et al. 2021

Front. Bioeng. Biotechnol.

195

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“…This treatment can improve the ecosystem processes including sediment microbial community activities, distribution, structure, abundance, and successions. The availability and distribution of bacterial communities in the sediment can help to improve and optimize the bioremediation process [8,41,42]. This study indicates that a couple of ecological activities including microorganism distribution patterns, nutrient dynamics, and contents of the OM were significantly influenced by the treatments…”

Section: Discussionmentioning

confidence: 75%

The relationship between benthic nutrient fluxes and bacterial community in Aquaculture Tail-water Treatment Systems

Nicholaus

Lukwambe

Yanga

et al. 2021

Preprint

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Constructed-wetlands, Biofilms, and sedimentation are potential aquaculture tail-water treatments however their roles on the distribution of benthic microbial community and the way they affect the interaction between microbial community and inorganic nutrient fluxes have not been fully explored. This study applied 16S rRNA high-throughput sequencing technology to investigate the microbial community distribution and their link with nutrient fluxes in an aquaculture tail- water bioremediation system . Results showed that bacterial community compositions were significantly different in constructed-wetland and biofilm treatments (p<0.05) relative to sedimentation. The composition of the 16S rRNA genes among all the treatments was enriched with Proteobacteria, Bacteroidetes, Firmicutes, and Flavobacteria . NMDS analysis showed that the bacterial composition in constructed-wetland and biofilm samples clustered separately compared to those in sedimentation. The Functional-Annotation-of-Prokaryotic-Taxa analysis indicated that the proportions of sediment-microbial-functional groups (aerobic-chemoheterophy, chemoheterotrophy, and nitrate-ammonification combined) in the constructed-wetland treatment were 47%, 32% in biofilm and 13% in sedimentation system. Benthic-nutrient fluxes for phosphate, ammonium, nitrite, nitrate and sediment oxygen consumption differed markedly among the treatments ( p<0.05 ). Canonical correspondence analysis indicated constructed-wetland had the strongest association between biogeochemical contents and the bacterial community relative to other treatments. This study suggests that the microbial community distributions and their interactions nutrient fluxes were most improved in the constructed-wetland followed by the area under biofilm and sedimentation treatment.

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“…Modern-day metagenomic approaches have developed in parallel with metaproteomics, metatranscriptomics, metabolomics, fluxomics, and metaphenomics. Metagenomic studies utilize different genomic approaches to characterize the microbial communities in environmental samples to reveal the genomes of uncultured microbes as well as diversity of taxonomically and phylogenetically relevant genes, catabolic genes and whole operons [ 109 ]. Metagenomics can offer a powerful lens for viewing the diversity of the microbial world in regions such as the Southern Ocean, chronically poorly characterized in terms of its microbiology.…”

Section: Emerging Trends In Genomic Studies Of Antarctic Marine MImentioning

confidence: 99%

“…Many studies have constructed metagenomic libraries for use in screening and identification of genes involved in bioremediation [ 109 ]. Such studies provide the initial stage in the identification and modification of microbes with valuable roles in enzyme, lipid and protein production, including biosurfactants, thereby enhancing bioremediation processes.…”

Section: Application Of Metagenomics In Marine Bioremediationmentioning

confidence: 99%

Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis

et al. 2021

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Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field we used VOSviewer software to analyze publication data obtained from the ScienceDirect database covering the period 1970 to the present, but with a primary focus on the years 2000–2020. A bibliometric analysis of the database allowed identification of the co-occurrence of keywords. There was an increasing trend over time for publications relating to oil bioremediation in maritime Antarctica, including both studies on marine bioremediation and of the metabolic pathways of hydrocarbon degradation. Studies of marine anaerobic degradation remain under-represented compared to those of aerobic degradation. Emerging keywords in recent years included bioprospecting, metagenomic, bioindicator, and giving insight into changing research foci, such as increasing attention to microbial diversity. The study of microbial genomes using metagenomic approaches or whole genome studies is increasing rapidly and is likely to drive emerging fields in future, including rapid expansion of bioprospecting in diverse fields of biotechnology.

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Applications of Metagenomics in Microbial Bioremediation of Pollutants

Cited by 110 publications

References 123 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 relationship between benthic nutrient fluxes and bacterial community in Aquaculture Tail-water Treatment Systems

Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis

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