Metagenomic tools in microbial ecology research

Taş, Neslihan; A, de Jong; Li, Yaoming; Trubl, Gareth; Xue, Yaxin; Dove, Nicholas C.

doi:10.1016/j.copbio.2021.01.019

Cited by 95 publications

(60 citation statements)

References 56 publications

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“…A rapidly growing number of microbial communities are captured by high-coverage metagenomic data as well as complementary ‘omics approaches. The large majority of existing tools and platforms that have been developed for the analysis of this new type of data concern early stages of data interpretation including assembly, gene calling, taxonomic assignment and functional predictions, typically at the single gene level [ 56 ]. Network analysis approaches allow contextualization of discrete functions (here metabolic conversions carried by enzymes) and are becoming an essential component in the study of microbial function both at species and community level.…”

Section: Discussionmentioning

confidence: 99%

NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data

et al. 2021

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The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.

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Section: Discussionmentioning

confidence: 99%

NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data

et al. 2021

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“…In the last decade, metagenomic methods have been increasingly applied to characterize microbial communities or target groups of microorganisms in different soil ecosystems and environmental compartments ( Mocali and Benedetti, 2010 ; Nesme et al, 2016 ; Jansson and Hofmockel, 2018 ; Taş et al, 2021 ). Sequencing the whole DNA [NGS, third-generation sequencing (TGS) techniques] isolated from a specific soil environment allows to evaluate the total genomic diversity, which is a different concept compared to total species diversity assessed with conventional molecular methods.…”

Section: Overview Of the Methodological Tools To Detect And Monitor Bioinocula In Soil: Challenges Limitations And Controversial Issuesmentioning

confidence: 99%

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Manfredini¹,

Malusà²,

Costa³

et al. 2021

Front. Microbiol.

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Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

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“…The use of function-based metagenomic strategies can be a potent tool in helping to exploit the unique microbial diversity of pesticide-contaminated environments, thereby assisting in the ongoing search for novel biosurfactants with potentially important bioremediation applications ( Yadav et al, 2019 ; Taş et al, 2021 ). Most research on biosurfactant producing microbes has been limited to soil isolates, primarily from the Pseudomonas and Bacillus species.…”

Section: Metagenomics: Unraveling the Structure And Composition Of Biosurfactant Producing Microbes And Their Role In Pesticide Remediatimentioning

confidence: 99%

Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability

2021

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Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.

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Metagenomic tools in microbial ecology research

Cited by 95 publications

References 56 publications

NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data

NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability

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