The New Science of Metagenomics: Revealing the Secrets of Microbial Physiology

Singh, Saurabh; Singh, Harpreet; Rout, Biswaranjan; Tripathi, Raja Babu Mani; Chopra, Chirag; Chopra, Reena Singh

doi:10.1007/978-981-15-6529-8_1

Cited by 5 publications

(7 citation statements)

References 100 publications

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“…Metagenomics plays a vital role in exploring distinctive biosurfactant-producing genes from bacteria in various surroundings and adopting different approaches for improved biosurfactant production. With the abundance and variety of biosurfactant-producing microbes present in cultured isolates, it is believed that utilizing metagenomics to investigate the even larger uncultured microbial community will lead to significant and novel discoveries of biosurfactants [161,163].…”

Section: Metagenomics Of Biosurfactants Applied In the Agricultural I...mentioning

confidence: 99%

Biosurfactants: Promising Biomolecules for Agricultural Applications

Silva,

Medeiros,

Converti

et al. 2024

Sustainability

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Population growth and the need for increased agricultural productivity pose a global problem. Therefore, the development of green compounds to ensure agricultural sustainability is an urgent necessity. Surfactant compounds hold significant commercial importance due to their diverse industrial uses. However, the synthetic origin of these agents limits their commercial application due to their toxicity. As a result, extensive research has focused on the production of microbial-originated green surfactants, known as biosurfactants, over the past fifteen years. These biomolecules not only offer a green alternative for agriculture but also exhibit reduced toxicity and excellent stability under specific environmental conditions. Biosurfactants can lower surface tension more effectively than synthetic surfactants. With properties such as detergency and foam formation, biosurfactants are suitable for various agricultural applications, particularly in pesticide and agrochemical formulations. They can function as biopesticides to manage pests, pathogens, phytopathogenic fungi, and weeds due to their antimicrobial activity. Moreover, plants can benefit from biosurfactant molecules and microorganisms as nutrients. They can also aid efficiently in the distribution of micronutrients and metals in the soil. They also stimulate plant immunity and are utilized for soil hydrophilization to ensure proper moisture levels and uniform fertilizer distribution. This review aims to provide valuable insights into the role and properties of biosurfactants as agricultural adjuvants, fostering the development of sustainable formulations to replace the chemical surfactants used in pesticides. For this purpose, the general aspects of global agricultural activity are initially described, followed by a discussion of pesticides, including herbicides, fungicides, and insecticide products. Next, the properties of chemical surfactants are discussed and the use of green surfactants, with emphasis on microbial biosurfactants, is demonstrated. The application of biosurfactants in the agricultural industry and trends are addressed and prospects for the application of these agents are discussed.

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Section: Metagenomics Of Biosurfactants Applied In the Agricultural I...mentioning

confidence: 99%

Biosurfactants: Promising Biomolecules for Agricultural Applications

Silva,

Medeiros,

Converti

et al. 2024

Sustainability

View full text Add to dashboard Cite

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“…Metagenomics assists in the investigation of unique biosurfactant-producing genes from the bacteria present in diverse environments and distinct pathways and approaches for improved biosurfactant production. These investigations helped in finding two novel biosurfactants; palmitoyl putrescine and N-acyl amino acids ( Jackson et al, 2015 ; Williams and Trindade, 2017 ; Hu et al, 2019 ; Singh et al, 2020b ). Given the amount and diversity of biosurfactant synthesizing microbes found in cultured isolates, it is believed that employing metagenomics to investigate the even larger uncultured component of the microbial community will lead to major novel biosurfactant discoveries ( Datta et al, 2020 ; Singh et al, 2020b ).…”

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

confidence: 99%

“…These investigations helped in finding two novel biosurfactants; palmitoyl putrescine and N-acyl amino acids ( Jackson et al, 2015 ; Williams and Trindade, 2017 ; Hu et al, 2019 ; Singh et al, 2020b ). Given the amount and diversity of biosurfactant synthesizing microbes found in cultured isolates, it is believed that employing metagenomics to investigate the even larger uncultured component of the microbial community will lead to major novel biosurfactant discoveries ( Datta et al, 2020 ; Singh et al, 2020b ). A group of researchers identified a new gene involved in biosurfactant synthesis and helps in hydrocarbon degradation.…”

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

confidence: 99%

“…Metagenomics delivers an adequate metagenomic database that will give a substantial stock of genes to develop novel microbial strains for targeted application in biosurfactant production and bioremediation ( Malla et al, 2018 ; Datta et al, 2020 ; Douglas et al, 2020 ; Kumar et al, 2021b ). Metagenomics coupled with bioinformatics removes all the obstacles faced in the process of genomic studies such as phylogenetic analysis, taxonomic profiling, molecular phylogeny, functional characterization of metagenomes, and enzymes and system biology studies, including genetic engineering through CRISPR or TALEN ( Singh et al, 2020b ). Quite a few bioinformatic pipelines have been developed ( Table 2 ), such as QIIME (quantitative insights into microbial ecology), PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), MG-RAST (metagenomic rapid annotations using subsystems technology), Mothur, CLARK, MetaPhlAn2 (metagenomic phylogenetic analysis), MICCA, Metaphyler, MOCAT 2 , TIPP2, mOTU sv2 , Bracken, etc., for sequence classification and taxonomic profiling of metagenomic data ( Liu et al, 2010 ; Albanese et al, 2015 ; Truong et al, 2015 ; Douglas et al, 2020 ; Singh et al, 2020b ).…”

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

confidence: 99%

“…Metagenomics coupled with bioinformatics removes all the obstacles faced in the process of genomic studies such as phylogenetic analysis, taxonomic profiling, molecular phylogeny, functional characterization of metagenomes, and enzymes and system biology studies, including genetic engineering through CRISPR or TALEN ( Singh et al, 2020b ). Quite a few bioinformatic pipelines have been developed ( Table 2 ), such as QIIME (quantitative insights into microbial ecology), PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), MG-RAST (metagenomic rapid annotations using subsystems technology), Mothur, CLARK, MetaPhlAn2 (metagenomic phylogenetic analysis), MICCA, Metaphyler, MOCAT 2 , TIPP2, mOTU sv2 , Bracken, etc., for sequence classification and taxonomic profiling of metagenomic data ( Liu et al, 2010 ; Albanese et al, 2015 ; Truong et al, 2015 ; Douglas et al, 2020 ; Singh et al, 2020b ). Metagenomics coupled with in-silico bioinformatic tools or repositories such as KEGG (Kyoto encyclopedia of genes and genomes), COG (clusters of orthologous groups), EAWAG-BBD pathway prediction system, enviPath, BIOWIN, etc., helps in predictive degradation of pesticides along with the metabolite/biosurfactant identification involved in degradation mechanism ( Awasthi et al, 2020 ; Rodríguez et al, 2020 ; Shah et al, 2021 ; Singh et al, 2021 ).…”

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

confidence: 99%

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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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Genus Bithynia: morphological classification to molecular identification

Huang,

Peng

2024

Parasites Vectors

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Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease’s transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms. Graphical Abstract

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The New Science of Metagenomics: Revealing the Secrets of Microbial Physiology

Cited by 5 publications

References 100 publications

Biosurfactants: Promising Biomolecules for Agricultural Applications

Biosurfactants: Promising Biomolecules for Agricultural Applications

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

Genus Bithynia: morphological classification to molecular identification

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