Metagenomics promises to provide new molecules and novel enzymes with diverse functions and enhanced features compared to the enzymes from the culturable microorganisms. 2. Here, we seek to provide a key background on metagenomic approaches and summarize how these tools have been employed to understand contaminated environments in an effort to inform the best practices for environmental cleanup. The search for bioactive molecules using a metagenomic approach has generally been conducted using either homology-based methods or functional screening. She has received IARDO and RACE-Bangkok Awards for Best Teacher (University Level). Hence, study of the microbial diversity using culture independent approaches become necessary. Researchers have isolated new antibiotics, one of such example is Turbomycin A and B from a metagenomic library of soil microbial DNA [83]. 7, pp. 74, no. Its advantage is the rapid and replicated evaluation of the samples [56] but while analyzing the soil or environmental sample there may be risk of cross hybridization. S. Biver, D. Portetelle, and M. Vandenbol, Characterization of a new oxidant-stable serine protease isolated by functional metagenomics, SpringerPlus, vol. D. B. Wilson, Cellulases and biofuels, Current Opinion in Biotechnology, vol. Cellulases are used in animal feeds for improving the nutritional quality and digestibility, in processing of fruit juices, and in baking, while de-inking of paper is yet another emerging application [80]. . But in recent years based on the relative proximity and influence to root the rhizosphere is refined to include three zones. also characterized a metagenome-derived halotolerant cellulase which is highly stable revealing the importance of metagenomics cellulases. At a given time, particular number of species significantly dominates over other and vice versa. Recommended read lengths for metagnomics applications. Highlights potential applications of metagenomics in microbial bioprospecting, environmental forensics, bioremediation and human health. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.. 34, no. Phosphatases are good indicator of soil fertility and are believed to play critical roles in P cycles [78]. [7]. Both data sets assessed the taxonomic diversity of the microbial population using 16S rRNA genes. In addition, the intensive use of land in production through multiple cropping, reduced fallow periods, excessive use of agrochemicals, spread of monocultures are components of management is perceived as leading to land degradation and the undermining of its long-term productive potential (www.fao.org). Metagenomics analysis is the genomic study of the collective microbial communities present in environmental, stool, oral, urogenital and other sample types. In these wells, the uranium concentrations ranged from non-detectable to 55.3mg/L. 2, pp. Of special notes are the recent developments in single cell isolation, whole-genome amplification, pyrosequencing, and database warehousing and the potential impact of these developments on our future understandings of microbial communities in nature. They are resultant of plant root exudates which attract them to colonize the roots. Shotgun metagenomic sequencing with the NextSeq 500 System provides insight into microbial responses to environmental changes in a water reservoir. This indicated that Geobacter spp. 321, no. Bioremediation is a microbially mediated processes employed to degrade and detoxify environmental contaminants [1]. This model was nearly perfect in its ability to bin samples into these three categories. Finally, we provide an overview of the obstacles encountered in the implementation of metagenomic-based knowledge into field applications and propose solutions to facilitate such a technology transfer. from Doodys, "recommended for life science researchers and all students in biology and medicine" from Arzneimittelforschung/Drug Research (2010) 60: 226-227, "expert reviews on the approach, tools and prospects of metagenomics, on detailed methodologies, on a number of translational applications exciting concluding remarks, outlining challenges and future perspectives highly recommended to students and practitioners of molecular biology, biochemistry, all branches of microbiology, bioinformatics, and, last but not least, medicine." Applications of metagenomics: The metagenomics studies are now in its preliminary phase but it is potential enough to penetrate in different fields to solve different problems. One data set was from groundwater samples collected from a uranium and nitrate-contaminated aquifer from the Bear Creek watershed in Oak Ridge, Tennessee [29]. Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. What is Metagenomics?. 166, no. The use of 16S rRNA sequencing and metagenomics has great potential to inform bioremediation strategies and provide deep insights into the microbial response to contamination or remediation techniques. Various investigations indicate that the species richness is the simplest measure of diversity. Soil metagenomic data will reveal potential activities present in microbial communities which can be harnessed for future good use. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as . However, to achieve long-term reduction of uranium, several injections of electron donor were required. 6, pp. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. This allows for optimization of these techniques to enriched targeted groups of microbes most important to the bioremediation process. Increased understanding of how microbial communities cope with pollutants could help to assess the potential of contaminated sites to recover from pollution and increase the chances of bioaugmentation or biostimulation trials to succeed. Additionally, genes involved in reduction of NO3, Mn(IV), Fe(III), U(VI), and SO4 were enriched post-injection, especially during times of peak U(VI) reduction. Phylum, class, order, family, subfamily, or OTU placement are determined when a clone surpasses similarity thresholds of 80, 85, 90, 92, 94, or 97%, respectively. ", "recommended for life science researchers and all students in biology and medicine", Arzneimittelforschung/Drug Research (2010) 60: 226-227, "expert reviews on the approach, tools and prospects of metagenomics, on detailed methodologies, on a number of translational applications exciting concluding remarks, outlining challenges and future perspectives highly recommended to students and practitioners of molecular biology, biochemistry, all branches of microbiology, bioinformatics, and, last but not least, medicine. GeoChip, a functional gene array is widely used which targets hundreds of functional genes involved in biogeochemical, ecological, and environmental analyses. In this application, certain conserved regions (16s rRNA, 18s rRNA, ITS regions) are amplified with PCR primers and sequenced. Following on from this, in this chapter we provide an analysis of the basic aspect of culture-independent tools to study microbial communities, the methods available to isolate environmental DNA and to establish metagenomic libraries which can further be used for extensive activity screens, and a number of the recent applications of this technology. Microbiology, Molecular Genetics, Industrial Microbiology, Bioinformatics, Over 10 million scientific documents at your fingertips, Not logged in 74067409, 2006. followed by the screening of biosurfactant producing clones. 3, pp. 69, part 9, pp. While high-throughput DNA sequence analysis will be an important tool for these studies, the immense richness and diversity of such communities present a strong mandate for the use of functional metagenomics strategies that involve a broad variety of screening methodologies to discover and study the currently unknown key biological processes. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Nucleic acid (DNA/RNA) hybridization using specific probes is another qualitative and quantitative tool in molecular bacterial ecology. We provide details of the information that is available from these resources, tools that support the use of the information, resources for data providers and the analytical pipelines that enrich these largely unannotated datasets. Microbial community structure was probed using high-throughput 16S rRNA sequencing. . This Oceanospirillales sp. Till date, biological measures of soil health have been centered on biological functions, such as respiration or nitrogen mineralization. This is a preview of subscription content, access via your institution. Evidence from the single amplified genomes revealed the presence of genes involved in n-alkane and cycloalkane degradation. He has published ten papers in journals including Oncogene, Science Bulletin and f1000Research, and a book chapter. 11, pp. A comprehensive study was done to characterize the relative abundance, diversity and composition of acidobacterial communities across a range of soil types using clone library analyses [67]. 24232431, 2013. This book addresses in a coherent manner the diverse and multiple aspects of metagenomics and the multiplicity of its potential applications. Samples were collected from the Gulf of Mexico during the Deepwater Horizon oil spill [41]. 40, no. Biological activity of the soil can be known by estimating dehydrogenase enzyme in the soils [75]. M.-N. Xing, X.-Z. The Potential for Investigation of Plant-microbe Interactions Using Metagenomics Methods. Table 2 shows the list of antibiotics that have been discovered using the metagenomic approach. Here, we attempt to briefly describe some of the omics techniques used to study environmental systems focusing on metagenomic approaches (Fig. Applications for analyzing RNA-based virus assemblages from sea-water have also been developed, and have revealed new groups of RNA-viruses that infect marine planktonic protists and animals. This effort has expanded to become a worldwide initiative and will be described in this chapter. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and in medicine. It gives an idea of phylogenetic community composition by assessing the range of phyla or classes [63]. 16S rRNA sequencing was performed to assess the impact of this amendment on the microbial community. Publishing on IntechOpen allows authors to earn citations and find new collaborators, meaning more people see your work not only from your own field of study, but from other related fields too. Metagenomics is the application of modern genomic techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species [2]. Shrinivas N. Sabale, Padmaja P. Suryawanshi and Krishnaraj P.U. 1. Metagenomics Analyses: A Qualitative Assessment Tool for Applications in Forensic Sciences, Realizing Bioremediation Through Metagenomics: A Technical Review, Metagenomics and Enzymes: The Novelty Perspective, Epidemiological Perspectives of Human Health Through Metagenomic Research, Metagenomic Applications of Wastewater Treatment, Metagenomics in Agriculture: State-of-the-Art, The Skin Metagenomes: Insights into Involvement of Microbes in Diseases, Computational Metagenomics: State-of-the-Art, Facts and Artifacts, Tax calculation will be finalised during checkout, Saurabh Singh, Harpreet Singh, Biswaranjan Rout, Raja Babu Mani Tripathi, Chirag Chopra, Reena Singh Chopra, Jyotsana Sharma, Sarmeela Sharma, Indu Sharma, Chirag Chopra, Varun Sharma, Daljeet Singh Dhanjal, Chirag Chopra, Reena Singh Chopra, Peta Pavan Kumar, Kiran Yadav, Varun Vevek, Harshit Khandal, Rajni Kumari, Devika Dileep, Aadya Ramesh, Aarshaa Sojan, Daljeet Singh Dhanjal, Harinder Kaur, Amandeep Kaur. The soil DNA was extracted and the two step PCR amplification was done using domain-specific primer, 515F/806R (for prokaryotes), F1427/R1616 (for eukaryotes) or ITSF1/ITSF2 (for fungi) followed by purification and amplicon sequencing using illumina platform for identification of soil bacterial and fungal community. isolated and characterized a novel metagenomic lipase from tidal flat sediments which evidence a new family of bacterial lipase [23]. 6, pp. E. Orhan, D. Omay, and Y. Gvenilir, Partial purification and characterization of protease enzyme from Bacillus subtilis and Bacillus cereus, Applied Biochemistry and Biotechnology A Enzyme Engineering and Biotechnology, vol. A technique has been devised for the cultivation of uncultured microorganisms from different environments that involved encapsulation of cells in gel micro-droplets for large-scale microbial cultivation under low nutrient flux conditions [13]. Changes in the functional diversity of the groundwater microbial community during acetate biostimulation were monitored using GeoChip [66]. The major limitation of the culture dependent techniques is that we are unable to study the microbes which cannot be grown on artificial media. J. Chow, F. Kovacic, Y. Dall Antonia et al., The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases, PLoS ONE, vol. Copyright 2014 Yasir Bashir et al. This analysis revealed that a diverse set of genes including genes for chemotaxis and hydrocarbon degradation were enriched in samples from the deep water plume compared to uncontaminated deep water. Microbes play an essential role in degrading lignocellulosic materials of plants in the rumen, which represents a potentially important resource of lignocellulose degrading enzymes. 207214, 2012. 2). 13, no. Lee et al. Soil community DNA is extracted, purified and amplified using either specific or universal primers, the resultant products are then separated by various ways and analyzed accordingly. 2019 The Author(s). The ultimate goal of the project is to understand the changes in the human microbiome which are associated with human health or disease. They also have the advantage of providing rigorous annotation for the various taxa/genes present on the chip alleviating the limitation of the need for good homologs in the database to achieve accurate classification. Salanitro JP, Johnson PC, Spinnler GE, Maner PM, Wisniewski HL, Bruce C, Klipp E, Liebermeister W, Wierling C, Kowald A, Herwig R (2016) Systems biology: a textbook. isolated turbomycins A and B from a metagenomic library, it demonstrated the feasibility of metagenomic approaches for searching novel antimicrobial compounds [45]. Its based on principles of collaboration, unobstructed discovery, and, most importantly, scientific progression. Among the hundreds of sequences encoding lipases that have been identified through recent metagenomic studies, it is notable that novel sequences are frequently reported. 9, pp. Overall, we conclude, metagenomics is a scientific approach that vindicates pluralism and has profound philosophical implications for fields within and without the life sciences. In fact, many investigators are engaged in this field to unlock the untapped genetic resources with funding from governments sector. These approaches have greatly expanded our understanding of the microbial processes involved in bioremediation as well as the impact of various response strategies for contaminant cleanup. Kumar V Metagenomics to Bioremediation Applications, Tools, 2022. . This methodology is of great potential for use in the studies of soil microbial communities and their functional genes, and in the discovery of new biocatalysts for industry. T. D. Ngo, B. H. Ryu, H. Ju et al., Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library, Acta Crystallographica D: Biological Crystallography, vol. Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. Lipases are triacylglycerol hydrolases that catalyze the hydrolysis and synthesis of long chain acyl glycerol with trioleyl glycerol being standard substrate [18]. Ontologically, metagenomics has implications for how we understand biological entities and their functions, as inquiry extends from more traditionally bounded entities, such as molecules and organisms, to multi-level communities interacting with planetary chemistry and geology. 53635372, 2010. Download it once and read it on your Kindle device, PC, phones or tablets. Get an email alert for Metagenomics Get the RSS feed for Metagenomics; Showing 1 - 13 of 588 View by: Cover Page List Articles. 390397, 2002. It represents the sequence variations other than the restriction sites also. Using a function-driven metagenomic approach, new metabolic pathways involved in the biodegradation of aromatic compounds can be discovered. Applications of metagenomics in bioremediation Environmental scientists consider metagenomic bioremediation as one of the potential tools to remove contaminants from the environment [ 13 - 15 ]. Many groups used targeted metagenomics as a tool to investigate the differences in the microbial community response to oil in these two distinct settings [51, 52]. A common point of agreement on the diversity is that, species richness and evenness aggregately estimates the diversity and these components should be defined so that they are independent of each other [46]. Conditioning of a treatment zone, A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer, Phylogenetic and functional biomarkers as indicators of bacterial community responses to mixed-waste contamination, Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site, Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico, Oil spill dispersants: efficacy and effects, Oil biodegradation and bioremediation: a tale of the two worst spills in US history, Microbial responses to the Deepwater Horizon oil spill: from coastal wetlands to the deep sea, Magnitude of the 2010 Gulf of Mexico oil leak, Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill, Golyshin PN (2007) Obligate oil-degrading marine bacteria, Tracking hydrocarbon plume transport and biodegradation at Deepwater Horizon, Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill, Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP, Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill, Health effects of uranium: new research findings, The biogeochemistry and bioremediation of uranium and other priority radionuclides, Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater, Monitoring microbial community structure and dynamics during in situ U(VI) bioremediation with a field-portable microarray analysis system, Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U (VI), Phase preference by active, acetate-utilizing bacteria at the rifle, CO integrated field research challenge site, Molecular analysis of the in situ growth rates of subsurface, High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment, Postbiostimulation microbial community structure changes that control the reoxidation of uranium, Microbial functional gene diversity with a shift of subsurface redox conditions during in situ uranium reduction, Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles, Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels, Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels, Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach, Evaluation of slow release substrates for anaerobic bioremediation, Evidence for multiple modes of uranium immobilization by an anaerobic bacterium, Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U (VI) reduction, Society for Industrial Microbiology 2016, This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (, Recent progress in adaptive laboratory evolution of industrial microorganisms, Data-based dynamic compartment model: Modeling of E. coli fed-batch fermentation in a 600 m, Bioindustrial manufacturing readiness levels (BioMRLs) as a shared framework for measuring and communicating the maturity of bioproduct manufacturing processes, Influence of nitrogen sources on the tolerance of Lacticaseibacillus rhamnosus to heat stress and oxidative stress, Microbial pigments: learning from the Himalayan perspective to industrial applications, Applied Genomics and Systems Biotechnology, Fermentation, Cell Culture and Bioengineering, Genetics and Molecular Biology of Industrial Organisms, Metabolic Engineering and Synthetic Biology, About the Journal of Industrial Microbiology and Biotechnology, About the Society for Industrial Microbiology and Biotechnology, https://doi.org/10.1007/s10295-016-1809-8, https://public.ornl.gov/orifc/FRC-conceptual-model.pdf, https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model, Receive exclusive offers and updates from Oxford Academic, Copyright 2022 Society for Industrial Microbiology and Biotechnology. It has been used to study microbial community composition and population changes due to agricultural practices. However by traditional techniques we can tap only known antibiotics identified from known organisms. Bioremediation approaches can be classified into three main categories separated by the intensity of intervention. Vzquez and co-workers collected the soil and sediment samples from the coastal region in response to diesel spill, based on DGGE analysis they selected six soils and two sediment samples for identification of bacterial community structure using clone library analyses [68]. 591594, 1993. Agriculture. This recent trend to access novel and natural sequences through the direct cloning of metagenomic DNA is significantly contributing to the screening and identification of hitherto unexplored microbial consortia for valuable bioactive compounds, biocatalysts, and other useful products and processes. In a comparison study regarding the PLFA analysis and 16S rRNA gene metabarcoding of bacterial communities across the biomes, the PLFA profiling has been found better in distinguishing bacterial community [18]. F. Niehaus, E. Gabor, S. Wieland, P. Siegert, K. H. Maurer, and J. Eck, Enzymes for the laundry industries: tapping the vast metagenomic pool of alkaline proteases, Microbial Biotechnology, vol. 121, no. However due to increased anthropogenic activity, accidental oil spills have impacted a number of marine settings [43, 44]. Garland and Mills developed a technique to assess the potential functional diversity of the bacterial population through Sole Source Carbon Utilization (SSCU) patterns [14]. Metagenomics. Metagenomics Applications. It has opened new horizons in the development of biotechnology based on the exploitation of uncultivated microbial species. Ninety-three wells were sampled for this study and the geochemistry and microbial community structure were determined for each well [9]. The industrial application of this enzyme is manifested by its properties including a broad pH profile, high pH stability, particularly at basic pH, and high substrate specificity including a lack of cellulase activity. 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