Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. Luo and is team reported whole-genome shotgun metagenomic analysis of microbial communities of temperate grassland soils that experienced 2C infrared heating for 10 years and observed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Furthermore, the degradation of synthetic compounds, essential to protect the environment from pollution, has been addressed by metagenomics. The microbial community in background groundwater was highly diverse. 91, no. The pattern thus obtained is compared to a reference FAME database to identify the fatty acids and their corresponding microbial signatures by multivariate statistical analyses [21]. This indicates that at early time points in the spill, the dominant physiologies were those involved in degradation of alkanes. Metagenomics to Bioremediation: Applications, Cutting Edge Tools, and Future Outlook provides detailed insight into metagenomics approaches to bioremediation in a comprehensive manner, which enables the analysis of microbial behavior at a community level under different environmental. T. M. Alvarez, J. H. Paiva, D. M. Ruiz et al., Structure and function of a novel cellulase 5 from sugarcane soil metagenome, PLoS ONE, vol. It was shown that the microbial community in the surface water was composed primarily of Cycloclasticus, Alteromonas, Halomonas, and Pseudoalteromonas [51, 52]. The Potential for Investigation of Plant-microbe Interactions Using Metagenomics Methods. 6, pp. 40, no. Proteases represent one of the three largest groups of industrial enzymes, and most of them are of bacterial origin [35]. Researchers have isolated new antibiotics, one of such example is Turbomycin A and B from a metagenomic library of soil microbial DNA [83]. Duan, L. Xian, G.-C. Zhao et al., Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens, Journal of Applied Microbiology, vol. 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. Thirty predicted primers with a high coverage rate (>90%) were identified [41] and can be successfully used for generating DGGE fingerprints. Stephen M Techtmann, Terry C Hazen, Metagenomic applications in environmental monitoring and bioremediation, Journal of Industrial Microbiology and Biotechnology, Volume 43, Issue 10, 1 October 2016, Pages 13451354, https://doi.org/10.1007/s10295-016-1809-8. Functional gene arrays are used in targeting genes involved in various biogeochemical cycling processes which help in determining the functional composition microbial communities. It is also a great place to network and discuss with other researchers working in related areas. The anticipated increase in metagenomic data available in the future will require high-throughput methods for data management and analysis of these large and complex microbial communities. It is used widely in ecology, environment conservation, infectious disease diagnosis, Environmental remediation, Biotechnology, and agriculture. qPCR is highly sensitive to starting template concentration and measures template abundance in a large dynamic range of around six orders of magnitude. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enzyme-catalyzed chiral synthesis is increasingly recognized. of novel genes, enzyme s, natural products, bioactive compounds, a nd bioprocesses that m ay . Therefore, such shift in microbial load can be estimated using different comparison tools. K. Jaeger and T. Eggert, Lipases for biotechnology, Current Opinion in Biotechnology, vol. She has received IARDO and RACE-Bangkok Awards for Best Teacher (University Level). J. Selvin, J. Kennedy, D. P. H. Lejon, G. S. Kiran, and A. D. W. Dobson, Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans, Microbial Cell Factories, vol. Evidence from the single amplified genomes revealed the presence of genes involved in n-alkane and cycloalkane degradation. 1, pp. 2). 2022 Springer Nature Switzerland AG. GeoChip analysis demonstrated that during acetate amendment, the microbial community proceeded from being dominated by pathways involved in iron reduction to sulfate reduction pathways, and finally to methanogenic pathways. 4, 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. REQUEST A CALL BACK. Yasir Bashir is grateful to Tezpur University, India, for providing the Institutional fellowship. followed by the screening of biosurfactant producing clones. To date our community has made over 100 million downloads. The rate of hybridization or re-association will depend on the similarity of sequences present. Further, there are two different microarray chips namely 16S rRNA gene microarray or PhyloChip and Functional gene microarray or GeoChip (Figure 4). Beyond Metagenomics: Integration of Complementary Approaches for the Study of Microbial Communities, Andrs Cubillos-Ruiz, Howard Junca, Sandra Baena, Ivonne Venegas and Mara Mercedes Zambrano. Oil is a natural part of the marine system [42]. Garland and Mills developed a technique to assess the potential functional diversity of the bacterial population through Sole Source Carbon Utilization (SSCU) patterns [14]. also isolated two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts [38], while Pushpam et al. The prediction of phylogenetic 18S rDNA and internal transcribed spacer (ITS) regions are increasingly used to study fungal communities. 14181423, 2013. Since microbes are the drivers of bioremediation, shifts in the composition and activity of a microbial community may impact the fate of a contaminant in the environment [2]. Thus, by employing the above described screening methods, it is likely that novel gene clusters involved in the biosurfactant production could be identified thereby accelerating the development of bioremediation technologies involving biosurfactants. Other efforts are examining those of animals including chickens, pigs and ruminants. 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 examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities. Many metal-reducing bacteria are able to reduce U(VI) to U(IV) using hydrogen, lactate, acetate, and ethanol among many others as electron donors [56]. Using NGS, it is possible to resolve highly complex microbiota compositions with greater accuracy, as well as to link microbial community diversity with niche function. Teresa Nogueira, Ana Botelho; Affiliations Teresa Nogueira Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal 3, pp. Soil metagenomic data will reveal potential activities present in microbial communities which can be harnessed for future good use. The version 5.0 GeoChip contains about 167,000 50-mer oligonucleotide probes covering ~395,000 coding sequences from >1590 functional genes related to various microbes, mineral cycling, energy metabolism, antibiotic resistance, metal homeostasis and resistance, secondary metabolism, organic remediation, stress responses, bacteriophages, and virulence [58]. In this chapter, I summarize a general framework of broad-sense metagenomics. Metagenomics is the study of genetic material recovered directly from environmental or clinical samples. By Ahmed Shuikan, Sulaiman Ali Alharbi, Dalal Hussien By Ral Enrique Valle-Gough, Blancka Yesenia Samanieg By Ayixon Snchez-Reyes and Jorge Luis Folch-Mallol, IntechOpen Limited This approach has been successfully explored for the assessment of the diazotrophs belonging to the rhizosphere of native red kidney beans (RKB) of the Western Indian Himalaya by targeting nifH [89]. A novel halotolerant lipase was isolated following a functional screening of a marine sponge fosmid metagenomic library by Selvin et al. A. Bhat, S. Riyaz-Ul-Hassan, N. Ahmad, N. Srivastava, and S. Johri, Isolation of cold-active, acidic endocellulase from Ladakh soil by functional metagenomics, Extremophiles, vol. In fact, the crystal structure of metagenomics derived RNase H1 has also been determined which indicated structure-based mutational shift at the active site of the motif [4]. Dr. Reena Singh Chopra is an Assistant Professor at the School of Bioengineering and Biosciences, Lovely Professional University. The design of primers is solemnly dependent on the sequence information of microsatellite regions. Contact our London head office or media team here. Whole-cells as well as microbial products such as . How to get more out of molecular fingerprints remains the question, because estimating the species diversity is the most important factor towards better understanding of the microbial load in the given soil environment. Soil provides shelter to various soil harboring insects, reptiles, animals and a huge volume of microbes within the soil aggregates. Over the years, several procedures has been devised for extracting the biomolecules such as nucleic acids but still there is the compromise in concentration or quality of the biomolecules. 10, pp. S. Biver, D. Portetelle, and M. Vandenbol, Characterization of a new oxidant-stable serine protease isolated by functional metagenomics, SpringerPlus, vol. Conservative fragments of available 16S rDNA sequences were mined and searched for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. 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. Additionally, the genes for degradation of BTEX compounds were expressed at relatively low levels in the plume. M. Schallmey, A. Ly, C. Wang et al., Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening, FEMS Microbiology Letters, vol. In fact there is a major funding from Department of Energy, USA, for three bioenergy research centers: one led by the Berkeley Argonne National Laboratory, one led by Oak Ridge National Laboratory, and one led by the University of Wisconsin that will study all aspects of liquid biofuel production from biomass sugars (http://genomicscience.energy.gov/centers/). [5860]. In 1990, William and his team developed a method which includes amplification of DNA fragments by using short arbitrary primer targeting multiple loci in genomic DNA, generating unique profile (amplicons of various lengths [28]). Each of these techniques investigates a particular biological molecule (DNA, RNA, or Protein). To deal with this issue, non-native organism or enzyme can be added to a system during bioaugmentation in an effort to enhance the rates of biodegradation. H. K. Allen, L. A. Moe, J. Rodbumrer, A. Gaarder, and J. Handelsman, Functional metagenomics reveals diverse -lactamases in a remote Alaskan soil, The ISME Journal, vol. 11631196, 2012. identified and characterized metagenomic alkaline serine protease from the metagenome of goat skin surface [39]. MetagenomicsCOMPUTATIONAL BIOLOGY 2. Neveu et al. There is ample demand for novel enzymes and biocatalysts, and metagenomics is currently thought to be one of the most likely technologies to provide the required candidate molecules [8, 9]. Y. S. Jeong, H. B. Na, S. K. Kim et al., Characterization of Xyn10J, a novel family 10 xylanase from a compost metagenomic library, Applied Biochemistry and Biotechnology, vol. 68, no. Amidases are used in the biosynthesis of -lactam antibiotics [85]. One of the most commonly used evenness measure is Pielous evenness index, evenness expresses how evenly the individuals in the community are distributed over the different species [47]. 16, pp. Part of Springer Nature. Functional screens have identified new enzymes (39, 52, 53, 67, 68, 72 . The fermentation products are then able to stimulate other community members. Oligonucleotide or polynucleotide probes designed from known sequences ranging in specificity from domain to species can be tagged with markers (fluorescent) at the 5-end [55]. [31], and Jeong et al. It can be used to determine gut microbial . However, to achieve long-term reduction of uranium, several injections of electron donor were required. Key metabolic pathways such as cellulose degradation (~13%), CO2 production (~10%), and to nitrogen cycling (~12%), were enriched under heating, which was consistent with independent physicochemical measurements. The following are some of the main enzymes that have been unlocked from genetically untapped resources. O. Lpez-Lpez, M. E. Cerdn, and M. I. Gonzalez-Siso, New extremophilic lipases and esterases from metagenomics, Current Protein and Peptide Science, vol. Increased understanding of bioaugmentation or biostimulation trials to succeed. The Use of Bioinformatic Tools in Symbiosis and Co Metagenomics-Based Phylogeny and Phylogenomic, University of Agricultural Sciences, Dharwad, Karnataka, India. Furthermore, Pelosinus strain UFO1, which was isolated from non-contaminated sediments at the Oak Ridge site, is able to reduce U(VI) [72, 73]. 91, no. With the advent of new frontiers in biotechnology, the spectrum of amylase applications has expanded into many other fields, such as clinical, medicinal, and analytical chemistry. 245256, 2009. We will also provide several recent examples of the application of metagenomics to bioremediation. . In fact, there are reports of metagenomics alkane hydroxylase enzyme degrading hydrocarbon that has been reported very recently [64]. Along with the microbial community samples, oil concentrations were measured. The rates of contaminant detoxification are dependent on a number of factors including the composition of the native microbial community, the environmental conditions, and the nature of the contaminant [, One of the limiting steps in systems biology is obtaining a comprehensive characterization of the various levels of the biological system of interest [, Systems biology approach to bioremediation, Cleaning up with genomics: applying molecular biology to bioremediation, Enhanced reductive dechlorination of polychlorinated biphenyl impacted sediment by bioaugmentation with a dehalorespiring bacterium, Field-scale demonstration of enhanced MTBE bioremediation through aquifer bioaugmentation and oxygenation, A unified initiative to harness Earths microbiomes, Beyond the Venn diagram: the hunt for a core microbiome, Natural bacterial communities serve as quantitative geochemical biosensors, Advances in monitoring environmental microbes, Deep-sea oil plume enriches indigenous oil-degrading bacteria, Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities, Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Ecosystem processes and interactions in a morass of diversity, Insights into the phylogeny and coding potential of microbial dark matter, Describing microbial communities and performing global comparisons in the omic era, GroopM: an automated tool for the recovery of population genomes from related metagenomes, Metagenomics meets time series analysis: unraveling microbial community dynamics, Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill, Disturbance and temporal partitioning of the activated sludge metacommunity, StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses, Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities, Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota, On the origin of the species by natural selection, In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions, Comparative metagenomics reveals impact of contaminants on groundwater microbiomes, Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization, 16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment, Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community, In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer, Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 17, no. Uranium-contaminated groundwater is of great concern due to releases associated with mining, milling, processing as well as from natural sources [54]. In shotgun metagenomics, the total genomic complement of an environmental community is probed through genomic sequencing (Fig. Phospholipid fatty acid analysis (PLFA) quantifies a set of biomarkers that track primarily viable biomass, avoids culturing of micro-organisms, and represents in-situ conditions. So far, metagenomic approaches able to scratch the surface of the genomic, metabolic and phylogenetic diversity stored in the soil metagenome. These discoveries have triggered extensive search operations for the quest of novel and biomedical important drugs as evidenced by various studies [4752]. In general, screening of soil metagenome libraries relies on metabolic activity (function-driven approach) or on nucleotide sequence (sequence driven approach) whichever is suitable and feasible. The work that is turned out by bacteria does benefit the plants and other living organisms. 635644, 2011. We now have the opportunity to explore the interactions between plants and microbes through cultivation independent study of the microbial communities. Based on this finding, many studies have sought to use community members as indicator species or biosensors of particular environmental features. In short, many cultivable areas have turned saline or uncultivable. Metagenomics provides a window into a world of unseen microbial diversity that is astonishing in its magnitude and is open to tap the vast genetic potential of microorganisms to obtain products and processes of biotechnological value. For example, Brevundimonas spp. Gut health. Following amplification and quantification of the 16S rRNA gene, a high-resolution melting curve analysis is obtained. Targeting the 16S rDNA is used extensively to study prokaryote diversity and allows identification of prokaryotes. 243251, 2009. It represents the sequence variations other than the restriction sites also. This article reviews the development and application of metagenomics detection technology. 121, no. 2). 150156, 2011. Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of . T. J. Neveu, C. Regeard, and M. S. Dubow, Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts, Applied Microbiology and Biotechnology, vol.
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