Metagenomic applications in environmental monitoring and bioremediation

Techtmann, Stephen M.; Hazen, Terry C.

doi:10.1007/s10295-016-1809-8

Cited by 120 publications

(50 citation statements)

References 70 publications

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“…It is easy to envision implementing metagenomic tools in the field of PHC remediation in order to: pre-assess the biodegradative capacity of an environment, monitor in situ biodegradation performance, assist with the selection of inoculants, identify new biodegradative pathways, and eventually to guide efforts in synthetic biology to develop new enzymatic activities (Baek et al, 2007; Yergeau et al, 2012; Uhlik et al, 2013; Dellagnezze et al, 2014; Sierra-Garcia et al, 2014). Having said this, there are still that need to be faced as the technologies mature and, for more information, the reader is referred to the following reviews (Desai et al, 2010; Hazen et al, 2013; Techtmann and Hazen, 2016). …”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

et al. 2016

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Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant–microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

et al. 2016

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“…Additionally, a better taxonomic resolution can be achieved, in comparison to taxonomic profiles generated by the 16S rRNA gene sequencing [8,9]. Research related to microbial ecology of perturbed sites, including the complete characterization of microbial diversity, the metabolic functions of microbes and other factors that influence their metabolism, could be useful in determining the genetic pool of enzymes necessary for pollution tolerance and survival [10,11]. In some cases, polluted sites may already include microorganism species that tolerate or transform the contaminant.…”

Section: Introductionmentioning

confidence: 99%

“…In some cases, polluted sites may already include microorganism species that tolerate or transform the contaminant. However, those species are not necessarily the most abundant, due to the lack of an appropriate carbon source [11]. The Apatlaco River is located in central México in the state of Morelos.…”

Section: Introductionmentioning

confidence: 99%

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

et al. 2020

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The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.

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“…This targeted metagenomic approach is also frequently employed to determine within a sample how diverse the small subunit rRNA sequence (16S/18S rRNA) are. Small subunit rRNA sequencing are routinely utilize by microbial ecologists to know and comprehend the different taxas and their diversity within an environment (Vieites et al, 2008;Techtmann and Hazen, 2016). In order to carryout targeted metagenomics, environmental DNA is extracted with the gene of interest being amplified (using PCR) by means of primers designed to amplify the greatest diversity of sequences for that gene of interest.…”

Section: Approaches In Metagenomicsmentioning

confidence: 99%

“…These libraries are then sequenced to determine the total genome of the sample. Shotgun metagenomics is a powerful tool where the functional potential of a community of microorganisms can be identified (Techtmann and Hazen 2016).…”

Section: Approaches In Metagenomicsmentioning

confidence: 99%

The application of metagenomics in hydrocarbon resource management

Gana¹,

Kure²,

Ahmadu³

2019

Braz. J. Biol. Sci.

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The last 5-10 years has witness a new proven field of research where explanation have been provided to non-cultured microbes. This uncultured microorganisms forms the major group of organisms found in most environment of the Earth. The science of metagenomics makes it possible to investigate resources which can be used to develop new enzymes, genes and several chemical compounds for use in biotechnology. Studies of microorganisms in pure laboratory culture for over a century have led to significant advances into microbial genetics and physiology, biotechnology and molecular biology. The rapid advancement in sequencing technology has brought about drastic reduction cost of sequencing thereby leading to increasing sequencing project been undertaken. This advancement has provided the privilege for the continual use of this sequencing technology to monitor microbes in the environment which before now are not available. While metagenomic applications have been used to consistently have a better understanding of ecology and microbial diversity, it is pertinent to note that its application in environmental monitoring and application is commonly increasing and has been one of the research areas in focus. To this end this article seek to provide a general overview of what metagenmics is, its principle and application in hydrocarbon resource management.

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Metagenomic applications in environmental monitoring and bioremediation

Cited by 120 publications

References 70 publications

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

The application of metagenomics in hydrocarbon resource management

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