The integration of sequencing and bioinformatics in metagenomics

Abbasian, Firouz; Lockington, Robin; Megharaj, Mallavarapu; Naidu, Ravi

doi:10.1007/s11157-015-9365-7

Cited by 15 publications

(15 citation statements)

References 241 publications

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“…Although this phenomenon can lead to tragic environmental problems such as contamination of water sources, these areas also become enriched sources of hydrocarbon degrading microbial populations and the corresponding genes for the degradation of hydrocarbon contaminants . Metagenomics analysis of such environments is a promising approach that allows analysis of these microbial communities and all the functional genes involved in both the adaptation of microorganisms to crude oil contamination and the degradation of aliphatic and aromatic hydrocarbons . In this study, a HiSeq Illumina platform was employed to investigate the microbial population of soil samples collected from a crude oil well field located in Perth, Australia.…”

Section: Discussionmentioning

confidence: 99%

“…Since microbial culture is limited to the isolation and identification of limited numbers of microorganisms, this technique is not suitable for investigation of whole microbial diversity and their genomes of all microorganisms present in a particular environment . However, recent metagenomic approaches enable researchers to analyze the whole microbial diversity, and the genetic capacity for the active metabolic pathways present in a given environment .…”

Section: Introductionmentioning

confidence: 99%

“…However, recent metagenomic approaches enable researchers to analyze the whole microbial diversity, and the genetic capacity for the active metabolic pathways present in a given environment . This technique is especially efficient for the study of the biodiversity and genome analysis of complex environmental samples where most of microorganisms cannot be cultured under normal laboratory conditions . Moreover, this system enable operators to establish a correlation between microbial diversity and the level of hydrocarbon(s) in a contaminated site .…”

Section: Introductionmentioning

confidence: 99%

“…This technique is especially efficient for the study of the biodiversity and genome analysis of complex environmental samples where most of microorganisms cannot be cultured under normal laboratory conditions . Moreover, this system enable operators to establish a correlation between microbial diversity and the level of hydrocarbon(s) in a contaminated site . Up to now, several studies have been performed on the microbial communities and metagenomic capacities of soils contaminated with crude oil and its derivatives .…”

Section: Introductionmentioning

confidence: 99%

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Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Abbasian¹,

Thavamani²,

Megharaj³

et al. 2016

Biotechnology Progress

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Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG-RAST, Actinomycetales (9.8%) were found to be the dominant microorganisms, followed by Rhizobiales (3.3%). Furthermore, several functional genes were found in this study, mostly belong to Actinobacteria (12.35%), which have a role in the metabolism of aliphatic and aromatic hydrocarbons (2.51%), desulfurization (0.03%), element shortage (5.6%), and resistance to heavy metals (1.1%). This information will be useful for assisting in the application of microorganisms in the removal of hydrocarbon contamination and/or for improving the quality of crude oil. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:638-648, 2016.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Abbasian¹,

Thavamani²,

Megharaj³

et al. 2016

Biotechnology Progress

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“…Upon extraction of the total environmental DNA it can either be examined at the sequence level or function driven. Sequence based analysis obviously requires the DNA to be sequenced, which commonly involves random shot gun sequencing (Abbasian et al, 2015). In contrast, when expressed heterologous, the metagenome can be screened for certain, desired activities by subjecting the metagenomic library to specifically designed screening assays (Gabor et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Bioprospecting plant-associated microbiomes

Müller

Obermeier

Berg

2016

Journal of Biotechnology

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There is growing demand for new bioactive compounds and biologicals for the pharmaceutical, agro- and food industries. Plant-associated microbes present an attractive and promising source to this end, but are nearly unexploited. Therefore, bioprospecting of plant microbiomes is gaining more and more attention. Due to their highly specialized and co-evolved genetic pool, plant microbiomes host a rich secondary metabolism. This article highlights the potential detection and use of secondary metabolites and enzymes derived from plant-associated microorganisms in biotechnology. As an example we summarize the findings from the moss microbiome with special focus on the genus Sphagnum and its biotechnological potential for the discovery of novel microorganisms and bioactive molecules. The selected examples illustrate unique and yet untapped properties of plant-associated microbiomes, which are an immense treasure box for future research.

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The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil

et al. 2016

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Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites.

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The integration of sequencing and bioinformatics in metagenomics

Cited by 15 publications

References 241 publications

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Bioprospecting plant-associated microbiomes

The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil

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