Dataset Information

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.

ABSTRACT: Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

SUBMITTER: Mukherjee A

PROVIDER: S-EPMC5430712 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.

Mukherjee Arghya A Chettri Bobby B Langpoklakpam James S JS Basak Pijush P Prasad Aravind A Mukherjee Ashis K AK Bhattacharyya Maitree M Singh Arvind K AK Chattopadhyay Dhrubajyoti D

Scientific reports 20170424 1

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological cha ...[more]

PMID: 28439121

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Project description:Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous pattern of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs) retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of pollution reduce fungal diversity and shape community composition in E. erythropoda. Our findings shed light on the effect of soil petroleum contamination on fungal endophytic communities and could help to develop strategies for improving phytoremediation using fungal endophytes.

Project description:Arbuscular mycorrhizal fungi (AMF) have been shown to play an important role in increasing plant fitness in harsh conditions. Therefore, AMF are currently considered to be effective partners in phytoremediation. However, AMF communities in high levels of petroleum pollution are still poorly studied. We investigated the community structures of AMF in roots and rhizospheric soils of two plant species, Eleocharis elliptica and Populus tremuloides, growing spontaneously in high petroleum-contaminated sedimentation basins of a former petrochemical plant (91,000 μg/Kg of C10-C50 was recorded in a basin which is 26-fold higher than the threshold of polluted soil in Quebec, Canada). We used a PCR cloning, and sequencing approach, targeting the 18S rRNA gene to identify AMF taxa. The high concentration of petroleum-contamination largely influenced the AMF diversity, which resulted in less than five AMF operational taxonomical units (OTUs) per individual plant at all sites. The OTUs detected belong mainly to the Glomerales, with some from the Diversisporales and Paraglomerales, which were previously reported in high concentrations of metal contamination. Interestingly, we found a strong phylogenetic signal in OTU associations with host plant species identity, biotopes (roots or soils), and contamination concentrations (lowest, intermediate and highest). The genus Rhizophagus was the most dominant taxon representing 74.4% of all sequences analyzed in this study and showed clear association with the highest contamination level. The clear association of Rhizophagus with high contamination levels suggests the importance of the genus for the use of AMF in bioremediation, as well as for the survey of key AMF genes related to petroleum hydrocarbon resistance. By favoring plant fitness and mediating its soil microbial interactions, Rhizophagus spp. could enhance petroleum hydrocarbon pollutant degradation by both plants and their microbiota in contaminated sites.

Dataset Information

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.

Publications

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.

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