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Analysis of Hydrocarbon-Contaminated Groundwater Metagenomes as Revealed by High-Throughput Sequencing

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Abstract

The tendency for chlorinated aliphatics and aromatic hydrocarbons to accumulate in environments such as groundwater and sediments poses a serious environmental threat. In this study, the metabolic capacity of hydrocarbon (aromatics and chlorinated aliphatics)-contaminated groundwater in the KwaZulu-Natal province of South Africa has been elucidated for the first time by analysis of pyrosequencing data. The taxonomic data revealed that the metagenomes were dominated by the phylum Proteobacteria (mainly Betaproteobacteria). In addition, Flavobacteriales, Sphingobacteria, Burkholderiales, and Rhodocyclales were the predominant orders present in the individual metagenomes. These orders included microorganisms (Flavobacteria, Dechloromonas aromatica RCB, and Azoarcus) involved in the degradation of aromatic compounds and various other hydrocarbons that were present in the groundwater. Although the metabolic reconstruction of the metagenome represented composite cell networks, the information obtained was sufficient to address questions regarding the metabolic potential of the microbial communities and to correlate the data to the contamination profile of the groundwater. Genes involved in the degradation of benzene and benzoate, heavy metal-resistance mechanisms appeared to provide a survival strategy used by the microbial communities. Analysis of the pyrosequencing-derived data revealed that the metagenomes represent complex microbial communities that have adapted to the geochemical conditions of the groundwater as evidenced by the presence of key enzymes/genes conferring resistance to specific contaminants. Thus, pyrosequencing analysis of the metagenomes provided insights into the microbial activities in hydrocarbon-contaminated habitats.

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Acknowledgments

The authors wish to thank the National Research Foundation for financial support and TIA (Dr James Sakwa and colleagues) for the pyrosequencing, Dr Rehana Shaik and Dr Algasan Govender for the sample collection and processing.

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  1. Discipline of Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000, Republic of South Africa

    Nathlee S. Abbai & Balakrishna Pillay

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  1. Nathlee S. Abbai
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  2. Balakrishna Pillay
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Correspondence to Balakrishna Pillay.

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Abbai, N.S., Pillay, B. Analysis of Hydrocarbon-Contaminated Groundwater Metagenomes as Revealed by High-Throughput Sequencing. Mol Biotechnol 54, 900–912 (2013). https://doi.org/10.1007/s12033-012-9639-z

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