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Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data

  • Environmental biotechnology
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Abstract

Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.

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Acknowledgement

This research was financially supported by Hong Kong General Research Fund (7190/12E). Yanping Mao and Yu Xia wish to thank The University of Hong Kong for the postgraduate scholarships. Zhiping Wang wishes to thank Hong Kong Scholar Program for financial support (XJ2012030).

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Authors and Affiliations

  1. Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, SAR, China

    Yanping Mao, Yu Xia, Zhiping Wang & Tong Zhang

  2. School of Environmental Science and Technology, Shanghai Jiao Tong University, Shanghai, China

    Zhiping Wang

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  1. Yanping Mao
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Correspondence to Tong Zhang.

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Mao, Y., Xia, Y., Wang, Z. et al. Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data. Appl Microbiol Biotechnol 98, 6885–6895 (2014). https://doi.org/10.1007/s00253-014-5756-x

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