Abstract
Microbial interactions have a key role in global geochemical cycles. Although we possess significant knowledge about the general biochemical processes occurring in microbial communities, we are often unable to decipher key functions of individual microorganisms within the environment in part owing to the inability to cultivate or study them in isolation. Here, we circumvent this shortcoming through the use of single-cell genome sequencing and a novel low-input metatranscriptomics protocol to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community. This methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus-far-uncharacterized biochemical process. The genome sequence of a dominant bacterial member of this community, belonging to the genus Smithella, was sequenced and served as the basis for subsequent analysis through metabolic reconstruction. Metatranscriptomic data generated from less than 500 pg of mRNA highlighted metabolically active genes during anaerobic alkane oxidation in comparison with growth on fatty acids. These data sets suggest that Smithella is not activating hexadecane by fumarate addition. Differential expression assisted in the identification of hypothetical proteins with no known homology that may be involved in hexadecane activation. Additionally, the combination of 16S rDNA sequence and metatranscriptomic data enabled the study of other prevalent organisms within the consortium and their interactions with Smithella, thus yielding a comprehensive characterization of individual constituents at the genome scale during methanogenic alkane oxidation.
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Acknowledgements
We thank Rohini Patel for technical assistance and Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences) for assistance with single-cell genome amplification. We also thank Pravin Shrestha and Derek Lovley (UMass, Amherst) for supplying total RNA of the Geobacter consortium. This work was supported by the Office of Science (BER), U.S. Department of Energy, award no. DE-SC0004485 and DE-SC0004917. This Whole-Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AWGX00000000. The version described in this paper is version AWGX01000000. Metatranscriptome analysis can be accessed through GEO, accession no. GSE49830.
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Embree, M., Nagarajan, H., Movahedi, N. et al. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J 8, 757–767 (2014). https://doi.org/10.1038/ismej.2013.187
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DOI: https://doi.org/10.1038/ismej.2013.187
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