Abstract
The phylum Chloroflexi is one of the most frequently detected phyla in the subseafloor of the Pacific Ocean margins. Dehalogenating Chloroflexi (Dehalococcoidetes) was originally discovered as the key microorganisms mediating reductive dehalogenation via their key enzymes reductive dehalogenases (Rdh) as sole mode of energy conservation in terrestrial environments. The frequent detection of Dehalococcoidetes-related 16S rRNA and rdh genes in the marine subsurface implies a role for dissimilatory dehalorespiration in this environment; however, the two genes have never been linked to each other. To provide fundamental insights into the metabolism, genomic population structure and evolution of marine subsurface Dehalococcoidetes sp., we analyzed a non-contaminated deep-sea sediment core sample from the Peruvian Margin Ocean Drilling Program (ODP) site 1230, collected 7.3 m below the seafloor by a single cell genomic approach. We present for the first time single cell genomic data on three deep-sea Chloroflexi (Dsc) single cells from a marine subsurface environment. Two of the single cells were considered to be part of a local Dehalococcoidetes population and assembled together into a 1.38-Mb genome, which appears to be at least 85% complete. Despite a high degree of sequence-level similarity between the shared proteins in the Dsc and terrestrial Dehalococcoidetes, no evidence for catabolic reductive dehalogenation was found in Dsc. The genome content is however consistent with a strictly anaerobic organotrophic or lithotrophic lifestyle.
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Acknowledgements
This project was funded by the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) and a fellowship to AK by C-DEBI and the Deutsche Forschungsgemeinschaft. We thank Jennifer Biddle (UC Delaware), Taiki Futagami and Fumio Inagaki (Kochi Institute for Core sample Research, Japan) for deep-sea sediment samples. We thank Ramunas Stepanauskas from the Bigelow Laboratory Single Cell Genomics Center for single cell sorting. We also thank Sergey Koren from the National Biodefense Analysis and Countermeasures Center for bioinformatics support.
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Kaster, AK., Mayer-Blackwell, K., Pasarelli, B. et al. Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. ISME J 8, 1831–1842 (2014). https://doi.org/10.1038/ismej.2014.24
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