Abstract
The Zetaproteobacteria are a candidate class of marine iron-oxidizing bacteria that are typically found in high iron environments such as hydrothermal vent sites. As much remains unknown about these organisms due to difficulties in cultivation, single-cell genomics was used to learn more about this elusive group at Loihi Seamount. Comparative genomics of 23 phylogenetically diverse single amplified genomes (SAGs) and two isolates indicate niche specialization among the Zetaproteobacteria may be largely due to oxygen tolerance and nitrogen transformation capabilities. Only Form II ribulose 1,5-bisphosphate carboxylase (RubisCO) genes were found in the SAGs, suggesting that some of the uncultivated Zetaproteobacteria may be adapted to low oxygen and/or high carbon dioxide concentrations. There is also genomic evidence of oxygen-tolerant cytochrome c oxidases and oxidative stress-related genes, indicating that others may be exposed to higher oxygen conditions. The Zetaproteobacteria also have the genomic potential for acquiring nitrogen from numerous sources including ammonium, nitrate, organic compounds, and nitrogen gas. Two types of molybdopterin oxidoreductase genes were found in the SAGs, indicating that those found in the isolates, thought to be involved in iron oxidation, are not consistent among all the Zetaproteobacteria. However, a novel cluster of redox-related genes was found to be conserved in 10 SAGs as well as in the isolates warranting further investigation. These results were used to isolate a novel iron-oxidizing Zetaproteobacteria. Physiological studies and genomic analysis of this isolate were able to support many of the findings from SAG analyses demonstrating the value of these data for designing future enrichment strategies.
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Acknowledgements
We thank Brian Thompson, Nicole Poulton, and Elizabeth Fergusson for their technical expertise and support in single-cell sorting and sequencing, as well as Anna Leavitt for her assistance with the physiologic studies. We also thank the captains, crew and operators of the R/V Kilo Moana, R/V Thomas N Thompson, and Jason II ROV without whom this work would not have been possible. Last, we appreciate the intellectual input provided by the members of the Single Cell Genomics Center and Geomicrobiology labs at Bigelow. This work was financially supported by the NASA EPSCoR program administered through the Maine Space Consortium Grant 10-EPSCoR-0005 and the National Science Foundation Grants OCE-0821374 and OCE-1155754. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Additional sequencing support for Bigelow Laboratory was provided through the Joint Genome Institute’s Community Sequencing Program, Project 560.
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Field, E., Sczyrba, A., Lyman, A. et al. Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J 9, 857–870 (2015). https://doi.org/10.1038/ismej.2014.183
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DOI: https://doi.org/10.1038/ismej.2014.183
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