Abstract
This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1–0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named ‘Nanohaloarchaea’. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.
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Acknowledgements
We thank Sue Welch and Dawn Cardace for sample collection assistance at Lake Tyrrell; Mike Dyall-Smith for generous access to reagents and laboratory equipment; Cheetham Salt Works (Lake Tyrrell, Australia) and South Bay Salt Works, Chula Vista (San Diego, CA) for permission to collect samples; Brian Collins (USFWS) for help with sample collection at South Bay Salt Works; Matt Lewis and the J Craig Venter Institute for library construction and sequencing; Nerida Wilson for assistance with phylogenetic trees; and the US Department of Energy Joint Genomes Institute for genome annotation support via the Integrated Microbial Genome Expert Review (IMG-ER) resource. We also thank Farooq Azam (SIO/UCSD) for kindly permitting use of the Nikon confocal microscope purchased with support from the Gordon and Betty Moore Foundation. Funding for this work was provided by NSF award number 0626526 (JFB, KBH, EEA) and NIH award R21HG005107-02 (EEA). JAU was supported by a Fulbright-Conicyt fellowship. CBA is supported by an Action Thématique et Incitative sur Programme of the French Centre National de la Recherche Scientifique (CNRS). 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.
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Narasingarao, P., Podell, S., Ugalde, J. et al. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6, 81–93 (2012). https://doi.org/10.1038/ismej.2011.78
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