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PMID: 21716304 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.

The ISME journal ·Vol. 6 ·No. 1 ·2012-01-00 ·Pages 81-93

Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE

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.

MeSH Terms
Australia Euryarchaeota/classification,genetics,isolation & purification,physiology Genome, Archaeal Lakes/microbiology Metagenomics Molecular Sequence Data Phylogeny Salinity Victoria
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Narasingarao Priya
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
Podell Sheila
Ugalde Juan A
Brochier-Armanet Céline
Emerson Joanne B
Brocks Jochen J
Heidelberg Karla B
Banfield Jillian F
Allen Eric E
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Article Info
Journal
The ISME journal
Abbr.
ISME J
ISSN
1751-7370
DOI
10.1038/ismej.2011.78
Published
2012-01-00
Epub
2011-00-30
Pages
81-93
Language
English
Region
England
NLM ID
101301086
PMCID
PMC3246234
Subset
IM
Grants
NHGRI NIH HHS · R21 HG005107 · United States
Databases
GENBANK
AEIX01000000, AEIY01000000, HQ197754, HQ197755, HQ197756, HQ197757, HQ197758, HQ197759, HQ197760, HQ197761, HQ197762, HQ197763, HQ197764, HQ197765, HQ197766, HQ197767, HQ197768, HQ197769, HQ197770, HQ197771, HQ197772, HQ197773, HQ197774, HQ197775, HQ197776, HQ197777, HQ197778, HQ197779, HQ197780, HQ197781, HQ197782, HQ197783, HQ197784, HQ197785, HQ197786, HQ197787, HQ197788, HQ197789, HQ197790, HQ197791, HQ197792, HQ197793, HQ197794
External Links
PubMed source DOI: 10.1038/ismej.2011.78 PMC Full Text View journal details
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