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. 2012 Jan;6(1):81-93.
doi: 10.1038/ismej.2011.78. Epub 2011 Jun 30.

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities (VSports在线直播)

Priya Narasingarao  1 , Sheila Podell, Juan A Ugalde, Céline Brochier-Armanet, Joanne B Emerson, Jochen J Brocks, Karla B Heidelberg, Jillian F Banfield, Eric E Allen
Affiliations

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

"VSports app下载" Priya Narasingarao et al. ISME J. 2012 Jan.

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 VSports手机版. 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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Figures

Figure 1
Figure 1
Length-weighted histogram of percent G+C for all scaffolds assembled from the LT community, binned in 1% GC increments. Symbols represent reference control points, indicating where five previously sequenced halophile genomes would have fallen, if they had been present in this data set. Data points are plotted based on total number of nucleotides in each scaffold (y axis) versus average percent GC for the entire scaffold (x axis). HA, Haloarcula marismortui; HQ, Haloquadratum walsbyi; HR, Halorubrum lacusprofundi; HS, Halobacterium salinarum R1; SR, Salinibacter ruber. Peaks labeled at 43% and 56% GC are the focus of this study.
Figure 2
Figure 2
FISH micrographs. (a) LT (0.1 to 3 μm filter fraction), (b) CV South Bay Salt Works (0.1 to 0.8 μm filter fraction). All cells are stained with 4′,6-diamidino-2-phenylindole (blue). Nanohaloarchaea cells shown are stained with lineage-specific Cy3 probe Narc_1214 (red). Scale bar=2 μm.
Figure 3
Figure 3
Unrooted maximum-likelihood 16S rRNA gene phylogenetic tree of the Euryarchaeota. Tree is based on 48 sequences, 1275 positions. Numbers of sequences in each collapsed node are indicated in parentheses. Numbers at nodes represent bootstrap values inferred by TreeFinder/PhyML. Bootstrap values <50% are indicated by a ‘–' sign. Scale bar represents 0.1 substitutions per site. A full, uncollapsed version of this tree is presented in Supplementary Figure S2a.
Figure 4
Figure 4
Phylogenetic distribution of non-self-protein BLAST matches for euryarchaeotal genomes. Searches against the GenBank nr database were classified by euryarchaeotal class, archaeal phylum, domain or no match using the DarkHorse algorithm, as described in Materials and methods section.
Figure 5
Figure 5
NM-MDS comparison of amino acid compositions. Euryarchaeal genomes were supplemented with four halophilic bacteria genomes. Symbols denote taxonomic classifications. Numbers rank genomes in increasing order of G+C content (1–10: 29–38%, 11–20: 38–43%, 21–30: 43–50%, 31–40: 50–60%, 41–53: 60–67%). Grey circles indicate hierarchical clustering, based on a 4% distance setting to define groups. A complete list of these genomes and their amino acid compositions is presented in Supplementary Table S6.
Figure 6
Figure 6
16S rRNA gene maximum likelihood tree of Nanohaloarchaea sequences recovered from worldwide hypersaline habitats. Tree is based on 709 nucleic acid positions in 77 sequences. Numbers at nodes represent bootstrap values (values <50% not shown). Scale bar shows average number of substitutions per site.
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