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

被引:245
作者
Narasingarao, Priya [1 ]
Podell, Sheila [1 ]
Ugalde, Juan A. [1 ]
Brochier-Armanet, Celine [2 ]
Emerson, Joanne B. [3 ]
Brocks, Jochen J. [4 ]
Heidelberg, Karla B. [5 ]
Banfield, Jillian F. [3 ,6 ]
Allen, Eric E. [1 ,7 ]
机构
[1] Univ Calif San Diego, Div Marine Biol Res, Scripps Inst Oceanog, La Jolla, CA 92093 USA
[2] Univ Aix Marseille, Univ Aix Marseille 1, CNRS,UPR 9043, Lab Chim Bacterienne,Inst Microbiol Mediterranee, Marseille, France
[3] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA
[4] Australian Natl Univ, Res Sch Earth Sci, Canberra, ACT, Australia
[5] Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA
[6] Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA
[7] Univ Calif San Diego, Div Biol Sci, La Jolla, CA 92093 USA
关键词
assembly; halophile; hypersaline; metagenome; Nanohaloarchaea; 16S RIBOSOMAL-RNA; GENE-SEQUENCES; GENOME; DIVERSITY; ENVIRONMENT; PHYLOGENY; BACTERIA; LIFE; LAKE; RECONSTRUCTION;
D O I
10.1038/ismej.2011.78
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
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 mu m 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 mu m 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. The ISME Journal (2012) 6, 81-93; doi:10.1038/ismej.2011.78; published online 30 June 2011
引用
收藏
页码:81 / 93
页数:13
相关论文
共 87 条
  • [1] Community genomics in microbial ecology and evolution
    Allen, EE
    Banfield, JF
    [J]. NATURE REVIEWS MICROBIOLOGY, 2005, 3 (06) : 489 - 498
  • [2] PHYLOGENETIC IDENTIFICATION AND IN-SITU DETECTION OF INDIVIDUAL MICROBIAL-CELLS WITHOUT CULTIVATION
    AMANN, RI
    LUDWIG, W
    SCHLEIFER, KH
    [J]. MICROBIOLOGICAL REVIEWS, 1995, 59 (01) : 143 - 169
  • [3] COMBINATION OF 16S RIBOSOMAL-RNA-TARGETED OLIGONUCLEOTIDE PROBES WITH FLOW-CYTOMETRY FOR ANALYZING MIXED MICROBIAL-POPULATIONS
    AMANN, RI
    BINDER, BJ
    OLSON, RJ
    CHISHOLM, SW
    DEVEREUX, R
    STAHL, DA
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1990, 56 (06) : 1919 - 1925
  • [4] [Anonymous], 2006, Primer
  • [5] [Anonymous], 2008, PROTEIN ADAPTATION E
  • [6] Lineages of acidophilic archaea revealed by community genomic analysis
    Baker, Brett J.
    Tyson, Gene W.
    Webb, Richard I.
    Flanagan, Judith
    Hugenholtz, Philip
    Allen, Eric E.
    Banfield, Jillian F.
    [J]. SCIENCE, 2006, 314 (5807) : 1933 - 1935
  • [7] Enigmatic, ultrasmall, uncultivated Archaea
    Baker, Brett J.
    Comolli, Luis R.
    Dick, Gregory J.
    Hauser, Loren J.
    Hyatt, Doug
    Dill, Brian D.
    Land, Miriam L.
    VerBerkmoes, Nathan C.
    Hettich, Robert L.
    Banfield, Jillian F.
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (19) : 8806 - 8811
  • [8] Review and re-analysis of domain-specific 16S primers
    Baker, GC
    Smith, JJ
    Cowan, DA
    [J]. JOURNAL OF MICROBIOLOGICAL METHODS, 2003, 55 (03) : 541 - 555
  • [9] Benlloch S, 2001, MICROB ECOL, V41, P12
  • [10] Bacterial diversity in the oral cavity of 10 healthy individuals
    Bik, Elisabeth M.
    Long, Clara Davis
    Armitage, Gary C.
    Loomer, Peter
    Emerson, Joanne
    Mongodin, Emmanuel F.
    Nelson, Karen E.
    Gill, Steven R.
    Fraser-Liggett, Claire M.
    Relman, David A.
    [J]. ISME JOURNAL, 2010, 4 (08) : 962 - 974