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PMID: 21908640 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Applied and environmental microbiology ·Vol. 77 ·No. 21 ·2011-11-00 ·Pages 7804-14

Youssef NH, Blainey PC, Quake SR, Elshahed MS

Abstract

Members of candidate division OP11 are widely distributed in terrestrial and marine ecosystems, yet little information regarding their metabolic capabilities and ecological role within such habitats is currently available. Here, we report on the microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell (ZG1) belonging to candidate division OP11. Genome analysis of the ∼270-kb partial genome assembly obtained showed that it had no particular similarity to a specific phylum. Four hundred twenty-three open reading frames were identified, 46% of which had no function prediction. In-depth analysis revealed a heterotrophic lifestyle, with genes encoding endoglucanase, amylopullulanase, and laccase enzymes, suggesting a capacity for utilization of cellulose, starch, and, potentially, lignin, respectively. Genes encoding several glycolysis enzymes as well as formate utilization were identified, but no evidence for an electron transport chain was found. The presence of genes encoding various components of lipopolysaccharide biosynthesis indicates a Gram-negative bacterial cell wall. The partial genome also provides evidence for antibiotic resistance (β-lactamase, aminoglycoside phosphotransferase), as well as antibiotic production (bacteriocin) and extracellular bactericidal peptidases. Multiple mechanisms for stress response were identified, as were elements of type I and type IV secretion systems. Finally, housekeeping genes identified within the partial genome were used to demonstrate the OP11 affiliation of multiple hitherto unclassified genomic fragments from multiple database-deposited metagenomic data sets. These results provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.

MeSH Terms
Bacteria, Anaerobic/genetics,isolation & purification Bacteriocins/genetics Cluster Analysis DNA, Bacterial/chemistry,genetics DNA, Ribosomal/chemistry,genetics Drug Resistance, Bacterial Genome, Bacterial Gram-Negative Bacteria/genetics,isolation & purification Heterotrophic Processes Hot Springs/microbiology Membrane Transport Proteins/genetics Oklahoma Open Reading Frames Phylogeny RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Sequence Homology
Chemicals
Bacteriocins DNA, Bacterial DNA, Ribosomal Membrane Transport Proteins RNA, Ribosomal, 16S
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Youssef Noha H
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA.
Blainey Paul C
Quake Stephen R
Elshahed Mostafa S
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
1098-5336
DOI
10.1128/AEM.06059-11
Published
2011-11-00
Epub
2011-00-09
Pages
7804-14
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC3209139
Subset
IM
Grants
NHGRI NIH HHS · R01 HG004863 · United States
NHGRI NIH HHS · 5R01HG004863-02 · United States
External Links
PubMed source DOI: 10.1128/AEM.06059-11 PMC Full Text View journal details
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