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PMID: 21364937 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.

PloS one ·Vol. 6 ·No. 2 ·2011-02-22 ·Pages e16626

Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR

Abstract

Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles.

MeSH Terms
Ammonia/metabolism Archaea/genetics,metabolism Codon/genetics Computational Biology Forecasting Genome, Archaeal Metagenomics/methods Molecular Sequence Annotation Oxidation-Reduction Phylogeny Salinity Salt Tolerance/genetics Sequence Analysis, DNA Single-Cell Analysis/methods
Chemicals
Codon Ammonia
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Blainey Paul C
Department of Bioengineering, Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America.
Mosier Annika C
Potanina Anastasia
Francis Christopher A
Quake Stephen R
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0016626
Published
2011-02-22
Epub
2011-00-22
Pages
e16626
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3043068
Subset
IM
Grants
NHGRI NIH HHS · R01 HG004863 · United States
Howard Hughes Medical Institute · United States
NHGRI NIH HHS · 5R01HG004863-02 · United States
External Links
PubMed source DOI: 10.1371/journal.pone.0016626 PMC Full Text View journal details
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