PMID- 21364937
OWN - NLM
STAT- MEDLINE
DCOM- 20110901
LR  - 20211020
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 6
IP  - 2
DP  - 2011 Feb 22
TI  - Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and 
      metagenomic analysis.
PG  - e16626
LID - 10.1371/journal.pone.0016626 [doi]
LID - e16626
AB  - 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  approximately 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 
       approximately 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.
FAU - Blainey, Paul C
AU  - Blainey PC
AD  - Department of Bioengineering, Howard Hughes Medical Institute, Stanford 
      University, Stanford, California, United States of America.
FAU - Mosier, Annika C
AU  - Mosier AC
FAU - Potanina, Anastasia
AU  - Potanina A
FAU - Francis, Christopher A
AU  - Francis CA
FAU - Quake, Stephen R
AU  - Quake SR
LA  - eng
GR  - R01 HG004863/HG/NHGRI NIH HHS/United States
GR  - HHMI/Howard Hughes Medical Institute/United States
GR  - 5R01HG004863-02/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20110222
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Codon)
RN  - 7664-41-7 (Ammonia)
SB  - IM
MH  - Ammonia/*metabolism
MH  - Archaea/*genetics/*metabolism
MH  - Codon/genetics
MH  - Computational Biology
MH  - Forecasting
MH  - *Genome, Archaeal
MH  - *Metagenomics/methods
MH  - Molecular Sequence Annotation
MH  - Oxidation-Reduction
MH  - Phylogeny
MH  - Salinity
MH  - Salt Tolerance/genetics
MH  - Sequence Analysis, DNA
MH  - *Single-Cell Analysis/methods
PMC - PMC3043068
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2011/03/03 06:00
MHDA- 2011/09/02 06:00
PMCR- 2011/02/22
CRDT- 2011/03/03 06:00
PHST- 2010/09/04 00:00 [received]
PHST- 2011/01/07 00:00 [accepted]
PHST- 2011/03/03 06:00 [entrez]
PHST- 2011/03/03 06:00 [pubmed]
PHST- 2011/09/02 06:00 [medline]
PHST- 2011/02/22 00:00 [pmc-release]
AID - PONE-D-10-01939 [pii]
AID - 10.1371/journal.pone.0016626 [doi]
PST - epublish
SO  - PLoS One. 2011 Feb 22;6(2):e16626. doi: 10.1371/journal.pone.0016626.