Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis
Open Access
- 22 February 2011
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 6 (2), e16626
- https://doi.org/10.1371/journal.pone.0016626
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.Keywords
This publication has 77 references indexed in Scilit:
- Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaeaProceedings of the National Academy of Sciences of the United States of America, 2010
- Shifting the genomic gold standard for the prokaryotic species definitionProceedings of the National Academy of Sciences of the United States of America, 2009
- A unique cell division machinery in the ArchaeaProceedings of the National Academy of Sciences of the United States of America, 2008
- A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot springProceedings of the National Academy of Sciences of the United States of America, 2008
- Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouthProceedings of the National Academy of Sciences of the United States of America, 2007
- Mechanosensitive channels in bacteria: signs of closure?Nature Reviews Microbiology, 2007
- Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosumProceedings of the National Academy of Sciences of the United States of America, 2006
- Archaeal nitrification in the oceanProceedings of the National Academy of Sciences of the United States of America, 2006
- Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbonProceedings of the National Academy of Sciences of the United States of America, 2006
- Optical trappingReview of Scientific Instruments, 2004