Genome Sequence of “Candidatus Nitrosopumilus salaria” BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

Abstract

Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the ammonia-oxidizing archaeon “Candidatus Nitrosopumilus salaria” BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

GENOME ANNOUNCEMENT

Ammonia-oxidizing archaea (AOA) are among the most abundant organisms on Earth and play important roles in the global carbon and nitrogen cycles. Nonetheless, AOA have proven difficult to isolate in culture, as evidenced by the fact that only two pure cultures (8, 15) have been documented, and many questions remain about their physiology, metabolism, and ecology within the environment.

Enrichment cultures targeting AOA were initiated from sediments in the San Francisco Bay estuary. “Candidatus Nitrosopumilus salaria” BD31 dominated cultures from site BD31 in the region of the estuary with variable salinity, depending on the amount of riverine freshwater input. The AOA grew chemoautotrophically by aerobic ammonia oxidation to nitrite. “Ca. Nitrosopumilus salaria” BD31 was closely related (98% 16S rRNA identity and 95% amoA identity) to Nitrosopumilus maritimus (8, 16) and more distantly related (96% 16S rRNA identity and 90% amoA identity) to “Candidatus Nitrosoarchaeum limnia” SFB1 (4, 10). Molecular surveys in San Francisco Bay showed that ammonia-oxidizing bacteria (AOB) were more abundant than AOA in sediments where “Ca. Nitrosopumilus salaria” BD31 was enriched (11). Genomic sequencing, assembly, and annotation of “Ca. Nitrosopumilus salaria” BD31 were performed by the J. Craig Venter Institute, supported by the Gordon and Betty Moore Foundation Marine Microbiology Initiative (http://camera.calit2.net/microgenome/).

The draft genome of “Ca. Nitrosopumilus salaria” BD31 is 1,572,957 bp in length and has a G+C content of 34%. The genome was sequenced with a half plate of a 454 FLX Titanium run and assembled with Newbler version 2.23. The final assembly resulted in 171 contigs with an N₅₀ size of 28,330 bp, an average contig size of 9,199 bp, and a coverage depth of 129×.

The genome contains 2,158 protein-coding genes, of which 45% are assigned predicted functions. The genome has 40 tRNA genes and single copies of the 5S, 16S, and 23S rRNA genes. The 5S rRNA gene is distantly located from the 16S and 23S rRNA genes, as seen in other AOA genomes (7, 16). One putative clustered regularly interspaced short palindromic repeat (CRISPR) was identified (5), as well as several phage integrase proteins.

To estimate the extent of genome completeness, predicted protein sequences were searched against a set of 53 highly conserved core gene functions previously identified as universally present in all archaeal genomes based on COG annotations (13). A total of 48 of the 53 COGs (90.5%) were identified in “Ca. Nitrosopumilus salaria” BD31, indicating partial genome coverage.

The “Ca. Nitrosopumilus salaria” BD31 genome contains genes of the modified 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon fixation (1–3, 6, 16). The genome codes for proteins putatively involved in ammonia oxidation, including ammonia monooxygenase, ammonium transporter, nitrite reductase, and several multicopper oxidase and blue copper domain-containing proteins. There was no evidence that “Ca. Nitrosopumilus salaria” BD31 has the ability to use urea as an alternative source of ammonia, because no genes encoding urea transporters or urease enzymes were identified in the genome.

The draft genome of “Ca. Nitrosopumilus salaria” BD31 contained genes coding for both the FtsZ and Cdv cell division systems, a feature unique to the Thaumarchaeota (9, 14), although recent evidence suggests that Cdv is the primary division system in N. maritimus (12). The draft genome was missing ectoine biosynthesis genes used to tolerate salt stress in N. maritimus (16) but did contain mechanosensitive ion channel genes. The “Ca. Nitrosopumilus salaria” BD31 genome did not contain a large number of motility genes as seen in “Ca. Nitrosoarchaeum limnia” SFB1 (4).

Nucleotide sequence accession numbers.

The draft genome sequence of “Ca. Nitrosopumilus salaria” BD31 is available in the NCBI GenBank database under accession number AEXL00000000. The raw sequence reads are available in the NCBI SRA database under accession number PRJNA50075.