Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle

Abstract

Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus sediminis” AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.

GENOME ANNOUNCEMENT

Ammonia-oxidizing archaea (AOA) belonging to the proposed new phylum Thaumarchaeota (2) are dominant ammonia-oxidizing microorganisms in marine and terrestrial environments that potentially play important ecological roles (11). They are capable of using ammonia as an energy source and performing carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate pathway (1). Despite these important contributions to the biogeochemical cycles of nitrogen and carbon, many unanswered questions on the physiology and ecology of these microbes remain. AOA are extremely fastidious; only a few cultures, from an aquarium (6), a water column (16), and sediment (13), have been reported. Whereas genome sequences from marine aquarium-cultivated archaeon “Candidatus Nitrosopumilus maritimus” and a symbiont of marine sponge “Ca. Cenarchaeum symbiosum” have been documented (4, 5, 15), none had been reported for sedimentary AOA prior to the present study.

Recently however, an ammonia-oxidizing culture was enriched from marine sediment obtained off Svalbard, within the Arctic Circle. Within this culture, “Ca. Nitrosopumilus sediminis” strain AR2 was found to be involved in ammonia oxidation, through which it grows chemolithoautotrophically (10). Its 16S rRNA gene sequence, it was discovered, is closely related to that of “Ca. Nitrosopumilus maritimus” (99% similarity) (6).

In the present study, mate-paired end sequences (8 kb; metagenomic library) and shotgun single sequences were produced with a 454 GS-FLX Titanium platform (Roche Applied Science). Preparation and sequencing of the sample and analytical processing were performed according to the manufacturer's instructions at the National Instrument Center for Environmental Management (NICEM), Seoul National University, Republic of Korea. Assembly was performed using the Roche GS De Novo Assembler (Newbler Assembler, version 2.3). Putative coding sequences (CDSs) were predicted using the MetaGeneAnnotator, COG, Pfam, and RAST (3, 8, 9, 12).

The size of the “Ca. Nitrosopumilus sediminis” AR2 draft genome is approximately 1.69 Mbp, with a G+C content of 33.6%. It contains 2,162 predicted CDSs, only 65.1% of which showed homology to “Ca. Nitrosopumilus maritimus” genes. The average nucleotide identity of strain AR2 to “Ca. Nitrosopumilus maritimus” was about 79%. Based on the genomic demarcation of species proposed by Konstantinidis and Tiedje (7), the AR2 strain can be considered to be a novel species of the genus “Ca. Nitrosopumilus.”

Genes for ammonia oxidation and an ammonium transporter, as well as those potentially involved in energy conservation (including genes encoding multicopper oxidase and blue copper domain-containing proteins), that were found in “Ca. Nitrosopumilus maritimus” also were observed in the AR2 genome. Significantly, a novel ammonia oxidation pathway could be postulated, based on the absence of genes coding for hydroxylamine oxidoreductase, which mediates conversion of hydroxylamine to nitrite in ammonia-oxidizing bacteria (15). Genes of the 3-hydroxypropionate/4-hydroxybutyrate pathway for carbon fixation were detected. And, interestingly, a complete set of genes involved in urea utilization was identified. The genes of the AR2 urease operon, in fact, encoded proteins with 46 to 86% amino acid identity to those encoded by the genome of “Ca. Cenarchaeum symbiosum.” Urea utilization might provide sedimentary AOA with a selective advantage, specifically by contributing to niche specialization through resource partitioning. However, detection of urea utilization genes in metagenomes of organisms in a marine water column (14) indicates that urea utilization is not unique to sedimentary AOA.

Nucleotide sequence accession number.

The draft genome sequence of “Ca. Nitrosopumilus sediminis” AR2 is available in the GenBank database (NCBI) under the accession number CP003843.