Genome of the haloarchaeon Natronomonas moolapensis, a neutrophilic member of a previously haloalkaliphilic genus.

The genus Natronomonas contains two species, one haloalkaliphile (N. pharaonis) and one neutrophile (N. moolapensis). Here, we report the genome sequence of N. moolapensis strain 8.8.11. The overall genome properties are similar for the two species. Only the neutrophile contains bacteriorhodopsin and a membrane glycolipid.

GENOME ANNOUNCEMENT

The two species currently assigned to the genus Natronomonas are N. pharaonis, a haloalkaliphile isolated from the Wadi Natrun in Egypt (1) (which was previously sequenced) (2), and N. moolapensis, a neutrophile that grows optimally at a pH of 7 to 7.5 and was recovered from a solar saltern in southeastern Australia (3). The genome of N. moolapensis strain 8.8.11 (JCM14361T = DSM18674T) was sequenced by the same strategy as described recently (4). Briefly, contigs from standard 454 whole-genome sequencing (171.4 Mb of raw data, assembled by Newbler into 118 contigs with 2.85 Mb and average coverage of 60.1-fold) were ordered by end-paired Sanger sequencing of cosmid clones (2,857 cosmid end sequences). Adjacent contigs were spanned by PCRs to close the genome. The final assembly was prepared using the Phred-Phrap-Consed package (5). The genome was annotated according to N. pharaonis and other haloarchaeal genomes maintained at a high annotation quality level within the HaloLex framework (6). Additional bioinformatic tools were used as described previously (4).

There is a single chromosome of 2.9 Mb with a G+C content of 64.5%, a single rRNA operon, 46 tRNA genes, and no plasmids. The sequence CTAG was strongly avoided. A partial tRNA-Glu gene is associated with a likely prophage (nucleotides [nt] 1501283 to 1545787).

The genome codes for 2,846 proteins, of which 1,930 (67.8%) have a bidirectional best BLAST match in N. pharaonis, with an average of 70% sequence identity.

The strain is motile and cells display intracellular gas vesicles (3), consistent with the presence of genes for flagella (e.g., flg1 to flg3), signal transduction (e.g., cheA, cheY), sensory rhodopsin, and a gas vesicle cluster. By microscopy, intracellular granules were observed in pyruvate-grown cells, consistent with the presence of polyhydroxyalkanoate biosynthesis genes. No Cas/CRISPR genes were found. The cell membrane of N. moolapensis contains a prominent glycolipid, consistent with the presence of bacteriorhodopsin, as described previously for Halobacterium (7, 8). By comparison, N. pharaonis and other haloalkaliphilic archaea have neither bop nor membrane glycolipids. Studies of haloarchaeal diversity in China and Iran revealed 16S rRNA sequences with 99% identity to N. moolapensis (accession no. GQ282622 and HQ425158), indicating a wide distribution of this species.

Several enzymes are found in N. moolapensis but not in N. pharaonis. Among these is a glycerol utilization cluster (glycerol kinase and heterotrimeric glycerol-3-phosphate dehydrogenase), explaining why N. moolapensis but not N. pharaonis can grow on glycerol. In contrast to N. pharaonis, N. moolapensis has most enzymes of the Entner-Doudoroff pathway. Despite this feature, however, the sequenced type strain (8.8.11) was not found to grow on glucose, while this is possible for a different strain of N. moolapensis, strain 4.03.5 (3). A puc gene cluster for urate-to- allantoin conversion occurs in N. moolapensis and only three other sequenced haloarchaeal genomes: those of Haloferax volcanii, Halalkalicoccus jeotgali, and Haloquadratum walsbyi. In the latter organism, it is found in the type strain C23, isolated from the same saltern as N. moolapensis, but not in the Spanish strain, HBS001 (4, 9).

Nucleotide sequence accession number.

The nucleotide sequence accession number is HF582854 (EMBL/GenBank).