Genome Sequence of Prosthecochloris sp. Strain HL-130-GSB from the Phylum Chlorobi.

The genome of the green sulfur bacterium Prosthecochloris sp. strain HL-130-GSB, isolated from a cyanobacterial mat obtained from Hot Lake, a saline meromictic lake in Washington, USA, comprises 2,437,774 bp in a single contig. The genome is predicted to encode 2,565 proteins and contain 47 tRNA genes and 2 rRNA operons.

GENOME ANNOUNCEMENT

Prosthecochloris sp. strain HL-130-GSB is a slightly thermotolerant, anaerobic, photoautotrophic green sulfur bacterium (GSB; phylum Chlorobi, family Chlorobiaceae). Strain HL-130-GSB was isolated from a microbial mat obtained from Hot Lake (Washington, USA; 48°58′23″N, 119°28′35″W), a shallow, meromictic salt lake dominated by MgSO4 (1, 2). The mat sample HL6812-130 was obtained from a depth of 55 cm, beneath the chemocline at a water temperature of 24°C on 8 June 2012. The strain was isolated using Pfennig’s medium supplemented with “Hot Lake salts,” containing 0.4 M MgSO4, 0.08 M Na2SO4, and 20 mM KCl, as well as 0.05% (wt/vol) Mg/NH4-acetate mix (1:1) in agar shakes in the light at room temperature. Growth was observed up to 45°C. Two rRNA operons were present in the genome; the 16S rRNA genes were identical and shared 99.5% nucleotide identity to those of Prosthecochloris sp. strain CHP 3401, which was isolated from a hypersaline lake in Spain (3). This strain is considered to represent an undescribed species with sequence similarities of 96.9% to three closest type strains, Prosthecochloris aestuarii DSM 271 (4), Prosthecochloris vibrioformis DSM 260 (5, 6), and Prosthecochloris indica JAGS6 (7).

Purified genomic DNA from Prosthecochloris sp. strain HL-130-GSB was sequenced using a PacBio RSII instrument in one single-molecule real-time (SMRT) cell that yielded 927,499,821 bp (91,952 subreads) and was assembled with the HGAP3 (8) workflow in the SMRT Analysis 2.3.0 package (https://github.com/PacificBiosciences/smrtmake). The assembly used for genome analysis contained a single contig with a length of 2,437,774 bp, with an average G+C content of 52% and mean coverage of 260-fold. Both the G+C content and genome size are similar to those of other phototrophic Chlorobi (9).

Annotation using RAST (10) predicted 2,565 protein-coding genes, 47 tRNA genes, and 2 rRNA operons. AmphoraNet (11) identified all 31 phylogenetic marker genes, which confirmed the phylogenetic assignment of this organism to the Chlorobiaceae.

Consistent with the photoautotrophic growth characteristics of this and other GSB, the genome encodes a type-1 photosynthetic reaction center (pscABCD), the bacteriochlorophyll a-binding Fenna-Matthews-Olson protein (fmoA), and chlorosomes (csmABCDFHIJX), as well as the diagnostic enzymes for the reductive tricarboxylic acid (TCA) cycle (aclAB, kor, and por). The strain contains photosynthetic pigments bacteriochlorophyll (BChl) a, c, and d (12) and carotenoids of the chlorobactene series. All genes necessary for the biosynthesis of these pigments (bchDEHIJM, bciABC, bchBLN, bchXYZ, bchCFG, chlG, bchKQRUV, crtBCPHQU, and cruACD) are present. The presence of genes encoding nitrogenase (nifABDEHKNV) indicates the ability to fix dinitrogen (13, 14). The genome contains genes for dissimilatory sulfur oxidation (sqr, dsrABCEFHJKLMNOP, and 2 genes encoding PSRLC3 [13]) but lacks genes for assimilatory sulfate reduction. Thiosulfate utilization was not observed, and a sox-type gene cluster for thiosulfate oxidation was absent (13, 15). Similar to other, mostly marine, GSB, strain HL-130-GSB contains genes encoding an Na+-transporting electron transport complex (rnfABCDEG), an Na+-transporting NADH:ubiquinone oxidoreductase (nqrABCDEF), and a multisubunit Na+/H+ antiporter (mnhABCDEFG) (13). The presence of numerous genes for oxidative stress response (e.g., cydAB, nox, roo, bcp-1, bcp-2, tpx-2, sodB, and msrA) is consistent with observations for other members of this group of strictly anaerobic bacteria (13).

Accession number(s).

The genome has been deposited at DDBJ/EMBL/GenBank under the accession no. CP020873.