Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat

Abstract

Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.

Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov.

“…All the members of genus Rhodoferax are motile by polar flagella except for Rhodoferax bucti [1][2][3][4][5][6][7]. This genetic evidence of motility by flagella and type IV pili in Rhodoferax antarcticus was found in previous observations by Baker et al [8], in which the genes coding proteins synthesizing polar flagella, fliEFGHIJKLMNPQR, were well studied.…”

“…Cell growth was investigated in different bacteriological media: R2A agar, tryptic soy agar (TSA; Difco, NJ, USA), Luria-Bertani (LB; Difco, NJ, USA) and nutrient agar (NA; Difco, NJ, USA). The growth temperature range was checked at 4,8,15,20,30,37 and 42 • C. The pH range for growth was determined by measuring the OD values of R2A broth cultures after 3 days. Then, pH was adjusted to 5-10 at intervals of 1 pH unit with appropriate biological buffers [18,19].…”

“…This means that some other enzyme together with PEP carboxylase assists in adding CO 2 to PEP [43]. light-harvesting complex and RuBisCo (ribulose 1, 5-bisphosphate carboxylase/oxygenase) genes [1,2,8,40,41]. Genes of complete sets of glycolysis and the citric acid cycle were identified in the genome of strain CHu59-6-5 T .…”

“…Two species in this genus, R. fermentans and R. antarcticus, grow photoheterotrophically using carbon sources such as acetate, pyruvate, lactate and succinate. Genomic features that provide photosynthesis gene clusters of the R. antarcticus have already been reported [8]. In contrast, R. ferrireducens is able to grow anaerobically using organic electron donors to reduce ferric iron (Fe +3 ) to ferrous (Fe +2 ) [1][2][3][4][5][6][7].…”

Genomic insights into a novel species Rhodoferax aquaticus sp. nov., isolated from freshwater

“…Members of the Rhodoferax species are capable of anoxygenic photoorganotrophy, anaerobic-dark fermentation, aerobic respiration and anaerobic growth via sugar fermentation, and the species in this genus are Gram-stain-negative, rod- or slightly curved rod-shaped bacteria containing ubiquinone-8 as the major respiratory quinone, and the G+C content is in the range of 59.5–62.8 mol% [1–7]. The genetic blueprint of a psychrophilic purple non-sulfur bacterium, Rhodoferax antarcticus ANT.BR T , has revealed that it has the photosynthetic machinery to survive under varying environmental conditions [8]. Here, we report on the analysis of the genome of a nonphototrophic strain, Gr-4 T , together with a taxonomic proposal based on its phylogenetic, genomic, physiological and chemotaxonomic characteristics.…”