Rhodobacter capsulatus

The discoverHans Molisch, a Czech-Austrian botanist. The microorganism, then named Rhodonostoc capsulatum, was identified in 1907 in his book Die Purpurbakterien nach neuen Untersuchungen.^[7] C. B. van Niel then characterized the species further in 1944 where it was renamed Rhodopseudomonas capsulata. Van Niel initially described 16 strains of R. capsulata that he was able to culture from mud samples collected in California and Cuba.^[8] In 1984, the species would be reclassified as Rhodobacter capsulatus with the introduction of the genus Rhodobacter. This genus was introduced to better differentiate Rhodopseudomonas species with distinct morphological differences such as those with vesicular intracytoplasmic membranes (membrane-bound compartments in the cell often involved in photosynthesis)^[9] like R. capsulatus and R. sphaeroides.^[1]

The R. capusulatus genome consists of one chromosome and one plasmid. Sanger sequencing was first used to assemble the genome. The complete genome was then analyzed using several programs, Critica, Glimmer, RNAmmer, tRNAscan, and ARAGORN. These programs all identify different groups of genes, including protein-coding, tRNA, tmRNA, and rRNA genes. The chromosome is approximately 3.7-Mb with 3,531 open reading frames (ORFs), while the plasmid is smaller at 133-kb and 154 ORFs. Within the 3,531 ORFs in the chromosome, 3,100 had a known function assigned. Another 610 ORFs had similarities to genes that are known, but their function is still not proven. The rest of the ORFs were novel, with nothing similar in UniRef90, NCBI-NR, COG, or KEGG databases used for comparison. The genetic material had a high GC content at 66.6%. R. capsulatus contains all of the genes necessary to produce all 20 amino acids, and also contains 42 transposase genes, and 237 phage genes, including the gene transfer agent (GTA). The chromosome can be found in the NCBI database under CP001312, and the plasmid is under accession number CP001313.^[10]

These bacteria prefer aqueous environments^[7] such as those around natural water sources or in sewage.^[11] R. capsulatus has been isolated from the United States and Cuba.^[12] Initially, this bacteria could be grown in the lab by plating samples from the environment onto RCVBN (DL-malic acid, ammonium sulfate, biotin, nicotinic acid, trace elements, and some additional compounds) medium and incubating them anaerobically with ample light. Colonies on these plates could then be isolated, grown in pure culture, and identified as R. capsulatus.^[11] With the sequencing of its genome, RNA and DNA sequencing can now be used to identify this species.^[6][13]

R. capsulatus is a phototrophic bacterium with some distinctive characteristics. They can grow either as rods or as motile coccobacilli, which is dependent on their environment. At pH levels below 7, the bacterium is spherical and forms chains. When the pH rises above 7, they switch to rod morphology. The length of the rod shaped bacteria is dependent on the pH as well; the cells elongate as the pH rises. In their rod shape, they also often form chains that are bent in nature. The original paper describes them as "zigzaggy" in shape.^[14] In response to the stress put on the cell at a pH of 8 or above, the cells display pleiomorphism, or abnormal, filamentous growth, and they produce a slimy substance for protection. Anaerobic culturing of the organism produces a brown color, on the spectrum of yellow-brown to burgundy. In media containing malonate, the reddish-brown, or burgundy, color is observed. When the organism is grown aerobically, a red color is produced. This species will not grow above 30 °C, and it will grow within 6 and 8.5 pH, although specific temperature and pH optima are not explicitly stated in the characterization paper.^[14] Although most Rhodobacter species are freshwater and have little salt tolerance, some strains of R. capsulatus appear to tolerate up to 0.3 M NaCl depending on their source of nitrogen.^[15]

As a purple non-sulfur bacterium, it is capable of aerobic growth without light, or anaerobic growth with light present, as well as fermentation.^[16] This species is also capable of fixing nitrogen.^[17] For carbon sources, R. capsulatus can utilize glucose, fructose, alanine, glutamic acid, propionate, glutaric acid, and other organic acids. However, it cannot use mannitol, tartrate, citrate, gluconate, ethanol, sorbitol, mannose, and leucine, which is unique to R. capsulatus when compared to other species in the genus. The most successful enrichments of this species come from propionate and organic acids.^[14] Under photoheterotrophic conditions, R. capsulatus strain B10 is capable of using acetate as its sole carbon source, but the mechanisms of this have not been identified.^[18] The strains studied do not hydrolyze gelatin.^[14]