The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships.

In a conserved culture of the purple sulfur bacterium Thiospirillum jenense DSM216T, cells of this species were easily recognized by cell morphology, large-size spirilla and visible flagellar tuft. The Tsp. jenense genome is 3.22 Mb in size and has a GC content of 48.7 mol%. It was readily identified as a member of the Chromatiaceae by the complement of proteins in its genome. A whole genome comparison clearly placed Tsp. jenense near Thiorhodovibrio and Rhabdochromatium species and somewhat more distant from Thiohalocapsa and Halochromatium species. This relationship was also found with the sequences of the photosynthetic reaction center protein PufM. The genome sequence supported important properties of this bacterium: the presence of ribulose-bisphosphate carboxylase and enzymes of the Calvin cycle of autotrophic carbon dioxide fixation but the absence of carboxysomes, an incomplete tricarboxylic acid cycle and the lack of malate dehydrogenase, the presence of a sulfur oxidation pathway including adenylylsulfate reductase (aprAB) but absence of assimilatory sulfate reduction, the presence of hydrogenase (hoxHMFYUFE), nitrogenase and a photosynthetic gene cluster (pufBALMC). The FixNOP type of cytochrome oxidase was notably lacking, which may be the reason that renders the cells highly sensitive to oxygen. Two minor phototrophic contaminants were found using metagenomic binning: one was identified as a strain of Rhodopseudomonas palustris and the second one has an average nucleotide identity of 82% to the nearest neighbor Rhodoferax antarcticus. It should be considered as a new species of this genus and Rhodoferax jenense is proposed as the name.

Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123T as the authentic type strain of this species.

The genus Rhodopseudomonas, containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called Rhodopseudomonas palustris. The type species R. palustris and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following Rhodopseudomonas species are well recognized: R. palustris (strains ATH 2.1.6T=DSM 123T=NBRC 100419T and BisB5), Rhodopseudomonas rutila (strains R1T, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), Rhodopseudomonas pentothenatexigens JA575T and Rhodopseudomonas faecalis JCM 11668T. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that R. palustris strain ATH 2.1.6T-KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123T of ATH 2.1.6T, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from R. palustris strain ATH 2.1.6T-KCM are in complete agreement with the translated genome sequences of R. palustris DSM 123T. In addition, the 16S rRNA gene sequence of R. palustris NBRC 100419T completely matches that of strain DSM 123T. In conclusion, the type strain of R. palustris ATH 2.1.6T is correctly represented by DSM 123T and NBRC 100419T. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic R. palustris, but rather indicate that this is a strain of R. rutila. The previously suggested assignment of the type strain of R. palustris DSM 123T to the new species R. pseudopalustris was incorrect because strain DSM 123T is the authentic type strain of R. palustris.

Anoxic growth optimization for metal respiration and photobiological hydrogen production by arsenic-resistant Rhodopseudomonas and Rhodobacter species.

The current research focuses on anaerobic respiration of arsenic and other toxic metals by purple nonsulfur bacteria (PNSB). Among the optimization assays performed were carbon utilization, cross metal resistance, and metal respiration, along with a comparison of each assay in photoheterotrophic and chemoheterotrophic growth. The bacteria were identified by the classification of 16S ribosomal RNA gene sequences. Rhodobacter sp. PI3 proved to be more versatile in carbon source utilization (acetate, lactate, citrate, and oxalate), whereas Rhodopseudomonas palustris PI5 proved to be more versatile in metal resistance (arsenate, arsenite, cobalt, lead, selenium, and nickel). Both the strains were found to be positive for photofermentative hydrogen production along with arsenic respiration. This study reveals that anaerobic conditions are more appropriate for better efficiency of PNSB. Our study demonstrates that R. palustris PI5 and Rhodobacter sp. PI3 can be promising candidates for the biohydrogen production along with metal detoxification using heavy metal-polluted effluents as a substrate.

Adaptation of Rhodopseudomonas acidophila strain 7050 to growth at different light intensities: what are the benefits to changing the type of LH2?

Typical purple bacterial photosynthetic units consist of light harvesting one/reaction centre 'core' complexes surrounded by light harvesting two complexes. Factors such as the number and size of photosynthetic units per cell, as well as the type of light harvesting two complex that is produced, are controlled by environmental factors. In this paper, the change in the type of LH2 present in the Rhodopsuedomonas acidophila strain 7050 is described when cells are grown at a range of different light intensities. This species contains multiple pucBA genes that encode the apoproteins that form light-harvesting complex two, and a more complex mixture of spectroscopic forms of this complex has been found than was previously thought to be the case. Femto-second time resolved absorption has been used to investigate how the energy transfer properties in the membranes of high-light and low-light adapted cells change as the composition of the LH2 complexes varies.

Rhodopseudomonas telluris sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.

A strain of anoxygenic phototrophic bacteria isolated from paddy soil (designated strain TUT3615T) was studied taxonomically in comparison with Rhodopseudomonasstrain ATCC 17005 as its nearest phylogenetic relative. Strains TUT3615T and ATCC 17005 had budding rod-shaped cells and showed in vivo absorption maxima at 804 and 860 nm in the near infrared region, indicating the presence of bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3615T and ATCC 17005 had a 99.7 % level of similarity to one another and were closest to Rhodopseudomonas palustris ATCC 17001T (98.6 % similarity) among the established species of the genus Rhodopseudomonas. Genomic DNA-DNA hybridization studies revealed that strains TUT3615T and ATCC 17005 had an average similarity level of 65 % to one another and of less than 40 % to the available type strains of Rhodopseudomonas species. Results of phenotypic studies showed that strains TUT3615T and ATCC 17005 could be differentiated from one another and from any previously described species of Rhodopseudomonas. The G+C contents of the genomic DNA of strain TUT3615T and ATCC 17005 were 66.3 and 66.5 mol%, respectively. Based on these data, we propose the name Rhodopseudomonas telluris sp. nov. for strain TUT3615T. The type strain is TUT3615T (=KCTC 23279T=NBRC 107609T). We suspend a proposal to reclassify strain ATCC 17005 as a novel species or subspecies until a genome-wide analysis provides more definite information on its taxonomic position.

Isolation and Characterization of a Purple Non-Sulfur Photosynthetic Bacterium Rhodopseudomonas faecalis Strain A from Swine Sewage Wastewater.

A purple non-sulfur photosynthetic bacterium (PNSB), PSB Strain A was isolated from swine sewage wastewater. Phylogenetic analysis revealed that PSB Strain A was most closely related to Rhodopseudomonas faecalis. Growth of the isolate under anaerobic-light conditions with a variety of carbon sources was investigated. Both PSB Strain A and the standard strain showed good growth with acetic acid, propionic acid, and n-butyric acid at a concentration of 20 mM. At the high concentration of 200 mM, PSB Strain A showed better growth in pyruvate, acetate, propionate, succinate and malate. By applying PSB Strain A to treat swine sewage wastewater, the concentration of VFAs, which were acetic acid and propionic acid, decreased from 158.0 mM to 120.2±2.9 mM, and 14.9 mM to 9.3±0.9 mM, respectively, after 216-h incubation. After 330-h incubation, the concentrations of TOC and ammonia nitrogen dropped from 4508.0 mg/L to 3104.0±451.5 mg/L, and 629.7 mg/L to 424.1±7.4 mg/L, respectively. The isolated PSB Strain A showed almost the same efficiency compared with the standard strain on the removal of VFAs and TOC. The results suggest the possibility of using the isolated strain to treat swine sewage wastewater.

[Isolation, Identification and Characteristics of a Rhodopseudomonas with High Ammonia-nitrogen Removal Efficiency].

A strain of photosynthetic bacterium named psb1 capable of ammonia-nitrogen degradation was isolated from a swamp in Yunnan. The psb1 was similar to Rhodopseudomonas sp. according to its cell morphological properties and absorption spectrum analysis of living cells. The alignment result of 16S rDNA amplification sequence with specific primers of photosynthetic bacteria showed that the homology between strain psb1 and Rhodopseudomonas sp. was 99%, and the alignment results of protein sequences of bacterial chlorophyll Y subunit showed that the strain psb1 and Rhodopseudomonas palustris were the most similar, with a similarity of 99%. But there was a great difference in the biological properties of the strains psb1 and Rhodopseudomonas palustris according to physiological biochemical characteristics and main fatty acid analysis. For example, strain psb1 could not utilize glucose and mannitol as carbon source, and had specific fatty acid C18:1ω6c. The results of single factor test showed that:the optimal growth was obtained at pH 7.0 and 40℃, the optimal nitrogen source was yeast extract. The optimal conditions for ammonia nitrogen biodegradation were as following:anaerobic, light, initial pH 6.0-7.0, temperature 30℃, inoculation volume 0.4%. Under that cultural condition, the degradation rate of ammonia nitrogen in wastewater could reach 99%. The results indicated that strain psb1 might be a novel bacterium in genus Rhodopseudomonas with high ammonia removal efficiency, and can be applied in the bioremediation of polluted landscape water.

A New Hydrogen-Producing Strain and Its Characterization of Hydrogen Production.

A newly isolated photo non-sulfur (PNS) bacterium was identified as Rhodopseudomonas palustris PB-Z by sequencing of 16S ribosomal DNA (rDNA) genes and phylogenetic analysis. Under vigorous stirring (240 rpm), the hydrogen production performances were greatly improved: The maximum hydrogen production rate and cumulative hydrogen production increased by 188.9 ± 0.07 % and 83.0 ± 0.06 %, respectively, due to the hydrogen bubbles were immediately removed from the culture medium. The effects of different wavelength of light on hydrogen production with stirring were much different from that without stirring. The ranking on the photo-hydrogen production performance was white > yellow > green > blue > red without stirring and white > yellow > blue > red > green under stirring. The best light source for hydrogen production was tungsten filament lamp. The optimum temperature was 35 °C. The maximal hydrogen production rate and cumulative hydrogen production reached 78.7 ± 2.3 ml/l/h and 1728.1 ± 92.7 mol H2/l culture, respectively, under 35 °C, 240 rpm, and illumination of 4000 lux. Pyruvate was one of the main sources of CO2 and has a great impact on the gas composition.

Reduction of selenite to red elemental selenium by Rhodopseudomonas palustris strain N.

The trace metal selenium is in demand for health supplements to human and animal nutrition. We studied the reduction of selenite (SeO3⁻²) to red elemental selenium by Rhodopseudomonas palustris strain N. This strain was cultured in a medium containing SeO3⁻² and the particles obtained from cultures were analyzed using transmission electron microscopy (TEM), energy dispersive microanalysis (EDX) and X ray diffraction analysis (XRD). Our results showed the strain N could reduce SeO3⁻² to red elemental selenium. The diameters of particles were 80-200 nm. The bacteria exhibited significant tolerance to SeO3⁻² up to 8.0 m mol/L concentration with an EC50 value of 2.4 m mol/L. After 9 d of cultivation, the presence of SeO3²â» up to 1.0 m mol/L resulted in 99.9% reduction of selenite, whereas 82.0% (p<0.05), 31.7% (p<0.05) and 2.4% (p<0.05) reduction of SeO3⁻² was observed at 2.0, 4.0 and 8.0 m mol/L SeO3²â» concentrations, respectively. This study indicated that red elemental selenium was synthesized by green technology using Rhodopseudomonas palustris strain N. This strain also indicated a high tolerance to SeO3⁻². The finding of this work will contribute to the application of selenium to human health.

Benzoyl coenzyme a pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris.

Photoheterotrophic metabolism of two meta-hydroxy-aromatic acids, meta-, para-dihydroxybenzoate (protocatechuate) and meta-hydroxybenzoate, was investigated in Rhodopseudomonas palustris. When protocatechuate was the sole organic carbon source, photoheterotrophic growth in R. palustris was slow relative to cells using compounds known to be metabolized by the benzoyl coenzyme A (benzoyl-CoA) pathway. R. palustris was unable to grow when meta-hydroxybenzoate was provided as a sole source of organic carbon under photoheterotrophic growth conditions. However, in cultures supplemented with known benzoyl-CoA pathway inducers (para-hydroxybenzoate, benzoate, or cyclohexanoate), protocatechuate and meta-hydroxybenzoate were taken up from the culture medium. Further, protocatechuate and meta-hydroxybenzoate were each removed from cultures containing both meta-hydroxy-aromatic acids at equimolar concentrations in the absence of other organic compounds. Analysis of changes in culture optical density and in the concentration of soluble organic compounds indicated that the loss of these meta-hydroxy-aromatic acids was accompanied by biomass production. Additional experiments with defined mutants demonstrated that enzymes known to participate in the dehydroxylation of para-hydroxybenzoyl-CoA (HbaBCD) and reductive dearomatization of benzoyl-CoA (BadDEFG) were required for metabolism of protocatechuate and meta-hydroxybenzoate. These findings indicate that, under photoheterotrophic growth conditions, R. palustris can degrade meta-hydroxy-aromatic acids via the benzoyl-CoA pathway, apparently due to the promiscuity of the enzymes involved.

Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., isolated from paddy soils.

Two strains (JA575(T) and JA576(T)) of orange- to pink-pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from paddy soils. Both strains contained bacteriochlorophyll a and carotenoids of spirilloxanthin series. Both strains had C(18 : 1)ω7c as the major cellular fatty acid, ubiquinone-10 (Q(10)) as the main quinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as polar lipids. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria. Strains JA575(T) and JA576(T) were genotypically (<35 % DNA-DNA relatedness) and phenotypically distinct from each other. Further, both strains showed less than 48 % DNA-DNA relatedness with the type strains of all recognized species of the genus Rhodopseudomonas. The molecular evidence is supported by phenotypic evidence. It is proposed that strains JA575(T) and JA576(T) be classified as representing two novel species of the genus Rhodopseudomonas with the species names Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., respectively. The type strains of the proposed novel species are JA575(T) (= NBRC 108862(T) = KCTC15143(T)) and JA576(T) (= NBRC 108863(T) = KCTC 15144(T)), respectively.

[Photosynthetic bacteria of Rhodopseudomonas palustris isolated from river sediment].

OBJECTIVE: One strain of photosynthetic bacteria associated with highly removal capability of pollutant was isolated, and investigated about its growth. METHODS: By using an enrichment culture and plate dilution method, one strain of bacteria, named VOTO1-G, was isolated from river sediment mainly received domestic wastewater. The VOTO1-C bacteria was researched about its growth law, and identified by molecular biology method, and further used to test its ability in the removing of nitrogen, phosphorus and organic compound from eutrophic water by 0.05 per thousand, 0.1 per thousand and 0.2 per thousand. RESULTS: By checking the individual morphology, colony culture characteristics, DNA sequencing and 16S rDNA gene bank, VOTO1-G was identified as Rhodopseudomonas palustris. The isolated bacteria strain had some nitrogen, phosphorus and organic compound removal ability. CONCLUSION: One strain of photosynthetic bacteria was successfully isolated from sewage sediments. Its removal capacity of nitrogen, phosphorus and organic compound from eutrophic water was good, which removed COD 12%, TP 25%, TN 13%.

Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.

Four strains (JA310(T), JA531(T), JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310(T) and JA531(T) was C(18:1)ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria. Strains JA531(T), JA447 and JA490 were genotypically (>80% related based on DNA-DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310(T) (33% related). Furthermore, all four strains had less than 48% relatedness (DNA-DNA hybridization) with type strains of members of the genus Rhodopseudomonas, i.e. Rhodopseudomonas palustris ATCC 17001(T), Rhodopseudomonas faecalis JCM 11668(T) and Rhodopseudomonas rhenobacensis DSM 12706(T). The genomic DNA G+C contents of strains JA310(T) and JA531(T) were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310(T) ( = NBRC 106083(T) = KCTC 5839(T)) and JA531(T) ( = NBRC 107575(T) = KCTC 5841(T)) be classified as the type strains of two novel species of the genus Rhodopseudomonas, Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123(T) ( = NBRC 100419(T)) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001(T) and other members of the genus Rhodopseudomonas. An emended description of R. palustris is also provided.

[Biological characteristics and phylogenetic analysis of a denitrifying photosynthetic bacterium].

OBJECTIVE: Nitrite accumulation in aquaculture water is toxic to reared animals. One of the solutions to this problem is to apply denitrifying bacteria. This paper is intended to get a strain of phototrophic bacteria for efficient removal of nitrite from aquaculture water. METHODS: We used soft agar to isolate and purify phototrophic bacteria. We investigated biological characteristics of the isolate by means of light and electronic observations, physical and chemical tests. We analyzed its phylogenetical position based on the sequences of 16S rDNA and the gene that codes for photosynthetic reaction center subunit M (pufM). RESULTS: A photosynthetic bacterial strain, named wps, showing high removal efficiency of nitrite, was isolated from the freshwater ponds. Cells were Gram-negative, rod-shaped, slightly curved, 0.4 - 0.6 x 1.5 - 4.0 microm, motile by means of polar multiple flagella. Intracellular membranes were of the lamellar type. It grew under facultative anaerobic conditions in the light with bacteriochlorophyll a and carotenoid of sppirilloxanthin series as photosynthetic pigment. The optimum growth was obtained at pH 5.5 - 8.5, in a range of 0 - 2% salinity and at 25 - 38 degrees C. The similarity of 16S rDNA between strain wps and Rhodopseudomonas palustris was 98.9% and 94.9% for pufM gene. However, there are significant differences between them in the morphological and physiological characteristics, i. e. grew at pH 5.5; no growth photoautotrophicaly with sodium hydrogen carbonate; could not utilize citrate or formate as only carbon source; required thiamine hydrochloride and calcium pantothenate as growth factors. CONCLUSION: Strain wps may represent a novel species in genus Rhodopseudomonas and possibly find its application in the bioremediation of polluted aquaculture water.

[Isolation, identification and degrading gene cloning of a pyrethroids-degrading bacterium].

OBJECTIVE: This study aimed to isolate, identify and clone degrading gene of a synthetic pyrethroids degrading bacterium. METHODS: A photosynthetic bacterial strain PSB07-21 capable of degrading several synthetic pyrethroids efficiently was isolated by an enrichment culture. PSB07-21 was identified based on its morphology, physiology and phylogenetic analysis of 16S rDNA sequence. The degradation ability of this strain was evaluated with gas chromatography.The degrading gene was cloned with PCR. RESULTS: PSB07-21 was closely related to Rhodopseudomonas sp. The optimum condition of degrading synthetic pyrethroidss was at 35 degrees C, pH 7 and 3000 lx. PSB07-21 could degrade fenpropathrin, cypermethrin and bipthenthrin by 66.63%, 43.25% and 50.18% in a concentration of 600 mg/L at day 15, respectively. We cloned a putative gene which was 326bp long with 37.0% identical to 20G-Fe (II) oxygenase gene. When compensating low concentration Fe (II) in PSB medium with synthetic pyrethroids, the degradation efficiency of PSB07-21 was enhanced. CONCLUSION: The strain has the potential application to synthetic pyrethroids bioremediation.

Intrageneric relationships of members of the genus Rhodopseudomonas.

The intrageneric structure of the genus Rhodopseudomonas was evaluated by studying sequence information on 16S rRNA genes, 16S-23S rRNA gene internal transcribed spacer (ITS) regions, and puf genes using 33 test strains. The topology of phylogenetic trees based on these sequences was similar to those of every other independent method for tree construction. These phylogenetic data indicated that the test strains were grouped into at least 7 clusters possibly at the species level. This was supported by genomic DNA-DNA similarities among 12 representative test strains selected from these clusters. Our molecular data confirmed that the currently available strains of Rhodopseudomonas (Rps.) palustris are genetically quite heterogeneous within the genus. For example, Rps. palustris strains DSM 123(T) and ATCC 17001(T) are different from each other at the species level despite their status as the type strain of the species. Rps. palustris strain ATCC 17005 and the full genome-sequenced strains BisA53, BisB18, BisB5, and HaA2 should be re-classified into different species from Rps. palustris or as novel species of the genus Rhodopseudomonas.

Hydrogen production with R. faecalis RLD-53 isolated from freshwater pond sludge.

The Rhodopseudomonas faecalis strain RLD-53 was isolated from freshwater pond sludge and was demonstrated it could produce hydrogen. This study to investigate their ability of hydrogen production under some conditions in batch culture experiments. At pH 7.0, temperature 35 degrees C and light intensity of 4000 lux, the H(2) yield was 2.64 mol-H(2)/mol-acetate, 2.34 mol-H(2)/mol-propionate, 1.75 mol-H(2)/mol-lactate and 3.55 mol-H(2)/mol-malate, respectively. The maximal H(2) production rate of 32.62 ml-H(2)/l/h and H(2) yield of 2.84 mol-H(2)/mol-acetate were achieved when beef extract was used as nitrogen source. Light intensity is the most important factor for H(2) production, H(2) production yield and rate decreased with increasing light intensity and reached highest under light intensity of 3000-5000 lux. Result indicated the strain RLD-53 was a high efficient bacteria for hydrogen production.

Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments.

The bacterial genus Rhodopseudomonas is comprised of photosynthetic bacteria found widely distributed in aquatic sediments. Members of the genus catalyze hydrogen gas production, carbon dioxide sequestration, and biomass turnover. The genome sequence of Rhodopseudomonas palustris CGA009 revealed a surprising richness of metabolic versatility that would seem to explain its ability to live in a heterogeneous environment like sediment. However, there is considerable genotypic diversity among Rhodopseudomonas isolates. Here we report the complete genome sequences of four additional members of the genus isolated from a restricted geographical area. The sequences confirm that the isolates belong to a coherent taxonomic unit, but they also have significant differences. Whole genome alignments show that the circular chromosomes of the isolates consist of a collinear backbone with a moderate number of genomic rearrangements that impact local gene order and orientation. There are 3,319 genes, 70% of the genes in each genome, shared by four or more strains. Between 10% and 18% of the genes in each genome are strain specific. Some of these genes suggest specialized physiological traits, which we verified experimentally, that include expanded light harvesting, oxygen respiration, and nitrogen fixation capabilities, as well as anaerobic fermentation. Strain-specific adaptations include traits that may be useful in bioenergy applications. This work suggests that against a backdrop of metabolic versatility that is a defining characteristic of Rhodopseudomonas, different ecotypes have evolved to take advantage of physical and chemical conditions in sediment microenvironments that are too small for human observation.

Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense.

The isolation of photoheterotrophic organism C3 from a saline microbial mat led to its taxonomic characterization. Strain C3 could be identified as a member of the species Rhodobium marinum due to the genetic and phenotypic similarities to the type strain of the species (DSM 2698(T)). As a result of a taxonomic study, it was observed that the currently classified species of the genus formed two separate clades, each of them deserving genus status. Rhodobium orientis and Rhodobium gokarnense may be considered as true members of the genus Rhodobium, whereas R. marinum and Rhodobium pfennigii should be reclassified into a new genus. In the light of the genetic and phenotypic evidence observed, we propose that both latter species are reclassified within the new genus Afifella gen. nov., as species Afifella marina comb. nov., and Afifella pfennigii comb. nov., with Af. marina the type species of the genus. In addition, the taxonomic study has revealed that strain DSM 11549, identified as the type strain of the species Rhodopseudomonas julia, may represent a genomovar of Af. marina. The fact that the author of the first classification of R. julia indicates that the strains deposited in the German Collection for Microorganisms (DSM 11549) and American Collection of Type Cultures (ATCC 51105) do not correspond to the original description, makes the authenticity of the strains doubtful. Due to this reason, it is not proposed to reclassify the species.

Composition and localization of bacteriochlorophyll a intermediates in the purple photosynthetic bacterium Rhodopseudomonas sp. Rits.

Rhodopseudomonas sp. Rits is a recently isolated new species of photosynthetic bacteria and found to accumulate a significantly high amount of bacteriochlorophyll (BChl) a intermediates possessing non-, di- and tetra-hydrogenated geranylgeranyl groups at the 17-propionate as well as normal phytylated BChl a (Mizoguchi T et al. (2006) FEBS Lett 580:137-143). A phylogenetic analysis showed that this bacterium was closely related to Rhodopseudomonas palustris. The strain Rits synthesizes light-harvesting complexes 2 and 4 (LH2/4), as peripheral antennas, as well as the reaction center and light-harvesting 1 core complex (RC-LH1 core). The amounts of these complexes were dependent upon the incident light intensities, which was also a typical behavior of Rhodopseudomonas palustris. HPLC analyses of extracted pigments indicated that all four BChls a were associated with the purified photosynthetic pigment-protein, as complexes described above. The results suggested that this bacterium could use these pigments as functional molecules within the LH2/4 and RC-LH1 core. Pigment compositional analyses in several purple photosynthetic bacteria showed that such BChl a intermediates were always detected and were more widely distributed than expected. Long chains in the propionate moiety of BChl a would be one of the important factors for assembly of LH systems in purple photosynthetic bacteria.