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Two Gram-stain-negative, aerobic, ovoid to short rod-shaped bacterial strains, designated as WL0062 T and WL0115, were isolated from coastal zone of the Yellow Sea, Jiangsu Province, PR China, respectively. Strain WL0062 T grew optimally at 28 °C, pH 7.0-8.0 and with 1.0-3.0% (w/v) NaCl. Strain WL0115 grew optimally at 28 °C, pH 6.0-7.0 and with 1.0-3.0% (w/v) NaCl. In the bac120 tree, strains WL0062 T and WL0115 clustered together with Sedimentimonas flavescens B57 T . The respiratory quinone of both strains was ubiquinone-10. The major polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, glycolipid, phosphatidylmonomethylethanolamine, and one unidentified polar lipid. The major fatty acids of strain WL0062 T were summed features 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c ). The major fatty acids of strain WL0115 were summed features 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c ), C 18 : 0 , iso-C 17 : 1  ω 5 c and C 20 : 4  ω 6/9/12/15 c (arachidonic acid). The G+C content of genomic DNA of strains WL0062 T and WL0115 was 64.0 mol% in both of them. Combined with the analysis of average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization, strain WL0062 T represents a novel species of the genus Rhodobacter , for which the name Rhodobacter flavimaris sp. nov is proposed. The type strain is WL0062 T (=MCCC 1K06014 T =JCM 34676 T =GDMCC 1.2427 T ). Strain WL0115 (=MCCC 1K07531=JCM 35568=GDMCC 1.3088) should belong to the same species as Sedimentimonas flavescens B57 T . In addition, on the basis of phylogenomic relationship and phenotypical characteristics, the genera Paenirhodobacter , Sedimentimonas , and Sinirhodobacter are proposed as synonyms of Rhodobacter .

Two bacterial strains, designated HSP-20 T and CCP-1 T , isolated from freshwater habitats in Taiwan, were characterized by polyphasic taxonomy. Both strains were Gram-stain-negative, aerobic, non-motile and rod-shaped. Cells of strains HSP-20 T and CCP-1 T formed pink and dark red coloured colonies, respectively. Both strains contained bacteriochlorophyll a , and showed optimum growth under anaerobic conditions by photoheterotrophy, but no growth by photoautotrophy. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences indicated that both strains belonged to the genus Rhodobacter . Analysis of 16S rRNA gene sequences showed that strains HSP-20 T and CCP-1 T shared 98.3 % sequence similarity and were closely related to Rhodobacter tardus CYK-10 T (96.0 %) and Rhodobacter flagellatus SYSU G03088 T (96.0 %), respectively. Both strains shared common chemotaxonomic characteristics including Q-10 as the major isoprenoid quinone, C 18 : 1  ω 7 c as the predominant fatty acid, and phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the main polar lipids. The DNA G+C content of both strains was 66.2 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Rhodobacter , for which the names Rhodobacter amnigenus sp. nov. (=BCRC 81193 T =LMG 31334 T ) and Rhodobacter ruber sp. nov. (=BCRC 81189 T =LMG 31335 T ) are proposed.

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5 T and CYK-10 T , were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae . Strain KMS-5 T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10 T is closest to Rhodobacter thermarum YIM 73036 T with 96.6 % sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set showed that strain KMS-5 T is affiliated with species in the genus Tabrizicola and strain CYK-10 T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485 T , Rhodobacter thermarum YIM 73036 T and Rhodobacter flagellatus SYSU G03088 T . These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C 18 : 1  ω 7 c as the main fatty acid. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. The obtained polyphasic taxonomic data suggested that strain KMS-5 T represents a novel species within the genus Tabrizicola , for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5 T (=BCRC 81196 T =LMG 31337 T ) as the type strain, and strain CYK-10 T should represent a novel species of the genus Rhodobacter , for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10 T (=BCRC 81191 T =LMG 31336 T ) as the type strain.

A Gram-stain-negative, aerobic, and motile strain, TJ48 T , was isolated from pakchoi-cultivated soil contaminated with Cd and Pb in Xinxiang (China). Cells of the strain were rod-shaped and colonies on LB agar were faint yellow. Strain TJ48 T was positive for catalase and oxidase and the optimal condition for growth was 28 °C, with 1% (w/v) NaCl and at pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TJ48 T was closely related to the genus Rhodobacter and the closest relatives were Rhodobacter ovatus JA234 T (97.4%, 16S rRNA gene sequence similarity) and Rhodobacter azotoformans KA25 T (96.5%). The DNA G + C content of strain TJ48 T was 64.7 mol%. Genome-to-genome distance calculations (GGDC) and ANIb values from genomic comparison between the genomes of strain TJ48 T and the related reference species were less than 70% and 95%, respectively. The major cellular fatty acids were summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c) and C 17:0 . The only isoprenoid quinone detected was Ubiquinone-10 (Q-10). The polar lipid profile contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipids, and three unidentified lipids. Strain TJ48 T significantly increased the dry weight of roots (26.2-66.3%) and shoots (16.7-37.8%) of pakchoi and reduced the Cd (50.2-60.1%) and Pb (55.6-60.9%) contents in pakchoi shoots and roots. On the basis of the physiological, genotypic and genomic characteristics, the strain TJ48 T represent a novel species of the genus Rhodobacter, and the name Rhodobacter xinxiangensis sp. nov. is proposed (type strain TJ48 T  = CCTCC AB2019120 T  = KCTC 72510 T ).

A thermophilic bacterium, designated SYSU G03088 T , was isolated from Moincer hot spring, Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position and genomic profiles of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that SYSU G03088 T showed highest sequence similarity to Rhodobacter blasticus CGMCC 1.3365 T (96.0 % sequence identity). The strain could be differentiated from most recognized species of the genus Rhodobacter by its slightly purple colony colour, distinct phenotypic characters and low ANI values. Cells were Gram-staining negative, and oval-to-rod shaped. Poly-β-hydroxybutyrate and vesicular intracytoplasmic membrane structures were formed inside cells. Growth occurred optimally at 45 °C and pH 7.0. Ubiquinone 10 was the only respiratory quinone. The major fatty acids (>10 %) were C 18 : 0 , C 18 : 1 ω7 c 11-methyl and summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ). The detected polar lipids of SYSU G03088 T included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The DNA G+C content of SYSU G03088 T was 67.7 % (genome). On the basis of the differences in the phenotypic characteristics and phylogenetic analyses, SYSU G03088 T is considered to represent a novel species of the genus Rhodobacter , for which the name Rhodobacter flagellatus sp. nov. is proposed. The type strain is SYSU G03088 T (=CGMCC 1.16876 T =KCTC 72354 T ).

A phototrophic bacterium, designated as strain JA983 T , was isolated from a freshwater pond in Gujarat, India. The strain was yellowish brown, catalase- and oxidase-positive, rod-to-oval shaped, Gram-stain-negative and motile. Growth was observed at 20-35 °C. NaCl was not required for optimum growth and up to 5 % was tolerated. Growth was observed at pH 6.0-8.0, with an optimum at pH 7.0. An unidentified glycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids (AL1, AL2) and two unidentified lipids (L1 and L2) are the polar lipids of JA983 T . Q10 is the only quinone. C 18 : 1  ω7 c /C 18 : 1  ω6 c is the major fatty acid. JA983 T showed highest 16S rRNA gene sequence similarity with the type strains of Rhodobacter sphaeroides (98.99%), Rhodobacter megalophilus (98.99 %), Rhodobacter johrii (98.99 %) and other members of the genus Rhodobacter with less than 98.7 % similarity. In a 16S rRNA gene sequence-based phylogenetic tree, JA983 T formed a different sub-clade with its nearest phylogenetic members of genus Rhodobacter . Phenotypic, chemotaxonomic, phylogenetic and genomic [average nucleotide identity (ANI) and digital DNA-DNA hybridization ( d DDH) differences indicated that JA983 T is significantly different from other species of the genus Rhodobacter and thus represents a novel species of the genus for which the name Rhodobacter sediminicola sp. nov. is proposed. The type strain is JA983 T (=KCTC 15782 T =NBRC 113843 T ).

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., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a sediment sample of a hot spring in Tibet, China. Cells of strain YIM 73036 T were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036 T grew optimally at pH 7.0-7.5 at 37-45 °C. Growth occurred in 0.5-3.5% (w/v) NaCl. Vitamins were not required for growth. The presence of photosynthesis genes pufL and pufM were shown and photosynthesis pigments were formed. Bacteriochlorophyll α, the bacteriopheophytin and carotenoids were present as photosynthetic pigments. Internal cytoplasmic membranes were of the lamellar type. The organism YIM 73036 T was able to grow chemo-organoheterophically, chemo-lithoautotrophically and photo-organoheterotrophically but photo-lithoautotrophic and fermentative growth were not demonstrated. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain YIM 73036 T is closely related to Rhodobacter blasticus ATCC 33485 T (96.65% sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae. Whole-genome sequence analyses based on the average nucleotide BLAST identity (ANI < 82%) indicated that this isolate belongs to a novel species. The genomic DNA G+C content of organism YIM 73036 T was determined to be 66.0 mol%. Strain YIM 73036 T contained Q-10 as the predominant ubiquinone and C 18:1 ω7c, C 18:1 ω7c 11-methyl and C 18:0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipid. Differential phenotypic and chemotaxonomic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 73036 T is distinguishable from other species of the genus Rhodobacter. On the basis of the data presented, strain YIM 73036 T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter thermarum sp. nov. [type strain YIM 73036 T (= KCTC 52712 T  = CCTCC AB 2016298 T )] is proposed.

An alkali-tolerant, Gram-stain-negative, motile, rod-to-oval-shaped, yellowish brown-colored, phototrophic bacterium, designated as strain JA916 T , was isolated from an alkaline brown pond in Gujarat, India. The DNA G + C content of the strain JA916 T was 65.1 mol%. Strain JA916 T grew well at pH 10. Respiratory quinone was Q-10 and major fatty acid was C 18:1 ω7c/C 18:1 ω6c, with significant quantities of C 15:0 2OH observed. Strain JA916 T shared the highest 16S rRNA gene sequence similarity with the type strains of Rhodobacter johrii (98.4%), followed by Rhodobacter megalophilus (98.3%), Rhodobacter sphaeroides (98.3%), Rhodobacter azotoformans (97.9%) and other members of the genus Rhodobacter (< 97%). 16S rRNA gene-based phylogenetic tree shows that strain JA916 T formed a distinct sub-clade with Rhodobacter johrii, Rhodobacter megalophilus, Rhodobacter sphaeroides and Rhodobacter azotoformans. Further, rpoB-based phylogenetic analysis showed lower similarity with closely related species (≤ 93.0%) of the genus Rhodobacter, which suggests that JA916 T is a novel species of the genus Rhodobacter. DNA-DNA hybridization values between strain JA916 T and related type strains were less than 40%. Phenotypic, chemotaxonomical and phylogenetic differences showed that strain JA916 T was distinct from other species of the genus Rhodobacter, suggesting strain JA916 T represents a new species of the genus for which the name Rhodobacter alkalitolerans sp. nov. is proposed. Type strain is JA916 T (= KCTC 15473 T  = LMG 28749 T ).

Three strains (JA826T, JA912T and JA913), which were yellowish brown colour, rod to oval shaped, Gram-stain-negative, motile, phototrophic bacteria with a vesicular architecture of intracytoplasmic membranes, were isolated from different pond samples. The DNA G+C content of the three strains was between 64.6 and 65.5 mol%. The highest 16S rRNA gene sequence similarity of all three strains was with the type strains of the genus Rhodobacter sensu stricto in the family Rhodobacteraceae. Strain JA826T had highest sequence similarity with Rhodobacter maris JA276T (98.5 %), Rhodobacter viridis JA737T (97.5 %) and other members of the genus Rhodobacter (<97 %). Strain JA912T had highest sequence similarity with Rhodobacter viridis JA737T (99.6 %), Rhodobacter sediminis N1T (99.3 %), Rhodobacter capsulatus ATCC 11166T (98.8 %) and less than 97 % similarity with other members of the genus Rhodobacter. The 16S rRNA gene sequence similarity between strains JA826T and JA912T was 96.9 %. DNA-DNA hybridization showed that strains JA826T and JA912T (values among themselves and between the type strains of nearest members <44 %) did not belong to any of the nearest species of the genus Rhodobacter. However, strains JA912T and JA913 were closely related (DNA-DNA hybridization value >90 %). The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics in order to propose strains JA826T (=KCTC 15478T=LMG 28758T) and JA912T (=KCTC 15475T=LMG 28748T) as new species in the genus Rhodobacter sensu stricto with the names Rhodobacter lacus and Rhodobacter azollae, respectively.

Two Gram-stain-negative, rod-shaped phototrophic bacteria (designated strains N1T and C7) were isolated from lagoon sediments. Both strains were positive for catalase and oxidase activity. Casein, starch, urea and Tween 20 were hydrolysed by both strains while chitin, gelatin and Tween 80 were not. In both strains, C16 : 0, C18 : 0,C16 : 1ω6c/C16 : 1ω7c and C18 : 1ω6c/ C18 : 1ω7c were the predominant fatty acids, with minor amounts of C8 : 0 3-OH, anteiso-C14 : 0, C17 : 0, C14 : 1ω5c, C17 : 1 10-methyl and C18 : 1ω5c. Strains N1T and C7 contained phosphatidylglycerol and phosphatidylethanolamine as major polar lipids with minor amounts of phosphatidylcholine, unidentified lipids and an unidentified phospholipid. The mean genomic DNA G+C content was 70.6±1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain N1T has a 16S rRNA gene sequence similarity of 99.2 % with Rhodobacter capsulatus ATCC 11166T, 99.1 % with Rhodobacter viridis JA737T and <96.6 % with other members of the genus Rhodobacter. Strain N1T and C7 shared 100 % 16S rRNA gene sequence similarity. DNA- DNA hybridization values between strain N1T and the type strains of the nearest species were clearly below the 70 % threshold. On the basis of phenotypic and genotypic data, it is proposed that strain N1T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter sediminis sp. nov. is proposed. The type strain is N1T (=KEMB 563-471T=JCM 31175T), and strain C7 is an additional strain of the species.

A Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped, non-photosynthetic bacterial strain, DW2-9(T), was isolated from soil. The highest 16S rRNA gene sequence similarities were found to Rhodobacter capsulatus ATCC 11166(T) (97.1%), Rhodobacter viridis JA737(T) (96.4%), Rhodobacter maris JA276(T) (96.2%), Rhodobacter veldkampii ATCC 35703(T) (96.0%), Haematobacter massiliensis CCUG 47968(T) (96.0%), Haematobacter missouriensis CCUG 52307(T) (95.9%) and Rhodobacter aestuarii JA296(T) (95.7%). The genomic DNA G+C content was 67.2 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>5%) were C(18 : 1)ω7c, C(16 : 0), C(19 : 0) cyclo ω8c and summed feature 3 (one or more of iso-C(15 : 0) 2-OH, C(16 : 1)ω6c and C(16 : 1)ω7c). However, unlike species of the genus Rhodobacter, strain DW2-9(T) neither formed internal photosynthetic membranes nor produced photosynthetic pigments. DNA-DNA hybridization between strain DW2-9(T) and R. capsulatus JCM 21090(T) showed a relatedness of 33%. Strain DW2-9(T) contained phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid as major polar lipids, which differed from those of species of the genera Rhodobacter and Haematobacter. In addition to the differences in phylogenetic position and polar lipid types, strain DW2-9(T) could be distinguished from species of the genus Haematobacter by the cultivation conditions. On the basis of our polyphasic taxonomic analysis, strain DW2-9(T) is considered to represent a novel genus and species, for which the name Paenirhodobacter enshiensis gen. nov., sp. nov. is proposed. The type strain of Paenirhodobacter enshiensis is DW2-9(T) ( = CCTCC AB 2011145(T) = KCTC 15169(T)). Emended descriptions of the genera Rhodobacter and Haematobacter are also proposed.

Deterioration of water wells due to clogging and corrosion over time is a common problem where solutions may be costly and ineffective. Pilot studies have suggested that impressed current or cathodic protection may be used to reduce microbially-induced declines in water well performance. Two water wells in an alluvial aquifer close to the North Saskatchewan River were selected to study the response of subsurface microbial communities to the application of an impressed current as an anti-fouling technology. The treated well was exposed to an impressed current while the untreated well was used as a reference site. Biofilms grown on in situ coupons under the influence of the impressed current were significantly (p < 0.05) thicker (mean thickness = 67.3 μm) when compared to the biofilms (mean thickness = 19.3 μm) grown outside the electric field. Quantitative PCR analyses showed significantly (p < 0.05) higher numbers of total bacteria, iron- and nitrate-reducers in the electrified zone. Molecular analysis revealed that the predominant bacteria present in biofilms grown under the influence of the impressed current belonged to Rhodobacter spp., Sediminibacterium spp. and Geobacter spp. In addition to favouring the growth of biofilms, direct microscopic and ICP-AES analyses revealed that the impressed current also caused the deposition of iron and manganese on, and in the vicinity of, the well screen. Together, these factors contributed to rapid clogging leading to reduced specific pumping capacities of the treated well. The study revealed that the impressed current system was not effective as an anti-fouling technology but actually promoted both microbial growth and physical clogging in this aquifer., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

A green phototrophic bacterium (strain JA737(T)), which was oval- to rod-shaped, Gram-negative and motile, was isolated from mud of a stream in the Western Ghats of India. Strain JA737(T) contained bacteriochlorophyll a, and the major carotenoid was neurosporene. The major quinone was Q-10 and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. Phylogenetic analysis showed that the strain clustered with members of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strain JA737(T) had highest sequence similarity with Rhodobacter capsulatus ATCC 11166(T) (98.8 %), Rhodobacter maris JA276(T) (97 %), Rhodobacter aestuarii JA296(T) (96.7 %) and other members of the genus Rhodobacter (<96 %). However, strain JA737(T) showed 22-55 % DNA-DNA relatedness with the above type strains. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, strain JA737(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter viridis sp. nov. is proposed. The type strain is JA737(T) ( = KCTC 15167(T) = MTCC 11105(T) = NBRC 108864(T)).

A novel non-sporulating, non-motile, catalase- and oxidase-positive, strictly aerobic, Gram-negative, rod-shaped bacterial strain, designated DCA-1(T), was isolated from activated sludge collected from a butachlor wastewater treatment facility. The strain was able to degrade about 85 % of 100 mg butachlor l(-1) within 5 days of incubation. Growth occurred in the presence of 0-6 % (w/v) NaCl [optimum, 1 % (w/v) NaCl] and at pH 5.5-9.0 (optimum, pH 7.0) and 15-35 °C (optimum, 25-30 °C). Vesicular internal membrane structures and photoheterotrophic growth were not observed. The major respiratory quinone was ubiquinone 10 (Q-10) and the major cellular fatty acids were C(18 : 1)ω7c and 11-methyl C(18 : 1)ω7c. The genomic DNA G+C content of strain DCA-1(T) was 62.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DCA-1(T) was a member of the family Rhodobacteraceae and was related most closely to the type strain of Catellibacterium aquatile (96.5 % sequence similarity). The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supports the suggestion that strain DCA-1(T) represents a novel species of the genus Catellibacterium, for which the name Catellibacterium caeni sp. nov. is proposed. The type strain is DCA-1(T) ( = CGMCC 1.7745(T)  = DSM 21823(T)). In addition, based on the characterization data obtained in this study, it is proposed that Rhodobacter changlensis should be reclassified as Catellibacterium changlense comb. nov. (type strain JA139(T)  = DSM 18774(T)  = CCUG 53722(T)  = JCM 14338(T)). An emended description of the genus Catellibacterium is also presented.

Measurements of dissolved, ascorbate-reducible and total Mn by ICP-OES revealed significantly higher concentrations during estuarine turbidity maxima (ETM) events, compared with non-events in the Columbia River. Most probable number (MPN) counts of Mn-oxidizing or Mn-reducing heterotrophs were not statistically different from that of other heterotrophs (10³ -10⁴ cells ml⁻¹) when grown in defined media, but counts of Mn oxidizers were significantly lower in nutrient-rich medium (13 cells ml⁻¹). MPN counts of Mn oxidizers were also significantly lower on Mn(III)-pyrophosphate and glycerol (21 cells ml⁻¹). Large numbers of Rhodobacter spp. were cultured from dilutions of 10⁻² to 10⁻⁵, and many of these were capable of Mn(III) oxidation. Up to c. 30% of the colonies tested LBB positive, and all 77 of the successfully sequenced LBB positive colonies (of varying morphology) yielded sequences related to Rhodobacter spp. qPCR indicated that a cluster of Rhodobacter isolates and closely related strains (95-99% identity) represented approximately 1-3% of the total Bacteria, consistent with clone library results. Copy numbers of SSU rRNA genes for either Rhodobacter spp. or Bacteria were four to eightfold greater during ETM events compared with non-events. Strains of a Shewanella sp. were retrieved from the highest dilutions (10⁻⁵) of Mn reducers, and were also capable of Mn oxidation. The SSU rRNA gene sequences from these strains shared a high identity score (98%) with sequences obtained in clone libraries. Our results support previous findings that ETMs are zones with high microbial activity. Results indicated that Shewanella and Rhodobacter species were present in environmentally relevant concentrations, and further demonstrated that a large proportion of culturable bacteria, including Shewanella and Rhodobacter spp., were capable of Mn cycling in vitro., (© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.)

An oval to rod-shaped, phototrophic, purple non-sulfur bacterium, strain JA192(T), was isolated from an enrichment culture of a pasteurized rhizosphere soil sample from a field cultivated with jowar (sorghum) collected from Godumakunta village near Hyderabad, India. Strain JA192(T) is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192(T) is closely related to Rhodobacter sphaeroides 2.4.1(T) (99.9 % sequence similarity), Rba. megalophilus JA194(T) (99.8 %) and Rba. azotoformans KA25(T) (98.1 %) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. sphaeroides DSM 158(T), Rba. megalophilus JA194(T) and Rba. azotoformans JCM 9340(T) showed relatedness of only 38-57 % with respect to strain JA192(T). On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data and morphological, physiological and chemotaxonomic characters, strain JA192(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192(T) (=DSM 18678(T) =JCM 14543(T) =MTCC 8172(T)).

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a brown-coloured microbial mat from the brackish water of Bhitarkanika mangrove forest, Dangmal, Orissa, India. Cells of strain JA296(T) were Gram-negative and motile, forming chains of four to eight cells. The colour of the cell suspension grown under anaerobic conditions in the light was yellowish green. Bacteriochlorophyll a and the carotenoids spheroidene and spheroidenone of the spirilloxanthin series were present as photosynthetic pigments. The bacterium was a facultative anaerobe and was able to grow photo-organoheterotrophically and chemo-organoheterotrophically. Thiamine was required as a growth factor. C(18 : 1)omega7c was the dominant fatty acid. Internal cytoplasmic membranes were of the vesicular type. Strain JA296(T) did not require NaCl for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA296(T) was most closely related to Rhodobacter capsulatus ATCC 11166(T) (95.5 % sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae, class Alphaproteobacteria. On the basis of 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA296(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter aestuarii sp. nov. is proposed; the type strain is JA296(T) (=JCM 14887(T) =CCUG 55130(T)).

Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.

Phototrophic iron(II) [Fe(II)]-oxidizing bacteria are present in modern environments and evidence suggests that this metabolism was present already on early earth. We determined Fe(II) oxidation rates depending on pH, temperature, light intensity, and Fe(II) concentration for three phylogenetically different phototrophic Fe(II)-oxidizing strains (purple nonsulfur bacterium Rhodobacter ferrooxidans sp. strain SW2, purple sulfur bacterium Thiodictyon sp. strain F4, and green sulfur bacterium Chlorobium ferrooxidans strain KoFox). While we found the overall highest Fe(II) oxidation rates with strain F4 (4.5 mmol L(-1) day(-1), 800 lux, 20 degrees C), the lowest light saturation values [at which maximum Fe(II) oxidation occurred] were determined for strain KoFox with light saturation already below 50 lux. The oxidation rate per cell was determined for R. ferrooxidans strain SW2 to be 32 pmol Fe(II) h(-1) per cell. No significant toxic effect of Fe(II) was observed at Fe(II) concentrations of up to 30 mM. All three strains are mesophiles with upper temperature limits of c. 30 degrees C. The main pigments were identified to be spheroidene, spheroidenone, OH-spheroidenone (SW2), rhodopinal (F4), and chlorobactene (KoFox). This study will improve our ecophysiological understanding of iron cycling in modern environments and will help to evaluate whether phototrophic iron oxidizers may have contributed to the formation of Fe(III) on early earth.

Two strains of phototrophic, purple non-sulfur bacteria capable of growing at low temperatures (5 degrees C) were isolated from the Himalayas. The two strains showed positive phototaxis and grew over a relatively wide temperature range (5-40 degrees C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA194T clustered with members of the genus Rhodobacter. Strain JA194T showed highest 16S rRNA gene sequence similarity with Rhodobacter sphaeroides DSM 158T (99 %). However, DNA-DNA hybridization experiments between Rba. sphaeroides DSM 158T and strain JA194T revealed a level of relatedness of only 67 %. The DNA base composition of strain JA194T was 66.67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological, physiological, Fourier transform infrared fingerprinting and DNA-DNA hybridization studies, strain JA194T (=KCTC 5602T =JCM 14598T) is sufficiently different from other Rhodobacter species to merit its description as the type strain of a novel species, for which the name Rhodobacter megalophilus sp. nov. is proposed.

During investigations into the diversity of anoxygenic phototrophic bacteria in marine habitats, an ovoid to rod-shaped purple non-sulfur bacterium, designated strain JA276(T), was isolated from enrichments under photoheterotrophic conditions from a marine sediment sampled from the seashore of Cochin, India. Strain JA276(T) is a Gram-negative, motile, chain-forming bacterium that shows optimum growth under photoheterotrophic conditions and is also able to grow chemoorganotrophically. Thiamine is required as a growth factor. Strain JA276(T) contains vesicular intracytoplasmic membranes, bacteriochlorophyll a and the carotenoids spheroidene and spheroidenone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA276(T) belongs to the genus Rhodobacter and is closely related to the type strain of Rhodobacter capsulatus (96.2 % sequence similarity). On the basis of the results of 16S rRNA gene sequence analysis and morphological and physiological data, strain JA276(T) is significantly different from other species of the genus Rhodobacter and represents a novel species of the genus, for which the name Rhodobacter maris sp. nov. is proposed. The type strain is JA276(T) (=JCM 14794(T) =ATCC BAA-1549(T) =CCUG 55129(T)).

Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly--the absorbance maximum extends from 432 to 465 nm, the pK(a) of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure-function relationships in the PYP family.

A novel ovoid, phototrophic, purple non-sulfur bacterium was isolated in pure culture from a sample of sediment from an industrially polluted pond (Noor Mohammad Kunta) in Hyderabad, India. Strain JA234(T) was found to be Gram-negative and non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon source/electron donor. Photo-organoheterotrophic and chemo-organoheterotrophic growth were demonstrated. Biotin and thiamine were required for growth of strain JA234(T). Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA234(T) is most closely related to Rhodobacter azotoformans (97.3 % sequence similarity) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. azotoformans JCM 9340(T) showed a relatedness of only 31.3 % with respect to strain JA234(T). On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data and morphological and physiological characteristics, strain JA234(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter ovatus sp. nov. is proposed. The type strain is JA234(T) (=JCM 14779(T)=CCUG 55049(T)).

A novel strain, alga-05, of alkaliphilic purple nonsulfur bacteria was isolated from sediments of a small saline (60 g/l) soda lake near Lake Algin (Barguzin Valley, Buryat Republic, Russia). These bacteria contain bacteriochlorophyll a and carotenoids of the alternative spirilloxanthin group with predominating demethylspheroidenone. They are facultative anaerobes; their photosynthetic structures are of the vesicular type and arranged along the cell periphery. Growth of this strain is possible in a salinity range of 5-80 g/l NaCl, with an optimum at 20 g/l NaCl. Best growth occurred at 20-35 degrees C. Analysis of the 16S rRNA gene sequences demonstrated that the studied isolate is closely related to the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis (99% similarity) isolated from soda lakes of the African Rift Zone. According to the results of DNA-DNA hybridization, strain alga-05 has a 52% similarity with the type species of the genus Rhodobaca. On the basis of the obtained genotypic data and some phenotypic properties (dwelling in a hypersaline soda lake of Siberia, moderate halophily, ability to grow at relatively low temperatures, etc.), the isolated strain of purple bacteria was described as a new species of the genus Rhodobaca, Rca. barguzinensis sp. nov.

A Gram-negative, non-motile, oval to rod-shaped, psychrotolerant, phototrophic, purple non-sulfur bacterium (designated strain JA139T) was isolated from a snow sample from Changla Pass in the Indian Himalayas. Strain JA139T had vesicular-type intracytoplasmic membrane structures and contained bacteriochlorophyll a and most probably spheroidene-like carotenoids. Biotin, niacin and thiamine were required for growth of strain JA139T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain clustered with species of the genus Rhodobacter but was distinctly separate from all recognized members of the family Rhodobacteraceae. Based on the genotypic and phenotypic differences observed between strain JA139T and recognized Rhodobacter species, strain JA139T is considered to represent a novel species of the genus, for which the name Rhodobacter changlensis sp. nov. is proposed. The type strain is JA139T (=DSM 18774T=CCUG 53722T=JCM 14338T).

A rod-shaped, phototrophic, purple non-sulfur bacterium was isolated in pure culture from seawater collected from the seashore of Visakhapatnam, on the east coast of India, in a medium that contained 2 % NaCl (w/v). Strain JA123(T) was Gram-negative and non-motile and had a requirement for NaCl. Photo-organoheterotrophic and chemo-organoheterotrophic growth occurred with organic compounds as carbon sources and electron donors. Photolithoautotrophic, chemolithoautotrophic and fermentative growth could not be demonstrated. Strain JA123(T) contained vesicular intracellular photosynthetic membrane structures. Bacteriochlorophyll a and probably carotenoids of the spheroidene series were present as photosynthetic pigments. Biotin was required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA123(T) clustered with species of the genus Rhodobacter. Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA123(T) is sufficiently different from other Rhodobacter species to propose a novel species, Rhodobacter vinaykumarii sp. nov., to accommodate this strain; the type strain is JA123(T) (=DSM 18714(T) =JCM 14544(T) =CCUG 54311(T)).

Twelve strains of gram-negative, nonfermenting rods recovered mainly from septicemic patients were studied using conventional and molecular methods. The phenotypic profiles of these strains most closely resembled Psychrobacter phenylpyruvicus. They produced catalase, oxidase, urease, and H(2)S (lead acetate paper) but did not produce indole, reduce nitrate or nitrite, or hydrolyze gelatin or esculin. No acid production was observed in a King's oxidation-fermentation base containing d-glucose, d-xylose, d-mannitol, sucrose, lactose, or maltose. All strains were nonmotile and nonpigmented. Most strains produced green discoloration on blood agar. All strains grew at 25 degrees C and 35 degrees C and most grew on MacConkey agar. They shared a common cellular fatty acid (CFA) profile characterized by large amounts (56% to 90%) of 18:1omega7c and the presence of 3-OH-10:0, 16:1omega7c, 16:0, and 19:0cycomega8c that overall was most similar to that of Rhodobacter species but was quite distinct from that of P. phenylpyruvicus. The MICs for most beta-lactams, fluoroquinolones, aminoglycosides, and carbapenems were low. MICs for aztreonam and piperacillin were higher, with MICs for some strains of > 64 mg/liter and > 128 mg/liter, respectively. Polyphasic analysis of these strains, including morphological, biochemical, CFA composition, DNA-DNA hybridization, 16S rRNA gene sequencing, and percent guanine-plus-cytosine (G+C) content analysis, demonstrated that these strains and Rhodobacter massiliensis represent a new genus, "Haematobacter" (proposed name), with the species H. missouriensis (type strain H1892(T) = CCUG 52307(T) = CIP 109176(T)) and H. massiliensis comb. nov. (type strain Framboise(T) = CCUG 47968(T) = CIP 107725(T)) and an unnamed genomospecies.

Selenium is essential element for humans and animals but is very toxic at higher concentrations. In four inorganic states of selenate [SeO4 2- ( VI)], selenite [SeO3 2- (IV)], elemental selenium [Se (0)] and selenide [Se2- (- II )], selenite is well known to be more soluble and higher toxic than other three forms. Many microorganisms have the capacity to reduce selenite to red elemental selenium, which provide the potential to cope with the detoxification of pollution and to use the biological availability of red elemental selenium. Strain S3 that was more resistant to sodium selenite was selected from 20 photosynthetic bacteria preserved in laboratory. The red granule produced by S3 was identified as elemental selenium ( Se) by transmission electron microscopy and Electron-Dispersive X-ray (EDX) analysis. The granule diameter of the red elemental selenium was 5nm - 200nm, similar as the Nano-Se that has bioavailability. Morphology, physiology and photosynthetic pigments analysis results showed that strain S3 was essentially consistent with Rhodobacter azotoformans . The 16S rDNA sequence analysis (GenBank accession number DQ402051) suggested that strain S3 was clustered together with R. azotoformans in phylogenetic tree, with the sequence identity of 99% . Based on all the results of taxonomy, strain S3 was identified as R. azotoformans S3. The effects of selenite on growth kinetics and the ability to resistant selenite of strain S3 were investigated. In contrast to Rhodospirillum rubrum which was reported not to reduce selenite until the end of exponential growth, strain S3 transformed selenite (1.25mmol/L) at the beginning of the growth, suggesting that strain S3 and Rs. rubrum may employ different strategies to reduce selenite. Strain S3 can grow in the presence of up to 125mmol/L sodium selenite, which is much higher than those which could be resisted to by other bacteria such as Escherichia coli ( < 20mmol/L) and Ralstonia metallidurans CH34 ( < 6mmol/L) . It is firstly reported that R. azotoformans has the capacity to reduce selenite to red elemental selenium.

The abundance of aerobic anoxygenic phototrophic (AAP) bacteria, cyanobacteria, and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific Gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of Prochlorococcus spp. and 10-fold higher than that of Synechococcus spp. In contrast, Prochlorococcus spp. outnumbered AAP bacteria 5- to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (Erythrobacter and Roseobacter spp.). Concentrations of bacteriochlorophyll a (BChl a) were low ( approximately 1%) compared to those of chlorophyll a in the North Atlantic. Although the BChl a content of AAP bacteria per cell was typically 20- to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, the pigment content of AAP bacteria approached that of Prochlorococcus in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy.

Aerobic anoxygenic phototrophic bacteria (AAnPs) were previously proposed to account for up to 11% of marine bacterioplankton and to potentially have great ecological importance in the world's oceans. Our data show that previously used primers based on the M subunit of anoxygenic photosynthetic reaction center genes (pufM) do not comprehensively identify the diversity of AAnPs in the ocean. We have designed and tested a new set of pufM-specific primers and revealed several new AAnP variants in environmental DNA samples and genomic libraries.

Certain species of marine sponges in the order Dictyoceratida harbor large populations of the cyanobacterial symbiont Oscillatoria spongeliae in the mesohyl (interior) of the sponge. We show that in four of these sponge species (Lamellodysidea herbacea, Lamellodysidea chlorea, Lendenfeldia chondrodes, and Phyllospongia papyracea) from Palau there is a consistent community of alpha-proteobacteria in addition to O. spongeliae that fall within the Rhodobacter group based on 16S rRNA gene analysis. Some of the alpha-proteobacteria in Lendenfeldia chondrodes and P. papyracea but not in the Lamellodysidea spp. contained site-specific insertions in the 16S rRNA gene. Reverse transcription-PCR experiments demonstrated that the largest insertion found in this study (63 bp) is present in the mature rRNA. Lendenfeldia chondrodes was the only sponge found to have another cyanobacterium in the tissue, a Synechocystis sp. We found that the Synechocystis sp. was present in both the pinacoderm (surface epithelial tissue) and mesohyl, in contrast to O. spongeliae, which was only found in the mesohyl through the use of specific fluorescence in situ hybridization experiments. Of the four sponge species, only P. papyracea was found to contain a significant number of gamma-proteobacteria. These results demonstrate that O. spongeliae-dominated bacterial communities in different sponge species can vary considerably and increase our understanding of the bacterial communities found in marine invertebrates.

We have studied photosynthetic membranes of wild type Rhodobacter blasticus, a closely related strain to the well studied Rhodobacter sphaeroides, using atomic force microscopy. High-resolution atomic force microscopy topographs of both cytoplasmic and periplasmic surfaces of LH2 and RC-LH1-PufX (RC, reaction center) complexes were acquired in situ. The LH2 is a nonameric ring inserted into the membrane with the 9-fold axis perpendicular to the plane. The core complex is an S-shaped dimer composed of two RCs, each encircled by 13 LH1 alpha/beta-heterodimers, and two PufXs. The LH1 assembly is an open ellipse with a topography-free gap of approximately 25 A. The two PufXs, one of each core, are located at the dimer center. Based on our data, we propose a model of the core complex, which provides explanation for the PufX-induced dimerization of the Rhodobacter core complex. The QB site is located facing a approximately 25-A wide gap within LH1, explaining the PufX-favored quinone passage in and out of the core complex.

On the basis of data from phenotypic and genotypic characterization and analysis of 16S rRNA gene sequences, two novel species belonging to the genus Sulfitobacter are described. Strains KMM 3584(T), a pale-yellowish, non-motile strain isolated from a starfish (Stellaster equestris), and KMM 3554(T), which is motile by means of a single subpolar flagellum and was isolated from sea grass (Zostera marina), are marine, Gram-negative, aerobic, rod-shaped organisms. Both strains have the ability to degrade gelatin, but not casein, chitin, agar, DNA, Tween 80 or starch. Strain KMM 3584(T) decomposed alginate and grew at NaCl concentrations of 1-8 % and temperatures of 12-37 degrees C, whereas strain KMM 3554(T) grew in 1-12 % NaCl and at temperatures of 10-30 degrees C. The predominant fatty acid was 18 : 1omega7, amounting to up to 80 % of the total fatty acids. The other characteristic feature was the presence of 18 : 2 isomers. The DNA G+C contents of KMM 3584(T) and KMM 3554(T) were respectively 60.0 and 63.7 mol%. The level of DNA similarity between the two strains was 33 %. DNA from KMM 3584(T) and KMM 3554(T) had hybridization values of 5-24 % and 10-41 %, respectively, with DNA from the type strains of Sulfitobacter pontiacus, Sulfitobacter brevis, Sulfitobacter mediterraneus and Staleya guttiformis. It is proposed that strains KMM 3584(T) (=LMG 20554(T)=ATCC BAA-321(T)) and KMM 3554(T) (=LMG 20555(T)=ATCC BAA-320(T)) represent two novel species, Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively.

From the nose of a patient with aspiration pneumonia, we isolated a new bacterium by amoebal co-culture using Acanthamoeba polyphaga. Based on phenotypic, 16S rRNA and phylogenetic analysis, we show that this isolate represents a new species within the genus Rhodobacter and and we have named it Rhodobacter massiliensis. The type strain has been deposited in the Collection de l'Institut Pasteur, Paris, France (CIP 107725), and in the Culture Collection of the University of Göteborg, Sweden (CCUG 47968), as strain Framboise.

Heterotrophic bacteria were isolated from a water sample taken from the North Sea, 2 km off the coast of the island of Helgoland, by direct plating of the serially diluted sample on complex marine media. Sixteen of 80 strains from the highest sample dilution belonged to the 'Roseobacter-Sulfitobacter-Silicibacter' group within the 2-subclass of the Proteobacteria on the basis of partial 16S rDNA sequence analysis. Phylogenetic analysis of nearly complete 16S rDNA sequences showed that the closest relative of two strains, Hel 10(T) and Hel 26, was Ketogulonicigenium vulgare (94.4% similarity). These strains were Gram-negative, non-motile rods, obligate aerobes, required sodium ions and 1-7% sea salts for growth and did not produce bacteriochlorophyll. Their optimal growth temperature was 25-30 degrees C. The strains had Q-10 as the dominant respiratory quinone. Chemotaxonomic analysis showed a combination of ester-linked 3-OH 10 : 0, 12 : 1 and amide-linked 3-oxo 14 : 0 (or 3-OH 14 : 1) and 3-OH 14 : 0 fatty acids, which appears to be a unique feature of strains Hel 10(T) and Hel 26 within this subsection of the 2-subclass of the Proteobacteria. Based on 16S rDNA sequence analysis and chemotaxonomic data, the strains are assigned to a new genus and species, Jannaschia helgolandensis gen. nov., sp. nov., with the type strain Hel 10(T) (= DSM 14858(T) = NCIMB 13941(T)).

Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp. strain PS9. Rhodobacter sp. strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J. A. Zahn, A. A. DiSpirito, Y. S. Do, B. E. Brooks, E. E. Copper, and J. L. Hatfield, J. Environ. Qual. 30:624-634, 2001). The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom. During the height of a bloom, the Rhodobacter sp. strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals. Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp. strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate. In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride.

Experimental and theoretical results in support of nonlinear dynamic behavior of photosynthetic reaction centers under light-activated conditions are presented. Different conditions of light adaptation allow for preparation of reaction centers in either of two different conformational states. These states were detected both by short actinic flashes and by the switching of the actinic illumination level between different stationary state values. In the second method, the equilibration kinetics of reaction centers isolated from Rhodobacter sphaeroides were shown to be inherently biphasic. The fast and slow equilibration kinetics are shown to correspond to electron transfer (charge separation) at a fixed structure and to combined electron-conformational transitions governed by the bounded diffusion along the potential surface, respectively. The primary donor recovery kinetics after an actinic flash revealed a pronounced dependence on the time interval (deltat) between cessation of a lengthy preillumination of a sample and the actinic flash. A pronounced slow relaxation component with a decay half time of more than 50 s was measured for deltat > 10 s. This component corresponds to charge recombination in reaction centers for which light-induced structural changes have not relaxed completely before the flash. The amplitude of this component depended on the conditions of the sample preparation, specifically on the type of detergent used in the preparation. The redox potential parameters as well as the structural diffusion constants were estimated for samples prepared in different ways.

The marine gram-negative non-photosynthetic bacterium, Agrobacterium ferrugineum IAM 12616(T) forms one cluster with the species of the photosynthetic genus Rhodobacter in phylogenetic trees based on molecules of 16S rRNA, 23S rRNA and DNA gyrases. Agrobacterium ferrugineum and Rhodobacter species are similar in that growth occurs without NaCl in the culture medium (optimal NaCl concentration for growth of P. ferrugineus is 1%) and their major hydroxy fatty acid compositions are 3-hydroxy decanoic acids (3-OH 10:0) and 3-hydroxy tetradecanoic acids (3-OH 14:1). However, A. ferrugineum differs from Rhodobacter species in G+C content (58 mol% in A. ferrugineum versus 64-73 mol% in Rhodobacter species), in having an insertion in its 16S rRNA gene sequence, and in lacking photosynthetic abilities, bacteriochlorophyll a and intracytoplasmic membrane systems. Furthermore, experiments using PCR and Southern hybridization show that A. ferrugineum does not have puhA gene and puf genes localized near the opposite ends of the photosynthesis gene cluster of Rhodobacter capsulatus. It suggests that A. ferrugineum may not have any genes for photosynthesis. We propose the transfer of A. ferrugineum IAM 12616(T) to the genus Pseudorhodobacter gen. nov. as Pseudorhodobacter ferrugineus comb. nov. Although Pseudorhodobacter ferrugineus disturbs the phylogenetic monophyly of the genus Rhodobacter, this taxonomic proposal seems adequate until it has been clarified whether P. ferrugineus possesses an incomplete photosynthetic apparatus.

Bacterial diversity among marine creatures, especially molluscs, as a source for searching out novel lineages of bacteria, was studied. Marine creatures were collected at the coasts of the Kanto area in Japan. A total of 116 strains of bacteria were isolated from the intestines of 19 species of marine creatures includings molluscs, pisces and protochordata. Partial sequencing of 16S rDNA revealed that most of the isolates belonged to the gamma subclass of the Proteobacteria and Cytophaga-Flavobacterium-Bacteroides group. The BLAST searches revealed that the complete 16S rDNA sequence of 17 strains out of 116 isolates showed less than 94% similarity with 16S rDNA sequences deposited in the database. Four strains out of the 17 isolates belonged to the Rhodobacter group, 8 strains to the Alteromonas group, and the remaining 5 strains to the Cytophaga-Flavobacterium-Bacteroides group. Phylogenetic positions of 6 strains belonging to the Alteromonas group, which were isolated from different marine creatures, were close to each other, and represented a novel 16S rDNA lineage within the gamma subclass of Proteobacteria. Therefore, it may be inferred that these 6 strains belong to a new genus of Proteobacteria. Phylogenetic positions of the other strains are also independent from neighboring taxa, and they were suggested to respectively form a novel lineage. From these results, it is clear that the biodiversity of bacteria in marine creatures is much wider than was previously thought, and unknown microbiological resources are buried in these organisms.

Early stages of surface colonization in coastal marine waters appear to be dominated by the marine Rhodobacter group of the alpha subdivision of the division Proteobacteria (alpha-Proteobacteria). However, the quantitative contribution of this group to primary surface colonization has not been determined. In this study, glass microscope slides were incubated in a salt marsh tidal creek for 3 or 6 days. Colonizing bacteria on the slides were examined by fluorescence in situ hybridization by employing DNA probes targeting 16S or 23S rRNA to identify specific phylogenetic groups. Confocal laser scanning microscopy was then used to quantify and track the dynamics of bacterial primary colonists during the early stages of surface colonization and growth. More than 60% of the surface-colonizing bacteria detectable by fluorescence staining (Yo-Pro-1) could also be detected with the Bacteria domain probe EUB338. Archaea were not detected on the surfaces and did not appear to participate in surface colonization. Of the three subdivisions of the Proteobacteria examined, the alpha-Proteobacteria were the most abundant surface-colonizing organisms. More than 28% of the total bacterial cells and more than 40% of the cells detected by EUB338 on the surfaces were affiliated with the marine Rhodobacter group. Bacterial abundance increased significantly on the surfaces during short-term incubation, mainly due to the growth of the marine Rhodobacter group organisms. These results demonstrated the quantitative importance of the marine Rhodobacter group in colonization of surfaces in salt marsh waters and confirmed that at least during the early stages of colonization, this group dominated the surface-colonizing bacterial assemblage.

Four bacterial strains that oxidize L-sorbose to 2-keto-L-gulonic acid, a key intermediate in the synthesis of vitamin C, were isolated from soils of geographically distinct locations. All were Gram-negative, facultatively anaerobic, chemoheterotrophic rods. Comparative analysis revealed nearly identical 16S rDNA sequences amongst them (99.7-100% identical) and identified them as members of the alpha-subclass of the Proteobacteria. Phylogenetic analysis identified the closest taxonomically defined genus as Roseobacter (92.1-92.8% identical). On the basis of phylogenetic, phenotypic and genotypic analyses, a new genus is proposed, Ketogulonigenium gen. nov. Based upon these analyses, we also propose the reclassification of strain DSM 4025TP, originally identified as Gluconobacter oxydans, to the genus Ketogulonigenium. Two species are proposed: the type species Ketogulonigenium vulgare gen. nov., sp. nov., consisting of strains 62A-12APP, 266-13BPP and the type strain K. vulgare DSM 4025TP, and Ketogulonigenium robustum gen. nov., sp. nov., consisting of the type strain K. robustum X6LTP (= NRRL B-21627 = KCTC 0858BP). The species affiliation of the fifth strain (291-19PP) remains unresolved.

It is becoming increasingly apparent from complete genome sequences that 16S rRNA data, as currently interpreted, does not provide an unambiguous picture of bacterial phylogeny. In contrast, we have found that analysis of insertions and deletions in the amino acid sequences of cytochrome c2 has some advantages in establishing relationships and that this approach may have broad utility in acquiring a better understanding of bacterial relationships. The amino acid sequences of cytochromes c2 and c556 have been determined in whole or in part from four strains of Rhodobacter sulfidophilus. The cytochrome c2 contains three- and eight-residue insertions as well as a single-residue deletion in common with the large cytochromes c2 but in contrast to the small cytochromes c2 and mitochondrial cytochromes. In addition, the Rb. sulfidophilus protein shares a rare six- to seven-residue insertion with other Rhodobacter cytochromes c2. The cytochrome c556 is a low-spin class II cytochrome c homologous to the greater family of cytochromes c', which are usually high-spin. The similarity of cytochrome c556 to other species of class II cytochromes is consistent with the relationships deduced from comparisons of cytochromes c2. Thus, our results do not support placement of Rb. sulfidophilus in a separate genus, Rhodovulum, which was proposed primarily on the basis of 16S rRNA sequences. Instead, the Rhodobacter cytochromes c2 are distinct from those of other genera and species of purple bacteria and show a different pattern of relationships among species than reported for 16S rRNA.

From enrichment cultures established for purple nonsulfur bacteria using water and sediment samples from Lake Bogoria and Crater Lake, two soda lakes in the African Rift Valley, three strains of purple nonsulfur bacteria were isolated; strain LBB1 was studied in detail. Cells of strain LBB1 were motile and spherical to rod-shaped, suggesting a relationship to Rhodobacter or Rhodovulum species, and the organism was capable of both phototrophic and chemotrophic growth on a wide variety of organic compounds. Phototrophically grown cultures were yellow to yellow-brown in color and grew optimally at pH 9 (pH range 7.5-10) and 1% NaCl (range 0-10%). In physiological studies of strain LBB1, neither photoautotrophy (H2- or sulfide-dependent) nor nitrogen fixation was observed. Absorption spectra revealed that all three strains contained bacteriochlorophyll a and carotenoids of the spheroidene pathway and synthesized only a light-harvesting (LH) I-type photosynthetic antenna complex. Electron microscopy of cells of strain LBB1 revealed a vesicular intracytoplasmic membrane system, although only a few vesicles were observed per cell. The G+C content of strain LBB1 DNA was 59 mol%, significantly lower than that of known Rhodobacter and Rhodovulum species, and its phylogeny as determined by ribosomal RNA gene sequencing placed it within the Rhodobacter/Rhodovulum clade yet distinct from all described species of either of these genera. The unique assemblage of properties observed in strain LBB1 warrants its inclusion in a new genus of purple nonsulfur bacteria and the name Rhodobaca bogoriensis is proposed herein, the genus name reflecting morphological characteristics and the species epithet referring to the habitat.

Roseobacter denitrificans has rough (R)-type lipopolysaccharide, containing 2-keto-3-deoxyoctonate but no hepatoses. Its lipid A has a glucosamine-containing, phosphorylated backbone. It contains the rare 3-oxotetradecanoic (3-oxomyristic) acid as the only amide-bound fatty acid and ester-bound 3-hydroxydecanoic acid, this pattern being characteristic for the alpha-3 subgroup of Proteobacteria. Treatment of the major outer-membrane protein (porin, apparent molecular mass 88 kDa) of Roseobacter denitrificans with EDTA (2 mM, 30 degrees C, 20 min) resulted in the dissociation of the oligomers into monomers (apparent molecular mass 35 kDa). EDTA-sensitive dissociation has so far been observed only within the alpha-3 subgroup of Proteobacteria. The 12 N-terminal amino acids of the monomers exhibit sequence homology with the porins of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas blastica. Renaming of Roseobacter denitrificans as Rhodobacter denitrificans is suggested.

Comparative sequence analysis of in vitro-amplified 16S rRNA genes of Thiosphaera pantotropha GB17T (T = type strain) and Paracoccus denitrificans LMG 4218T revealed identical 16S rRNA primary structures for the two organisms. The level of overall DNA similarity of Thiosphaera pantotropha GB17T and P. denitrificans DSM 65T is 85%, as determined by quantitative DNA-DNA hybridization. Therefore, we propose the transfer of Thiosphaera pantotropha to P. denitrificans. The closest relative of Thiosphaera pantotropha and P. denitrificans is Thiobacillus versutus, as revealed by comparative 16S rRNA sequence analysis. These organisms are members of the alpha subclass of the Proteobacteria. Within this subclass, Thiosphaera pantotropha, P. denitrificans, and Thiobacillus versutus form a phylogenetic group with Rhodobacter sphaeroides, Rhodobacter capsulatus, and "Erythrobacter longus."

The 16S rRNA or rRNA gene sequences of the type strains of 5 species of Rhodobacter, Rhodopseudomonas blastica and Paracoccus denitrificans were determined. The sequence analysis revealed that Rhodobacter species, whose intracytoplasmic membrane systems were characteristically vesicular, composed a sole cluster. Rhodopseudomonas blastica, whose intracytoplasmic membrane system was lamellar, was included in the cluster of Rhodobacter. The phylogenetic co-clustering of these bacteria conformed to their possessing of the identical types of carotenoids. Paracoccus denitrificans, which is nonphototrophic, is a right member of the Rhodobacter cluster. Rhodobacter species, Rhodopseudomonas blastica and Paracoccus denitrificans are apart from the other phototrophic bacteria and have the common deletions of 21 bases at the positions 1258 to 1278 (Escherichia coli numbering system). It was demonstrated that the morphological character "intracytoplasmic membrane structure", that has been regarded as a generic criterion does not reflect the phylogeny in the phototrophic bacteria. The transfer of Rhodopseudomonas blastica to the genus Rhodobacter is proposed.