Rhodobacter amnigenus sp. nov. and Rhodobacter ruber sp. nov., isolated from freshwater habitats.

Two bacterial strains, designated HSP-20T and CCP-1T, 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-20T and CCP-1T 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-20T and CCP-1T shared 98.3 % sequence similarity and were closely related to Rhodobacter tardus CYK-10T (96.0 %) and Rhodobacter flagellatus SYSU G03088T (96.0 %), respectively. Both strains shared common chemotaxonomic characteristics including Q-10 as the major isoprenoid quinone, C18 : 1 ω7c 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 81193T=LMG 31334T) and Rhodobacter ruber sp. nov. (=BCRC 81189T=LMG 31335T) are proposed.

Rhodobacter xinxiangensis sp. nov., isolated from pakchoi-cultivated soil contaminated with heavy metal and its potential to reduce Cd and Pb accumulation in pakchoi (Brassica campestris L.).

A Gram-stain-negative, aerobic, and motile strain, TJ48T, 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 TJ48T 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 TJ48T was closely related to the genus Rhodobacter and the closest relatives were Rhodobacter ovatus JA234T (97.4%, 16S rRNA gene sequence similarity) and Rhodobacter azotoformans KA25T (96.5%). The DNA G + C content of strain TJ48T was 64.7 mol%. Genome-to-genome distance calculations (GGDC) and ANIb values from genomic comparison between the genomes of strain TJ48T and the related reference species were less than 70% and 95%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C17:0. 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 TJ48T 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 TJ48T represent a novel species of the genus Rhodobacter, and the name Rhodobacter xinxiangensis sp. nov. is proposed (type strain TJ48T = CCTCC AB2019120T = KCTC 72510T).

Rhodobacter sediminicola sp. nov., isolated from a fresh water pond.

A phototrophic bacterium, designated as strain JA983T, 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 JA983T. Q10 is the only quinone. C18 : 1 ω7c/C18 : 1 ω6c is the major fatty acid. JA983T 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, JA983T 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 (dDDH) differences indicated that JA983T 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 JA983T (=KCTC 15782T=NBRC 113843T).

Rhodobacter flagellatus sp. nov., a thermophilic bacterium isolated from a hot spring.

A thermophilic bacterium, designated SYSU G03088T, 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 G03088T showed highest sequence similarity to Rhodobacter blasticus CGMCC 1.3365T (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-ß-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 C18 : 0, C18 : 1ω7c 11-methyl and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The detected polar lipids of SYSU G03088T included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The DNA G+C content of SYSU G03088T was 67.7 % (genome). On the basis of the differences in the phenotypic characteristics and phylogenetic analyses, SYSU G03088T 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 G03088T (=CGMCC 1.16876T=KCTC 72354T).

Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae.

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5T and CYK-10T, were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae. Strain KMS-5T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10T is closest to Rhodobacter thermarum YIM 73036T 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-5T is affiliated with species in the genus Tabrizicola and strain CYK-10T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485T, Rhodobacter thermarum YIM 73036T and Rhodobacter flagellatus SYSU G03088T. These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C18 : 1 ω7c 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-5T represents a novel species within the genus Tabrizicola, for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5T (=BCRC 81196T=LMG 31337T) as the type strain, and strain CYK-10T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10T (=BCRC 81191T=LMG 31336T) as the type strain.

Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring.

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 73036T were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036T 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 73036T 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 73036T is closely related to Rhodobacter blasticus ATCC 33485T (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 73036T was determined to be 66.0 mol%. Strain YIM 73036T contained Q-10 as the predominant ubiquinone and C18:1ω7c, C18:1ω7c 11-methyl and C18:0 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 73036T is distinguishable from other species of the genus Rhodobacter. On the basis of the data presented, strain YIM 73036T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter thermarum sp. nov. [type strain YIM 73036T (= KCTC 52712T = CCTCC AB 2016298T)] is proposed.

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.

Rhodobacter alkalitolerans sp. nov., isolated from an alkaline brown pond.

An alkali-tolerant, Gram-stain-negative, motile, rod-to-oval-shaped, yellowish brown-colored, phototrophic bacterium, designated as strain JA916T, was isolated from an alkaline brown pond in Gujarat, India. The DNA G + C content of the strain JA916T was 65.1 mol%. Strain JA916T grew well at pH 10. Respiratory quinone was Q-10 and major fatty acid was C18:1ω7c/C18:1ω6c, with significant quantities of C15:02OH observed. Strain JA916T 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 JA916T 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 JA916T is a novel species of the genus Rhodobacter. DNA-DNA hybridization values between strain JA916T and related type strains were less than 40%. Phenotypic, chemotaxonomical and phylogenetic differences showed that strain JA916T was distinct from other species of the genus Rhodobacter, suggesting strain JA916T represents a new species of the genus for which the name Rhodobacter alkalitolerans sp. nov. is proposed. Type strain is JA916T (= KCTC 15473T = LMG 28749T).

Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.

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.

Rhodobacter sediminis sp. nov., isolated from lagoon sediments.

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.

Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter.

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.

Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream.

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)).

Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River.

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.

Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium.

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.

Physiology of phototrophic iron(II)-oxidizing bacteria: implications for modern and ancient environments.

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.

Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.

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.

[Screening and identification of a photosynthetic bacterium reducing selenite to red elemental selenium].

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.

Rhodobacter massiliensis sp. nov., a new amoebae-resistant species isolated from the nose of a patient.

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.

A preliminary report of phylogenetic diversity of bacterial strains isolated from marine creatures.

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.

Proposal of Pseudorhodobacter ferrugineus gen nov, comb nov, for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter.

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.