Rheinheimera lutimaris sp. nov., a marine bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-2T, was isolated from coastal sediment sampled in Jiangsu Province and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 28 °C (range 4-38 °C) and pH 7 (pH 6-10). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YQF-2T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera pacifica KMM 1406T (98.6%), followed by Rheinheimera aestuarii H29T (98.4%), Rheinheimera japonica KMM 9513T (98.3%), Rheinheimera aquimaris SW-353T (98.3%), Rheinheimera hassiensis E48T (97.8%) and Rheinheimera muenzenbergensis E49T (97.7%). The 16S rRNA gene sequence identities between strain YQF-2T and other members of the genus Rheinheimera were below 97.2%. The digital DNA-DNA hybridization value between strain YQF-2T and R. pacifica KMM 1406T was 23.3±2.3%. The average nucleotide identity value between strain YQF-2T and R. pacifica KMM 1406T was 79.7%. The unique respiratory quinone was ubiquinone-8. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The strain had summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C12:0 3-OH and iso-C17:0 3-OH as major fatty acids. The G+C content of the genomic DNA was 50.0 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-2T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera lutimaris sp. nov. is proposed, with the type strain YQF-2T (=KCTC 72184T=MCCC 1K03663T).

Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan.

A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40-56 °C) and pH 7.2 (range, pH 7-8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum. The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae. The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).

Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-1T, was isolated from coastal sediment in Jiangsu Province (PR China) and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range 4-40 °C) and pH 7 (range pH 6-11). Phylogenetic analysis based on 16S rRNA gene sequence indicated that YQF-1T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera mesophila DSM 29723T (98.5 %), followed by Rheinheimera tangshanensis DSM 19460T (98.4 %), Rheinheimera tilapiae Ruye-90T (97.9 %), Rheinheimera soli BD-d46T (97.9 %), Rheinheimera aquatica GR5T (97.4 %), Rheinheimera coerulea TAPG2T (97.3 %) and Rheinheimera texasensis A62-14BT (97.1 %). The 16S rRNA gene sequence identities between YQF-1T and other members of the genus Rheinheimera were below 97.0 %. The digital DNA-DNA hybridization value between YQF-1T and Rheinheimera mesophila DSM 29723T was 25.1±2.3 %. The average nucleotide identity (ANI) value between YQF-1T and Rheinheimera mesophila DSM 29723T was 81.4 %. The major respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, two unidentified aminolipids and three unidentified lipids. The strain had summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0, and anteiso-C17 : 1 ω9c as the major fatty acids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-1T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera sediminis sp. nov. is proposed, with the type strain YQF-1T (=KCTC 72183T=MCCC 1K03646T).

Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment.

A Gram-stain-negative, rod-shaped, motile and strictly aerobic bacterium, designated LHK132T, was isolated from a mangrove sediment sample collected in Haikou, Hainan Province, PR China. Strain LHK132T was able to grow at temperatures of 10-45 °C, at salinities of 0-7.0 % (w/v) and at pH 6.0-9.0. Catalase and oxidase activities, H2S production, urease and methyl red reaction were positive. Indole, nitrate reduction, hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. According to 16S rRNA gene sequence analysis, strain LHK132T had 98.3, 97.5, 97.4, 97.2 and 97.1% similarities to Rheinheimera soli BD-d46T, Rheinheimera sediminis YQF-1T, Rheinheimera tangshanensis JA3-B52T, Rheinheimera mesophila IITR-13T and Rheinheimera arenilitoris J-MS1T, respectively. Phylogenetic analyses indicated that strain LHK132T formed a distinct lineage with R. soli BD-d46T within the genus Rheinheimera. The average nucleotide identity and digital DNA-DNA hybridization values between strain LHK132T and related species of the genus Rheinheimera were well below the thresholds for species delineation. The DNA G+C content was 46.7 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic data, strain LHK132T is considered a representative of a novel species in the genus Rheinheimera, for which the name Rheinheimera mangrovi sp. nov. is proposed. The type strain is LHK132T (=KCTC 62580T=MCCC 1K03529T).

In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.

Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.

Rheinheimera riviphila sp. nov., isolated from a freshwater stream.

Strain KYPC3T, isolated from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPC3T belonged to the genus Rheinheimera. Strain KYPC3T exhibited 16S rRNA gene sequence similarity values of 94.8-97.9% to the type strains of species of the genus Rheinheimera. Strain KYPC3T was most closely related to Rheinheimera chironomi K19414T with 16S rRNA gene sequence similarity of 97.9%. Cells of strain KYPC3T were Gram-stain negative, aerobic, motile by means of a single-polar flagellum, non-spore forming, coccoid or short rods surrounded by a thick capsule and forming off-white coloured colonies. Growth occurred at 15-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5% NaCl (optimum, 0%). The major fatty acids (> 10%) of strain KYPC3T were C12:0 3-OH, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized lipid. The major isoprenoid quinone was Q-8. The draft genome was approximately 4.75 Mb in size with a G + C content of 49.8 mol%. The DNA-DNA relatedness of strain KYPC3T with respect to recognized species of the genus Rheinheimera was significantly less than 70%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPC3T should be classified as a novel species of the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. is presented. The type strain is KYPC3T (= BCRC 81008T = LMG 29729T = KCTC 52440T).

Rheinheimera marina sp. nov., isolated from a deep-sea seamount.

A bacterial strain designated TP462T, isolated from a seamount near the Yap Trench in the tropical western Pacific, was characterized using a polyphasic taxonomic approach. Strain TP462T was found to be Gram-stain-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 4-37 °C (optimum, 25-30 °C) and with 0-4.0 % NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP462T was related to the genus Rheinheimera and had the highest 16S rRNA gene sequence similarity with the type strain Rheinheimera tangshanensis JA3-B52T (96.8 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and C16 : 0. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain TP462T was 48.7 mol%. On the basis of the evidence presented in this study, strain TP462T represents a novel species of the genus Rheinheimera, for which we propose the name Rheinheimera marina sp. nov. (type strain TP462T=KACC 18560T=CGMCC 1.15399T).

Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera.

A Gram-negative, rod-shaped bacterium, designated KH87T, was isolated from a fishing hook that had been baited and suspended in seawater off O'ahu, Hawai'i. Based on a comparison of 1524 nt of the 16S rRNA gene sequence of strain KH87T, its nearest neighbours were the GammaproteobacteriaRheinheimera nanhaiensis E407-8T (96.2 % identity), Rheinheimera chironomi K19414T (96.0 %), Rheinheimera pacifica KMM 1406T (95.8 %), Rheinheimera muenzenbergensis E49T (95.7 %), Alishewanella solinquinati KMK6T (94.9 %) and Arsukibacterium ikkense GCM72T (94.6 %). Cells of KH87T were motile by a single polar flagellum, strictly aerobic, and catalase- and oxidase-positive. Growth occurred between 4 and 39 °C, and in a circumneutral pH range. Major fatty acids in whole cells of strain KH87T were cis-9-hexadecenoic acid, hexadecanoic acid and cis-11-octadecenoic acid. The quinone system contained mostly menaquinone MK-7, and a minor amount of ubiquinone Q-8. The polar lipid profile contained the major lipids phosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine, an unidentified aminolipid, and a lipid not containing phosphate, an amino group or a sugar moiety. Putrescine was the major polyamine. Physiological, biochemical and genomic data, including obligate halophily, absence of amylolytic activity, a quinone system dominated by MK-7 and DNA G+C content (42.0 mol%) distinguished KH87T from extant Rheinheimera species; strain KH87T was also distinguished by a multi-locus sequence analysis of aligned and concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences. Based on phenotypic and genotypic differences, the species Rheinheimera salexigens sp. nov. is proposed to accommodate KH87T as the type strain (=ATCC BAA-2715T=CIP 111115T). An emended description of the genus Rheinheimera is also proposed.

Rheinheimera coerulea sp. nov., isolated from a freshwater creek, and emended description of genus Rheinheimera Brettar et al. 2002.

A bacterial strain designated TAPG2T was isolated from a freshwater creek in Taiwan and characterized using the polyphasic taxonomic approach. Cells of TAPG2T were Gram-stain negative, aerobic, motile, non-spore forming, short rods surrounded by a thick capsules and forming cream to dark-green colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 6.5-8 (optimum, pH 7) and with 0-1 % NaCl (optimum, 0.5 %). The major fatty acids (>10 %) of TAPG2T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid, an uncharacterized aminolipid and an uncharacterized lipid. The polyamine profile was composed of the major compound putrescine and moderate amounts of spermidine. The only isoprenoid quinone was Q-8. The DNA G+C content was 53.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that TAPG2T represented a member of the genus Rheinheimera and was most closely related to Rheinheimera aquatica GR5T and Rheinheimera texasensis A62-14BT with 98.6 and 98.2 % 16S rRNA gene sequence identities, respectively. However, DNA-DNA hybridization values of TAPG2T with type strains of the species with validly published names were lower than 30 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that TAPG2T should be classified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera coerulea sp. nov. is presented. The type strain is TAPG2T (=BCRC 81054T=LMG 30056T=KCTC 52815T).

Imhoffiella gen. nov., a marine phototrophic member of the family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov.

A coccoid-shaped phototrophic purple sulfur bacterium, strain AK35T, was isolated from a coastal surface water sample collected from Visakhapatnam, India. Cells were Gram-stain-negative, motile and purple, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16 : 0, C18 : 1ω7c, and C16 : 1ω7c and/or iso-C15 : 0 2OH (summed feature 3). Strain AK35T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and six unidentified lipids as polar lipids. The G+C content of the DNA of strain AK35T was 63.1 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae. 16S rRNA gene sequence analysis indicated that strain AK35T is phylogenetically distinctly positioned outside the groups of most members of the genus Thiorhodococcus, clustered with members of the genera Marichromatium and Phaeochromatium, but was most closely related to Thiorhodococcus bheemlicus with a pairwise sequence similarity of 98.75 %. Based on DNA-DNA hybridization between strain AK35T and Thiorhodococcus bheemlicus MTCC 8120T a relatedness of 39.46 % was established. Distinct morphological, physiological and genotypic differences from these previously described taxa supported the classification of the new isolate as a representative of a novel species in a new genus, for which the name Imhoffiella purpurea gen. nov., sp. nov. is proposed. The type strain of Imhoffiella purpurea is AK35T (=JCM 18851T=KCTC 15575T=MTCC 12304T). In addition, Thiorhodococcus bheemlicus is recognized as another species of this genus and transferred to Imhoffiella bheemlica comb. nov.

Antibacterial low-molecular-weight compounds produced by the marine bacterium Rheinheimera japonica KMM 9513T.

Strain KMM 9513T was isolated from a sediment sample collected from the Sea of Japan seashore and selected due to its ability to inhibit indicator bacterial growth. The strain KMM 9513T has been recently described as a novel species Rheinheimera japonica. This study was undertaken to determine which substances produced by strain KMM 9513T could be responsible for its antimicrobial activity. Eight compounds were obtained from an ethyl acetate extract of R. japonica KMM 9513T. The structures of five diketopiperazines (4-8) and diisobutyl-, dibutyl- and bis(2-ethylhexyl) phthalates (1-3) were established on the basis of detailed interpretation of NMR data, by Marfey method and optical rotation data. The structures of diketopiperazines were determined as cyclo-(L-valyl-L-proline), cyclo-(L-valyl-D-proline), cyclo-(L-phenylalanyl-L-proline), cyclo-(L-leucyl-L-proline), and cyclo-(L-phenylalanyl-D-proline). Compounds 1-3, 5 and 8 revealed antimicrobial activities against Bacillus subtilis and/or Enterococcus faecium and Staphylococcus aureus. In this paper, we describe the isolation and structural elucidation of the isolated compounds 1-8. This is the first report of the characterisation of low molecular weight antibacterial metabolites produced by a member of the genus Rheinheimera.

'Candidatus Tenderia electrophaga', an uncultivated electroautotroph from a biocathode enrichment.

Biocathode communities are of interest for a variety of applications, including electrosynthesis, bioremediation, and biosensors, yet much remains to be understood about the biological processes that occur to enable these communities to grow. One major difficulty in understanding these communities is that the critical autotrophic organisms are difficult to cultivate. An uncultivated, electroautotrophic bacterium previously identified as an uncultivated member of the family Chromatiaceae appears to be a key organism in an autotrophic biocathode microbial community. Metagenomic, metaproteomic and metatranscriptomic characterization of this community indicates that there is likely a single organism that utilizes electrons from the cathode to fix CO2, yet this organism has not been obtained in pure culture. Fluorescence in situ hybridization reveals that the organism grows as rod-shaped cells approximately 1.8 × 0.6 µm, and forms large clumps on the cathode. The genomic DNA G+C content was 59.2 mol%. Here we identify the key features of this organism and propose 'Candidatus Tenderia electrophaga', within the Gammaproteobacteria on the basis of low nucleotide and predicted protein sequence identity to known members of the orders Chromatiales and Thiotrichales.

Rheinheimera gaetbuli sp. nov., a Marine Bacterium Isolated from a Tidal Flat.

A gram-staining-negative, strictly aerobic, rod-shaped, and motile bacterium with a single polar flagellum, designated H26(T), was isolated from tidal flat sediment in Jeju Island, South Korea. Growth of strain H26(T) was observed at 4-35 °C (optimum, 20-25 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0), and 1-4 % NaCl (optimum, 2-3 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H26(T) formed a phyletic lineage within the genus Rheinheimera, family Chromatiaceae. Strain H26(T) was most closely related to Rheinheimera baltica OSBAC1(T), Rheinheimera aestuarii H29(T), Rheinheimera muenzenbergensis E49(T), and Rheinheimera aquimaris SW-353(T) with 98.5, 98.1, 97.8, and 97.5 % of 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness levels between strain H26(T) and the type strains of R. baltica, R. aestuarii, R. muenzenbergensis, and R. aquimaris were 35.5 ± 3.2, 33.4 ± 1.5, 31.2 ± 2.2, and 28.7 ± 0.9 %, respectively. The major fatty acids of strain H26(T) were iso-C15:0 3-OH, summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c), C16:0, summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c), iso-C17:0 3-OH, and C12:0 3-OH and the strain contained ubiquinone (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, and an aminolipid were identified as the major polar lipids and the G + C content of the genomic DNA was 52.0 mol%. Based on the phenotypic, chemotaxonomic, and molecular properties, strain H26(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera gaetbuli sp. nov. is proposed. The type strain was H26(T) (=KACC 18254(T) = JCM 30403(T)).

A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode.

Biocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2 reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortia in situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2 for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided between Alpha- and Gammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, with Marinobacter, Chromatiaceae, and Labrenzia the most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified from Chromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed for Chromatiaceae. These findings represent the first description of putative EET and CO2 fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.

Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan.

Two gram-negative, aerobic, brown-pigmented, motile rod-shaped bacteria KMM 9512 and KMM 9513(T) were isolated from a sediment sample collected from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis, novel strains KMM 9512 and KMM 9513(T) positioned within the genus Rheinheimera (class Gammaproteobacteria) as a separate subline adjacent to Rheinheimera baltica DSM 14885(T) sharing highest gene sequence similarities of 98.6-97.6 % to their closest phylogenetic relatives, Rheinheimera muenzenbergensis LMG 27269(T), R. baltica DSM 14885(T), Rheinheimera aquimaris JCM 14331(T), Rheinheimera nanhaiensis KACC 14030(T), and Rheinheimera pacifica KMM 1406(T). Strains KMM 9512 and KMM 9513(T) belong to the same separate genospecies on the basis of the 16S rRNA gene sequence similarity (99.8 %) and their DNA relatedness to each other (89 %) and to closely related Rheinheimera species (25-53 %). The major isoprenoid quinone was Q-8, polar lipids consisted of phosphatidylserine, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, unknown aminophospholipids, unknown phospholipids, and unknown lipids, and major fatty acid were C16:0, C16:1 ω7c, C17:1 ω8c, C12:0 3-OH followed by C17:0 and C18:1 ω7c in both strains. Strains KMM 9512 and KMM 9513(T) revealed a remarkable antagonistic activity toward a number of gram-positive and gram-negative microorganisms. On the basis of phylogenetic analysis, DNA-DNA hybridization results, and phenotypic differences, strains KMM 9512 and KMM 9513(T) are proposed to be classified as a novel species of the genus Rheinheimera, Rheinheimera japonica sp. nov. The type strain of this species is KMM 9513(T) = NRIC 0918(T).

Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site.

A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA-DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp).

Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments.

A novel purple sulfur bacterium, strain AX1YPE(T), was isolated from marine sediments sampled at 47 m depth in Callao Bay, Perú. Strain AX1YPE grew anaerobically, synthesizing bacteriochlorophyll a and carotenoid pigments of the spirilloxanthin series. Cells were Gram-stain-negative rods and actively motile by a polar flagellum. Strain AX1YPE was able to grow photolithoautotrophically with sulfide and thiosulfate as electron donors. This new phototrophic organism utilized ammonium salt, N2, urea and glutamate as nitrogen sources. Strain AX1YPE had a DNA base composition of 63.9 mol% G+C. Analysis of the 16S rRNA gene sequence indicated that strain AX1YPE clusters in a separate branch within the genus Allochromatium of the family Chromatiaceae. Strain AX1YPE showed 16S rRNA gene sequence similarities of 98.2% with Allochromatium vinosum DSM 180(T) and Allochromatium minutissimum DSM 1376(T), 98.1% with Allochromatium phaeobacterium JA144(T), 97.3% with Allochromatium renukae DSM 18713(T) and 96.8% with Allochromatium warmingiiDSM 173(T). DNA-DNA hybridization values to the type strains of its closest relatives, A. vinosum and A. minutissimum, were 59 and 64%, respectively. The predominant fatty acid of strain AX1YPE(T) was C18 : 1ω;7c and it notably possessed C20 : 1 as a minor component. PCR-based molecular typing (Box A1R and randomly amplified polymorphic DNA) produced a unique banding pattern for strain AX1YPE(T) in comparison with the type strains of A. vinosum and A. minutissimum. Based on data from this polyphasic taxonomic study, which also includes average nucleotide identity comparison of five concatenated housekeeping genes, strain AX1YPE(T) is considered to represent a novel species of the genus Allochromatium for which the name Allochromatiumhumboldtianum sp. nov. is proposed. The type strain is AX1YPE(T) ( = DSM 21881(T) = KCTC 15448(T)).

Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment.

A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10-40 °C (optimum, 20-25 °C) and pH 6.0-9.0 (optimum, pH 7.0-8.0), and in the presence of 1-4% (w/v) NaCl (optimum, 2-3%). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8%, 97.6%, 97.4% and 97.2% 16S rRNA gene sequence similarities, respectively. However, DNA-DNA hybridization values of strain H29T with type strains of these species were lower than 70%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimeraaestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).

Thiorhodococcus fuscus sp. nov., isolated from a lagoon.

A brown, moderately halophilic, photoautotrophic bacterium designated strain JA363T was purified from a photoheterotrophic enrichment obtained from sediment from Chilika lagoon, Odisha, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. Strain JA363T had an obligate requirement for NaCl and could tolerate up to 7 % (w/v) NaCl. Strain JA363T had complex growth factor requirements. Internal photosynthetic membranes were present as vesicles. Strain JA363T contained bacteriochlorophyll a and spirilloxanthin series carotenoids with rhodopin as a major (>85 %) component. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c and C16 : 0 were the major fatty acids and phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. Q8 was the predominant quinone system of strain JA363T. The DNA G+C content was 64 mol%. The highest 16S rRNA gene sequence similarity of strain JA363T was found with the type strains of Thiorhodococcus kakinadensis (98.7 %), Thiohalobacter thiocyanaticus (98.2 %), Thiophaeococcus fuscus (97.4 %) and Thiorhodococcus bheemlicus (96.3 %). However, the phylogenetic trees generated firmly placed strain JA363T in the genus Thiorhodococcus, which was further supported by phenotypic and chemotaxonomic evidence. Consequently, strain JA363T is described as representing a novel species of the genus Thiorhodococcus as Thiorhodococcus fuscus sp. nov. The type strain is JA363T ( = KCTC 5701T = NBRC 104959T).

Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample.

A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2% pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8-94.8%. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T).