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).

Microbial Community Composition during a Bloom of Purple Bacteria in Intertidal Sediments in Vigo (Northwest Spain).

In summer 2019, a large, bright pink microbial mat was visible on top of macroalgal deposits in muddy sediments of an urban beach (Playa do Adro, Vigo). In order to characterize the dominant organisms in these colored mats, results from microscopic observations, photosynthetic pigments, and molecular analysis were gathered. Light microscopy examination revealed pinkish microbial aggregates with minor contributions of larger protists and cyanobacteria. High-performance liquid chromatography (HPLC) pigment analysis documented the dominance of bacteriochlorophyll a and carotenoids whose spectra were compatible with those described in photosynthetic purple bacteria. 16S rRNA gene amplicon sequencing confirmed that the vast majority of reads belonged to Proteobacteria (73.5%), and among them, nearly 88% of those reads belonged to purple sulfur bacteria (Gammaproteobacteria). A single family, Chromatiaceae, constituted the bulk of this assemblage, including the genera Thiohalocapsa (32%), Marichromatium (12.5%), Phaeochromatium (5%), and Halocromatium (2%) as main contributors. Nonetheless, a considerable number of sequences could not be assigned to a particular genus, stressing the large biological diversity in these microbial mats and the potential presence of novel taxa of purple sulfur bacteria. IMPORTANCE Urban beaches are valuable recreational areas particularly vulnerable to human disturbance. In these areas, the intertidal sediments harbor a diverse community of microorganisms, including virus, bacteria, fungi, and protozoa. In this sense, pollution events can introduce pathogenic allochthonous microbes which may constitute a human health risk. Visual and sensory observations, such as a weird color or bad smell, are usually appreciated as a warning by beachgoers and authorities, as indeed was the case at do Adro beach in 2019. The observed proliferation seems to be common in summertime, but its dimension alerted beachgoers and media. The obtained results allowed for the identification of purple sulfur bacteria as responsible for the pink-violet top layer staining the intertidal zone. These blooms have never been associated with public health risks. Beyond solving the sanitary concern, other important findings were its diversity and large proportion of novel taxa, illustrating the complexity of these ecosystems.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake.

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.

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).

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).

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).

Seasonal dynamics of Chironomus transvaalensis populations and the microbial community composition of their egg masses.

Chironomids (Diptera; Chironomidae) are the most abundant insects in freshwater environments and are considered natural reservoirs of Vibrio cholerae. We monitored the annual dynamics of chironomid populations along with their microbiota in order to better understand host-microbiota interactions. Chironomus transvaalensis populations peaked biannually in August and May-June. The composition of the endogenous bacterial communities of their egg masses clustered in two groups according to the sampling periods August-November and May-July. Nevertheless, a core bacterial community (43%) was present in all egg-mass samples. The most abundant phyla were: Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. The abundance of several genera (e.g. Rheinheimera and Pseudomonas) was positively correlated with C. transvaalensis population dynamics, while a predator-prey interaction was observed between the relative abundance of Vibrio OTUs and C. transvaalensis population size. Chironomids are known to tolerate toxic and stress conditions, and our results demonstrated that bacterial genera that may protect the insect under these conditions are present in the egg masses. After hatching, the first larval meal is the gelatinous matrix that surrounds the eggs. This meal contains a probiotic consortium that may protect the larva during its metamorphosis. The results provide important insights into the host-microbe interactions of chironomids.

First description of a new uncultured purple sulfur bacterium colonizing marine mangrove sediment in the Caribbean: Halochromatium-like PSB from Guadeloupe.

Here, we report the first description of a marine purple sulfur bacterium (PSB) from sulfide-rich sediments of a marine mangrove in the Caribbean. TEM shows that this new isolate contains intracytoplasmic vesicular membrane systems (containing bacteriochlorophyll a) and larger internal sulfur granules, confirmed by EDXS analyses performed using ESEM. The sulfur distribution and mapping obtained for this PSB strain has allowed us to conclude that elemental sulfur is formed as an intermediate oxidation product and stored intracellularly. SEM shows that the bacterial cells are ovoid and extremely motile via lophotrichous flagella. Phylogenetic characterization, based on the analysis of 16S rDNA and functional gene pufM sequences, demonstrate that this strain belongs to the Chromatiaceae and may be a representative of a new species of the genus Halochromatium. Thus, reduced sediments of marine mangrove represent a sulfide-rich environment that sustains the development of Chromatiaceae, in addition to sulfur-oxidizing bacteria and cyanobacteria, as previously reported.

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).

Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community.

Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.

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 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).

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.

Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases.

Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography-tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin-like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20 °C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity.

Succession Processes in the Anoxygenic Phototrophic Bacterial Community in Lake Kislo-Sladkoe (Kandalaksha Bay, White Sea).

The community of anoxygenic phototrophic bacteria (APB) in the water column of Lake Kislo- Sladkoe (Kandalaksha Bay, White Sea), which has recently become separated from the sea, was investigated in March-April 2012, March-April 2013, and in September 2013. The lake, which was previously considered meromictic, was in fact mixed and was strongly affected by the sea. In winter the lake is sometimes washed off with seawater, and this together with the seasonal cycles of succession processes determines the succession of the community. The consequences of the mixing in autumn 2011 could be observed in the APB community as late as autumn 2013. Green-colored green sulfur bacteria (GSB) usually predominated in the chemocline. In winter 2013 stagnation resulted in turbidity of water under the ice, which was responsible for both predom- inance of the brown GS B forms and the changes ratio of the species of purple sulfur bacteria (PS B) in anoxic water layers. Production of anoxygenic photosynthesis in the lake was at least 240 mg C m-2 day-- in September and 0-20 mg C m-2 day- in March-April, which corresponded to 40 and 69%, respectively, of oxygenic photosynthesis. Okenone-containing purple sulfur bacteria, strain TcakPS12 were isolated in 2012 from lake water. The ells of this strain form filaments of not separated cells. Strain TcakPS12 exhibited 98% similarity with the type strains of Thiocapsapendens DSM.236 and Thiocapsa bogorovii BBS, as well as with the strains AmPS10 and TcyrPS 10, which were isolated from Lake Kislo-Sladkoe in 2010.