Methanomethylovorans uponensis sp. nov., a methylotrophic methanogen isolated from wetland sediment

A novel mesophilic, methylotrophic, methanogenic archaeon, designated strain EK1^T, was enriched and isolated from wetland sediment. Phylogenetic analysis showed that strain EK1^T was affiliated with the genus Methanomethylovorans within the family Methanosarcinaceae, and shared the highest 16S rRNA and methyl-coenzyme M reductase alpha-subunit gene sequence similarity with the type strain of Methanomethylovorans hollandica (98.8 and 92.6 %, respectively). The cells of strain EK1^T were observed to be Gram-negative, non-motile and irregular cocci that did not lyse in 0.1 % (w/v) sodium dodecyl sulfate. Methanol, mono-, di- and trimethylamine, dimethyl sulfide and methanethiol were found to be used as catabolic and methanogenic substrates, whereas H₂/CO₂, formate, 2-propanol and acetate were not. Growth was observed at 25–40 °C (optimum, 37 °C), at pH 5.5–7.5 (optimum, pH 6.0–6.5) and in the presence of 0–0.1 M NaCl (optimum, 0 M). Growth and methane production rates were stimulated in the presence of H₂/CO₂ although methane production and growth yields were not significantly affected; acetate, formate, 2-propanol and CO/CO₂/N₂ did not affect methane production. CoCl₂ (0.6–2.0 μM) and FeCl₂ (25 mg/l) stimulated growth, while yeast extract and peptone did not. The DNA–DNA hybridization experiment revealed a relatedness of <20 % between EK1^T and the type strains of the genus Methanomethylovorans. The DNA G+C content of strain EK1^T was determined to be 39.2 mol%. Based on the polyphasic taxonomic study, strain EK1^T represents a novel species belonging to the genus Methanomethylovorans, for which the name Methanomethylovorans uponensis sp. nov. is proposed. The type strain is strain EK1^T(=NBRC 109636^T = KCTC 4119^T = JCM 19217^T).     

Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea

A slightly creamy, melanogenic, gram-negative, aerobic bacterium was isolated from seawater sample collected in the Karadag Natural Reserve of the Eastern Crimea, the Black Sea. The novel organism was chemoorganotrophic, had no obligate requirement in NaCl, tolerated to 12% NaCl, grew between 10 and 45 degrees C, was slightly alkaliphilic, and was not able to degrade starch, gelatin, agar, and Tween 80. 16S rRNA gene sequence-based analyses of the new organism revealed that Oceanimonas doudoroffii ATCC 27123T, Oceanimonas baumanii ATCC 700832T, and Oceanisphaera litoralis DSM 15406T were the closest relatives (similarity around 97%-96%). The G + C content of the DNA of the strain 31-13T was 55.5mol%. Phosphatidylethanolamine (49.0%), phosphatidylglycerol (41.8%), and diphosphatidylglycerol (9.2%) were the predominant phospholipids. The major fatty acids were 16:0 (24.1%), 16:1omega7 (40.3%), and 18:1omega7 (29.2%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Oceanimonas smirnovii sp. nov. is proposed. The type strain is 31-13T (UCM B-11076T = LMG 22147T = ATCC BAA-899T).     

Salinisphaera shabanensis gen. nov., sp. nov., a novel,moderately halophilic bacterium from the brine-seawater interface of the Shaban Deep,Red Sea

A novel, moderately halophilic bacterium was isolated from the brine-seawater interface of the Shaban Deep, northern Red Sea. A polyphasic approach was used for the taxonomic characterization of this isolate, with the phenotypic and phylogenetic data clearly showing the distinctiveness of this bacterium. Cells of isolate E1L3A were Gram-negative, monotrichous cocci that showed a remarkable physiological flexibility, as could be seen by the quite broad growth ranges for oxygen, temperature, NaCl, and, to a smaller degree, pH. In addition, it was able to grow from atmospheric pressure up to 15 MPa, making it a piezotolerant bacterium. Phylogenetically, strain E1L3A represents a new, deeply branching lineage within the gamma-Proteobacteria, as determined by 16S rRNA gene sequence analysis. No close relatives are known so far, with sequence similarity to other cultivated members of the gamma-Proteobacteria being lower than 88%. The creation of the new genus Salinisphaera and the new species Salinisphaera shabanensis (DSM 14853; JCM 11575) for this new and highly versatile microorganism is therefore proposed.     

Alteromonas australica sp. nov., isolated from the Tasman Sea

A non-pigmented, motile, Gram-negative bacterium designated H 17^T was isolated from a seawater sample collected in Port Phillip Bay (the Tasman Sea, Pacific Ocean). The new organism displayed optimal growth between 4 and 37 °C, was found to be neutrophilic and slightly halophilic, tolerating salt water environments up to 10 % NaCl. Strain H 17^T was found to be able to degrade starch and Tween 80 but unable to degrade gelatin or agar. Phosphatidylglycerol (27.7 %) and phosphatidylethanolamine (72.3 %) were found to be the only associated phospholipids. The major fatty acids identified are typical for the genus Alteromonas and include C_16:0, C_16:1ω7, C_17:1ω8 and C_18:1ω7. The G+C content of the DNA was found to be 43.4 mol%. A phylogenetic study, based on the 16S rRNA gene sequence analysis and Multilocus Phylogenetic Analysis, clearly indicated that strain H 17^T belongs to the genus Alteromonas. The DNA?DNA relatedness between strain H 17^T and the validly named Alteromonas species was between 30.7 and 46.4 mol%. Based on these results, a new species, Alteromonas australica, is proposed. The type strain is H 17^T (= KMM 6016^T = CIP 109921^T).     

Methanobrevibacter filiformis sp. nov., a filamentous methanogen from termite hindguts

A morphologically distinct, filamentous methanogen was isolated from hindguts of the subterranean termite, Reticulitermes flavipes (Kollar) (Rhinotermitidae), wherein it was part of the microbiota colonizing the hindgut wall. Individual filaments of strain RFM-3 were 0.23–0.28 μm in diameter and usually > 50 μm in length and aggregated into flocs that were often ≥ 0.1 mm in diameter. Optimal growth of strain RFM-3 was obtained at pH 7.0–7.2 and 30° C with a yeast-extract-supplemented, dithiothreitol-reduced medium in which cells produced stoichiometric amounts of methane from H₂ + CO₂. The morphology and gram-positive staining reaction of strain RFM-3, as well as its resistance to cell lysis by various chemical agents and its restriction to H₂ + CO₂ as an energy source, suggested that it was a member of the Methanobacteriaceae. The nucleotide sequence of the SSU-rRNA-encoding gene of strain RFM-3 confirmed this affiliation and also supported its recognition as a new species of Methanobrevibacter, for which the epithet filiformis is herewith proposed. Although M. filiformis was one of the dominant methanogens in R. flavipes collected from Woods Hole (Mass., USA), cells of similar morphology were not consistently observed in R. flavipes collected from different geographical locations. Received: 15 September 1997 / Accepted: 20 November 1997     

Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from Chinese rice field soil

Background

Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.).

Methodology/Principal Findings

By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254^T was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAE^T was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4–2.8 µm long and by 0.2–0.3 µm in width. They grew at 37–60°C (optimally at 55°C) and salinity of 0–5 g NaCl l⁻¹ (optimally at 0–1 g NaCl l⁻¹). The pH range for growth was 6.4–7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5–7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254^T utilized H₂/CO₂ but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254^T and SANAE^T were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254^T as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254^T ( = CGMCC 1.5162^T = JCM 17849^T = DSM 24694^T).

Conclusions/Significance

Strain HZ254^T could potentially serve as an excellent laboratory model for studying Methanocellales due to its fast growth and consistent cultivability.     

Hoeflea halophila sp. nov., a novel bacterium isolated from marine sediment of the East Sea, Korea

A Gram-negative, aerobic, motile, straight or curved rod-shaped marine bacterium was isolated from marine sediment of the East Sea, Korea. The isolated strain, JG120-1^T, grows with 0–5 % (w/v) NaCl and at 15–30 °C and pH 6–9. α-galactosidase activity test was positive. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Alphaproteobacteria and was the most closely related to Hoeflea alexandrii AM1 V30^T, Hoeflea phototrophica DFL-43^T and Hoeflea marina LMG 128^T (98.9, 97.9 and 97.0 % 16S rRNA gene sequence similarities, respectively). Strain JG120-1^T was found to possess summed feature 8 (C18:1ω7c/C18:1ω6c, 71.11 %) as the major cellular fatty acid. The major ubiquinone was determined to be Q-10. Polar lipids include phosphatidylglycerol, phosphatidylethanolamine, sulfoquinovosyl diacylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. The G+C content of the genomic DNA of strain JG120-1^T was determined to be 57.8 mol %. DNA–DNA relatedness data indicated that strain JG120-1^T represents a distinct species that is separate from H. phototrophica DFL-43^T, H. marina LMG128^T and H. alexandrii AM1 V30^T. On the basis of polyphasic evidences, it is proposed that strain JG120-1^T (= KCTC 23107^T = JCM 16715^T) represents the type strain of a novel species, Hoeflea halophila sp. nov.     

Arthrospiribacter ruber gen. nov., sp. nov., a novel bacterium isolated from Arthrospira cultures

Polyphasic analysis of ten isolates of the red-pigmented bacteria isolated from ten Arthrospira cultures originating from different parts of the world is described. The 16S rRNA analysis showed <95 % identity with the known bacteria on public databases, therefore, additional analyses of fatty acids profiles, MALDI-TOF/MS, genome sequencing of the chosen isolate and following phylogenomic analyses were performed. Gram-stain-negative, strictly aerobic rods were positive for catalase, negative for oxidase, proteolytic and urease activity. Major fatty acids were 15 : 0 iso, 17:0 iso 3 OH and 17:1 iso w9c/16:0 10-methyl. The whole phylogenomic analyses revealed that the genomic sequence of newly isolated strain DPMB0001 was most closely related to members of Cyclobacteriaceae family and clearly indicated distinctiveness of newly isolated bacteria. The average nucleotide identity and in silico DNA–DNA hybridisation values were calculated between representative of the novel strains DPMB0001 and its phylogenetically closest species, Indibacter alkaliphilus CCUG57479 (LW1)^T (ANI 69.2 % is DDH 17.2 %) and Mariniradius saccharolyticus AK6^T (ANI 80.02 % isDDH 26.1 %), and were significantly below the established cut-off <94 % (ANI) and <70 % (isDDH) for species and genus delineation.The obtained results showed that the analysed isolates represent novel genus and species, for which names Arthrospiribacter gen nov. and Arthrospiribacter ruber sp. nov. (type strain DPMB0001 = LMG 31078 = PCM 3008) is proposed.     

Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea

Four strains of obligately heterotrophic bacteria isolated from the oxygen-sulfide interface of the Black Sea are characterized. The bacteria are aerobic, Gram-negative, with lemon-like, nonmotile cells. Bacteriochlorophyll a is not detected. They are mesophilic and neutrophilic with a temperature range of 8–35 °C (optimum 25) and pH range of 6.5–8.5 (optimum 7.8). Their growth is NaCl dependent within a range of 5 and 60 (optimum 20) g l⁻¹. They are able to oxidize thiosulfate, sulfide and elemental sulfur to sulfate and to use metabolic energy from these reactions (lithoheterotrophy). According to the level of DNA reassociation of more than 40%, all isolates represent a single generic group. The G+C content of the DNA was in the range of 67.5–69.2 mol%. According to phylogenetic analysis, the new isolates form a separate branch in the alpha-3 subdivision of the Proteobacteria together with two undescribed marine bacterial strains. On the basis of phenotypical and genomic properties, the new isolates are described as a new genus and species Citreicella thiooxidans gen. nov., sp. nov. The type strain is CHLG 1^T (=DSM 10146, UNIQEM U 228).     

Streptosporangium nanhuense sp. nov., a novel actinomycete isolated from soil

A novel actinomycete, designated strain NEAU-NH11^T, was isolated from muddy soil collected from a lake and characterized using a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain NEAU-NH11^T belongs to the genus Streptosporangium, and was most closely related to Streptosporangium amethystogenes subsp. amethystogenes DSM 43179^T (99.0 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-NH11^T formed a monophyletic clade with Streptosporangium purpuratum CY-15110^T (98.3 %) and Streptosporangium yunnanense CY-11007^T (98.0 %), an association that was supported by a bootstrap value of 80 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, the low level of DNA–DNA relatedness allowed the strain to be differentiated from S. amethystogenes subsp. amethystogenes DSM 43179^T, S. purpuratum CY-15110^T and S. yunnanense CY-11007^T. Moreover, strain NEAU-NH11^T could also be differentiated from its closest related strains by phenotypic characteristics. Therefore, it is proposed that strain NEAU-NH11^T represents a novel Streptosporangium species, Streptosporangium nanhuense sp. nov. The type strain of S. nanhuense is NEAU-NH11^T. (=CGMCC 4.7131^T = DSM 46674^T).     

Sporosarcina siberiensis sp. nov., isolated from the East Siberian Sea

A Gram-stain positive, non-motile, rod-shaped bacterium, designated strain 1111S-42^T, was isolated from the East Siberian Sea. The organism was found to grow at 4–30 °C, pH 7.0–8.5 and in 0–8 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 7.5 and in 1 % NaCl. Based on 16S rRNA gene sequence similarity studies, strain 1111S-42^T was found to belong to the genus Sporosarcina and to be most closely related to Sporosarcina contaminans CCUG53915^T (97.3 %) and Sporosarcina soli I80^T (97.2 %). The main polar lipids were found to include diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant menaquinone was identified as MK-7. The major cellular fatty acids were identified as anteiso-C_15:0 (34.4 %), iso-C_15:0 (29.8 %) and anteiso-C_17:0 (22.4 %). The DNA G+C content of strain 1111S-42^T was determined to be 39 mol %. The values of DNA–DNA relatedness between the strain 1111S-42^T and related type strains of the genus Sporosarcina were less than 30 %. Based on the phylogenetic analysis, along with extensive physiological and chemotaxonomic testing, we conclude that the bacterium represents a novel species of the genus Sporosarcina, for which the name Sporosarcina siberiensis sp. nov. is proposed. The type strain is strain 1111S-42^T (=CGMCC 1.12516^T = LMG 27494^T).     

Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin

A novel anaerobic methylotrophic halophilic methanogen strain SLHTYRO^T was isolated from a deep hypersaline anoxic basin called “Tyro” located in the Eastern Mediterranean Sea. Cells of SLHTYRO^T were motile cocci. The strain SLHTYRO^T grew between 12 and 37 °C (optimum 30 °C), at pH between 6.5 and 8.2 (optimum pH 7.5) and salinity from 45 to 240 g L⁻¹ NaCl (optimum 135 g L⁻¹). Strain SLHTYRO^T was methylotrophic methanogen able to use methylated compounds (trimethylamine, dimethylamine, monomethylamine and methanol). Strain SLHTYRO^T was able to grow at in situ hydrostatic pressure and temperature conditions (35 MPa, 14 °C). Phylogenetic analysis based on 16S rRNA gene and mcrA gene sequences indicated that strain SLHTYRO^T was affiliated to genus Methanohalophilus within the order Methanosarcinales. It shared >99.16% of the 16S rRNA gene sequence similarity with strains of other Methanohalophilus species. Based on ANIb, AAI and dDDH measurements, and the physiological properties of the novel isolate, we propose that strain SLHTYRO^T should be classified as a representative of a novel species, for which the name Methanohalophilus profundi sp. nov. is proposed; the type strain is SLHTYRO^T (=DSM 108854 = JCM 32768 = UBOCC-M-3308).     

Altuibacter lentus gen. nov., sp. nov., a novel member of family Flavobacteriaceae isolated from deep seawater of the South China Sea

A novel chemoheterotrophic, aerobic, Gram-negative, rod-shaped, yellow-pigmented, bacterial strain JLT2010^T was isolated from deep seawater of the South China Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain JLT2010^T belongs to the family Flavobacteriaceae and is most closely related to Ulvibacter antarcticus IMCC3101^T with 95.7 % similarity. Some phenotypic characteristics such as the absence of flexirubin-type pigments, growth at 37 °C, hydrolysis of casein differentiated strain JLT2010^T from the genus Ulvibacter as well as other genera in the family Flavobacteriaceae. The DNA G+C content of the strain JLT2010^T was found to be 35.7 mol% and the major respiratory quinone was found to be MK-6. On the basis of phenotypic and phylogenetic features, JLT2010^T is classified as a novel genus and species within the family Flavobacteriaceae, for which the name Altuibacter lentus gen. nov., sp. nov. is proposed. The type strain is JLT2010^T (=JCM 18884^T = CGMCC 1.12167^T).     

Aestuariihabitans beolgyonensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment

A Gram-negative, non-motile and rod-shaped bacterial strain, designated BB-MW15^T, was isolated from a tidal flat of the southern coast of the Korean peninsula, and its taxonomic position was investigated by using a polyphasic taxonomic approach. Strain BB-MW15^T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2–3 % (w/v) NaCl. Strain BB-MW15^T exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Marivita byunsanensis (96.8 %), Thalassobius maritimus (96.6 %), Sulfitobacter marinus (96.4 %) and Marinovum algicola (96.3 %). Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-MW15^T forms an independent lineage within the evolutionary radiation encompassed by the Roseobacter clade of the class Alphaproteobacteria. Strain BB-MW15^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c as the predominant fatty acid. The major polar lipids detected in strain BB-MW15^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain BB-MW15^T is 62.7 mol%. Based on phylogenetic, chemotaxonomic and other phenotypic characteristics, strain BB-MW15^T represents a new genus and a new species within Alphaproteobacteria, for which the name Aestuariihabitans beolgyonensis gen. nov., sp. nov. is proposed. The type strain of A. beolgyonensis is BB-MW15^T (= KCTC 32324^T = CCUG 63829^T).