Cohnella panacarvi sp. nov., a xylanolytic bacterium isolated from ginseng cultivating soil

A Gram-positive, aerobic, rod-shaped, nonmotile, endospore-forming bacterium, designated Gsoil 349T, was isolated from soil of a ginseng field and characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that the strain Gsoil 349T belongs to the family Paenibacillaceae, and the sequence showed closest similarity with Cohnella thermotolerans DSM 17683T (94.1%) and Cohnella hongkongensis DSM 17642T (93.6%). The strain showed less than 91.3% 16S rRNA gene sequence similarity with Paenibacillus species. In addition, the presence of MK-7 as the major menaquinone and anteiso-C(15:0), iso-C(16:0), and C(16:0) as major fatty acids suggested its affiliation to the genus Cohnella. The G+C content of the genomic DNA was 53.4 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 349T should be treated as a novel species within the genus Cohnella for which the name Cohnella panacarvi sp. nov. is proposed. The type strain is Gsoil 349T (=KCTC 13060T = DSM 18696T).     

Sedimenticola selenatireducens, gen. nov., sp. nov., an anaerobic selenate-respiring bacterium isolated from estuarine sediment

The respiration of selenate, as a terminal electron acceptor has been known for over a decade, but the microorganisms involved in this respiration are largely unknown. Here we characterize a novel selenate-respiring bacterium, strain AK4OH1, isolated from an estuarine sediment enrichment culture. Strain AK4OH1 has the unique capability to oxidize aromatic acids, such as benzoate, 4-hydroxybenzoate and 3-hydroxybenzoate, coupled to selenate respiration. This novel respiratory coupling has not been described before. Reduction of selenate is followed by stoichiometric accumulation of selenite. The strain grows in agar shake tubes forming bright red colonies due to precipitation of elemental selenium. Strain AK4OH1 is a strictly anaerobic bacterium, which can also respire nitrate and nitrite via denitrification. Analysis of the 16S rRNA gene sequence shows that this strain clusters with another selenate-reducing bacterium and a (per) chlorate reducing bacterium, within the Gammaproteobacteria, along with symbionts of bivalves and tubeworms. Based on its unique physiological capabilities and its 16S rRNA gene sequence phylogeny, we classify this strain AK4OH1 as a new genus and species with the proposed name Sedimenticola selenatireducens.     

Weizmannia acidilactici sp. nov., a lactic acid producing bacterium isolated from soils

The strains designed PP-18^T, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced l-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18^T, JC-4 and JC-7 were closely related to Weizmannia coagulans LMG 6326^T (97.27–97.64%) and W. acidiproducens KCTC 13078^T (96.46–96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained meso-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18^T were iso-C_15:0, anteiso-C_17:0, iso-C_16:0 and anteiso-C_15:0. The ANIb and ANIm values among the genomes of strains PP-18^T, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and W. coagulans LMG 6326^T and W. acidiproducens KCTC 13078^T were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7–23.6% when compared with W. coagulans LMG 6326^T and W. acidiproducens DSM 23148^T. The DNA G + C contents of strains PP-18^T, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18^T, JC-4 and JC-7 should be represented as a novel species within the genus Weizmannia for which the name Weizmannia acidilactici sp. nov. is proposed. The type strain is PP-18^T (=KCTC 33974^T = NBRC 113028^T = TISTR 2515^T).     

Ectothiorhodospira vacuolata sp. nov., a new phototrophic bacterium from soda lakes

A new phototrophic bacterium was isolated from Jordanian and Kenyan alkaline salt lakes. Cells are rod shaped, 1.5 m wide and 2–4 m long, and motile by polar flagella. They divide by binary fission, and possess photosynthetic membranes as lamellar stacks similar to those in the other species of the genus Ectothiorhodospira and the brown colored Rhodospirillum species. The presence of bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series is indicated by the absorption spectra of living cells. Under certain growth conditions the cells form gas vacuoles, may become immotile and float to the top of the culture medium. Sulfide and thiosulfate are used as photosynthetic electron donors. During the oxidation of sulfide to sulfate, elemental sulfur is formed, which is accumulated outside the cells. The organisms are strictly anaerobic, do not require vitamins, are moderately halophilic and need alkaline pH-values for growth. The new species Ectothiorhodospira vacuolata is proposed.     

Chromohalobacter moromii sp. nov., a moderately halophilic bacterium isolated from lupine-based moromi fermentation

Three moderately halophilic strains, TMW 2.2308^T, TMW 2.2299 and TMW 2.2304, were isolated from a lupine-based moromi fermentation. Initial identification based on their low molecular sub-proteome using mass spectrometry showed relation to the genus Halomonas, however, low score values indicated novelty. The comparison of 16S rRNA gene sequences placed these strains within the genus Chromohalobacter with C. japonicus CECT 7219^T (99.67% 16S rRNA sequence similarity to strain TMW 2.2308^T), C. canadensis DSM 6769^T (99.54%) and C. beijerinckii LMG 2148^T (99.32%) being their closest relatives. However, average nucleotide highest identity values of TMW 2.2308^T to C. beijerinckii LMG 2148^T of 93.12% and 92.88% to C. japonicus CECT 7219^T demonstrate that it represents a novel species within the genus Chromohalobacter with additional strains TMW 2.2299 (96.91%) and TMW 2.2304 (96.98%). The isolated strains were non-spore-forming, motile and able to grow at temperatures from 5 to 45 °C with an optimum at 37 °C. Growth of TMW 2.2308^T occurs at 5 to 25% (w/v) NaCl with optimum growth between 10 and 12.5%. The genome of TMW 2.2308^T has a size of 3.47 Mb and a G + C content of 61.0 mol%. The polyphasic evidence lead to the classification of TMW 2.2308^T, TMW 2.2299 and TMW 2.2304 as members of a novel species of the genus Chromohalobacter. We propose a novel species as Chromohalobacter moromii sp. nov., with TMW 2.2308^T (=DSM 113153^T =CECT 30422^T) as the type strain.     

Caldimonas taiwanensis sp. nov., a amylase producing bacterium isolated from a hot spring

During screening for amylase-producing bacteria, a strain designated OnlT was isolated from a hot spring located in Pingtung area, which is near the very southern part of Taiwan. Cells of this organism were Gram-negative rods motile by means of a single polar flagellum. Optimum conditions for growth were 55 degrees C and pH 7. Strain On1(T) grew well in minimal medium containing starch as the sole carbon source, and its extracellular products expressed amylase activity. The 16S rRNA gene sequence analysis indicates that strain On1(T) is a member of beta-Proteobacteria. On the basis of a phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, physiological and biochemical characteristics, as well as fatty acid compositions, the organism belonged to the genus Caldimonas and represented a novel species within this genus. The predominant cellular fatty acids of strain On1(T) were 16:0 (about 30%), 18:1 omega 7c (about 20%) and summed feature 3 (16:1 omega 7c or 15:0 iso 2OH or both [about 31%]). Its DNA base ratio was 65.9 mol% G + C. We propose to classify strain On1(T) (= BCRC 17405T = LMG 22827T) as Caldimonas taiwanensis sp. nov.     

Lysinibacillus mangiferahumi sp. nov., a new bacterium producing nematicidal volatiles

A Gram-positive bacterium, designated M-GX18^T, was isolated from the rhizosphere soil of mango (Guangxi Province, China). The isolate produced nematicidal volatile compounds with activities against the root-knot nematode Meloidogyne incognita. The organism was motile, catalase- and oxidase-positive, spore-forming and rod shaped. The predominant menaquinone was MK-7 and the major cellular fatty acid profiles were iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. The DNA G+C content was 38.9%. A phylogenetic analysis based on 16S rRNA gene sequences showed that this organism represented a new species of the genus Lysinibacillus. Strain M-GX18^T exhibited high 16S rRNA gene sequence similarity with its closest neighbors Lysinibacillus sphaericus (98.5%), Lysinibacillus fusiformis (98.1%) and Lysinibacillus xylanilyticus (98.6%). The physiological, biochemical and chemotaxonomic data, including DNA–DNA hybridization relatedness data, indicate that strain M-GX18^T can be distinguished from all the related species of the genus Lysinibacillus. Therefore, on the basis of the polyphasic taxonomic data presented, a new species of the genus Lysinibacillus, Lysinibacillus mangiferahumi, with the type strain M-GX18^T (=DSM 24076^T = CCTCC AB 2010389^T) is proposed.     

Methanothrix soehngenii gen. nov. sp. nov., a new acetotrophic non-hydrogen-oxidizing methane bacterium

A new genus of methanogenic bacteria is described, which was isolated from a mesophilic sewage digester. It is most probably the filamentous bacterium, earlier referred to asMethanobacterium soehngenii, fat rod or acetate organism. The single non-motile, non-sporeforming cells are rod-shaped (0.8×2 m) and are normally combined end to end in long filaments, surrounded by a sheath-like structure. The filaments form characteristic bundles.Methanothrix soehngenii decarboxylates acetate, yielding methane and carbon dioxide. Other methanogenic substrates (H₂–CO₂, formate, methanol, methylamines) are not used for growth or methane formation. Formate is split into hydrogen and carbon dioxide. The temperature optimum for growth and methane formation is 37°C and the optimal pH range is 7.4–7.8. Sulfide and ammonia serve as sulfur and nitrogen source respectively. Oxygen completely inhibits growth and methane formation, but the bacteria do not loose their viability when exposed to high oxygen concentrations. 100 mg/l vancomycin showed no inhibition of growth and methanogenesis. No growth and methane formation was observed in the presence of: 2-bromoethanesulfonic acid, viologen dyes, chloroform, and KCN. The bacterium has a growth yield on acetate of 1.1–1.4 g biomass per mol acetate. The apparent K _S of the acetate conversion system to methane and carbon dioxide is 0.7 mmol/l. The DNA base composition is 51.9 mol% guanine plus cytosine. The nameMethanothrix is proposed for this new genus of filamentous methane bacterium. The type species,Methanothrix soehngenii sp. nov., is named in honor of N. L. Söhngen.     

Succinate decarboxylation byPropionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment

Enrichments on succinate plus yeast extract under anoxic conditions from intertidal mud-flat sediments yielded cultures dominated by oval to round-ended rod-shaped cells. Strain 10succ1, obtained in pure culture, was characterized in detail. The non-motile cells possessed a gram-negative cell wall and did not form spores. Carbohydrates were fermented to formate, acetate, ethanol, and lactate. Succinate was decarboxylated to propionate. Other organic and amino acids were variously fermented to formate, acetate, propionate, and butyrate. Sulfur, sulfate, thiosulfate, and nitrate were not used as electron acceptors. Growth required the presence of yeast extract and at least 5 g/l NaCl, and was possible only in the absence of oxygen. No cytochromes were detected. The DNA base ratio was 40 mol% G+C. Phylogenetically, strain 10succ1 is closely related to Propionigenium modestum, as revealed by 16S rDNA analysis, but is physiologically distinct. Accordingly, strain 10succ1 (DSM 9537) is described as the type strain of a new species of the genus Propionigenium, P. maris sp. nov. Received: 12 January 1995 / Accepted: 24 February 1995     

Frigoriflavimonas asaccharolytica gen. nov., sp. nov., a novel psychrophilic esterase and protease producing bacterium isolated from Antarctica

Antonie van Leeuwenhoek - The rod-shaped and Gram-stain-negative bacterial strain 16FT, isolated from an air sample collected at King George Island, maritime Antarctica, was investigated to...     

Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap

Zymobacter palmae gen. nov., sp. nov. was proposed for a new ethanol-fermenting bacterium that was isolated from palm sap in Okinawa Prefecture, Japan. The bacterium is gram-negative, facultatively anaerobic, catalase-positive, oxidase-negative, nonspore-forming and peritrichously flagellated. It requires nicotinic acid for growth. It ferments hexoses, -linked di- and tri-saccarides, and sugar alcohols (fructose, galactose, glucose, mannose, maltose, melibiose, saccharose, raffinose, mannitol and sorbitol). Fifteen percent of maltose in broth medium is effectively fermented, whereas glucose with a concentration higher than 10% delayed growth initiation and decreased growth rates. Maltose is fermented to produce ethanol and CO₂ with a trace amount of acids. Approximately 2 mol of ethanol are produced from 1 mol moiety of hexose of maltose. The organism possesses ubiquinone-9. The G+C content of the DNA is 55.8+-0.4 mol%. Major cellular fatty acids were palmitic and oleic acids and cyclopropanic acid of C_19:0. Characteristic hydroxylated acid was 3-hydroxy dodecanoic acid. The bacterium is distinct from other ethanol-fermenting bacteria belonging to the genera Zymomonas Kluyver and van Niel 1936 and Saccharobacter Yaping et al. 1990 with respect to chemotaxonomic and other phenotypic characters to warrant to compose a new genus and a new species. The type strain is strain T109 (= IAM 14233).Abbreviation IAM IAM Culture Collection, Institute of Applied Microbiology. The University of Tokyo     

Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov.

A new xylanolytic bacterium designated strain HESP1T (T = type strain) was isolated from a methanogenic digester. Strain HESP1T was a motile, rod shaped, spore-forming bacterium, which possessed a Gram-positive type cell wall. Glucose, fructose, lactose, trehalose, maltose, raffinose, sucrose, xylan, mannitol, cellobiose, galactose, mannose, melibiose, ribose were fermented to produce, acetate, butyrate, H2, CO2, formate, isobutyrate, and ethanol. Fumarate was fermented to acetate. Glycerol and methanol were also utilized. Sulfate, thiosulfate, nitrate, sulfur and fumarate were not used as electron acceptors. Strain HESP1T had a G + C content of 40 mol% and grew optimally at 37 degrees C and pH 7 on a fructose containing medium. Phylogenetically, strain HESP1T was most related to Clostridium aminovalericum (similarity of 94%) than to C. populeti, C. herbivorans and Eubacterium xylanophilum (average similarity of 92%), all members of subcluster XIVa of the low G + C containing Gram-positive branch. However, strain HESP1T shared little phenotypic and genotypic traits with C. aminovalericum and on the basis of this and phylogenetic evidence, we propose to tentatively designate strain HESP1T as a new species of the genus Clostridium, Clostridium xylanovorans sp. nov. The type strain is HESP1T (= DSM 12503).     

Desulforhopalus vacuolatus gen. nov., sp. nov., a new moderately psychrophilic sulfate-reducing bacterium with gas vacuoles isolated from a temperate estuary

A new type of gas-vacuolated, sulfate-reducing bacterium was isolated at 10° C from reduced mud (E₀ < 0) obtained from a temperate estuary with thiosulfate and lactate as substrates. The strain was moderately psychrophilic with optimum growth at 18–19° C and a maximum growth temperature of 24° C. Propionate, lactate, and alcohols served as electron donors and carbon sources. The organism grew heterotrophically only with hydrogen as electron donor. Propionate and lactate were incompletely oxidized to acetate; traces of lactate were fermented to propionate, CO₂, and possibly acetate in the presence of sulfate. Pyruvate was utilized both with and without an electron acceptor present. The strain did not contain desulfoviridin. The G+C content was 48.4 mol%. The differences in the 16S rRNA sequence of the isolate compared with that of its closest phylogenetic neighbors, bacteria of the genus Desulfobulbus, support the assignment of the isolate to a new genus. The isolate is described as the type strain of the new species and genus, Desulforhopalus vacuolatus. Received: 4 March 1996 / Accepted: 17 June 1996     

Cytophaga xylanolytica sp. nov., a xylan-degrading,anaerobic gliding bacterium

Gliding bacteria attached in masses to, and dominated the fermentation of, xylan powder in methanogenic and sulfidogenic enrichments from various freshwater sediments. Isolates of such bacteria were all gram-negative, slender rods (0.4×4-24 m) that formed no endospores, microcysts or fruiting bodies. Representative strain XM3 was a mesophilic, aeroduric anaerobe that grew by fermentation of mono-, di-, and poly-saccharides (but not cellulose) in a mineral medium containing up to 3% NaCl. However, CO₂/HCO _inf3 ^sup- was required in media for consistent initiation of growth. Fermentation products included acetate, propionate, succinate, CO₂, and H₂. Xylan-grown cells had xylanase and various glycosidase activities that were mainly or almost entirely cell-associated, respectively. Strain XM3 was weakly catalase positive, but oxidase negative; it possessed sulphonolipids and carotenoid, but not flexirubin, pigments; and its total cellular fatty acids were dominated by C_15:0 anteiso (75%), n (13%) and iso (2%) isomers. Strain XM3 had 45.5 mol% G+C in its DNA, and partial sequencing of its 16S rRNA placed XM3 within the Bacteroides-Flavobacterium phylogenetic group. Similar strains were isolated from marine sediments. Strain XM3 is herewith proposed as the type strain of the new species, Cytophaga xylanolytica. Results, which are discussed in terms of our current concept of the genus Cytophaga, suggest that the importance of C. xylanolytica in anaerobic biopolymer decomposition has not been fully appreciated.Dedicated to Professor Norbert Pfennig, in whose laboratory this project was initiated and who recently retired after more than four decades of contributions to microbiology     

Characterization of Halanaerobaculum tunisiense gen. nov., sp. nov., a new halophilic fermentative, strictly anaerobic bacterium isolated from a hypersaline lake in Tunisia

A new halophilic anaerobe was isolated from the hypersaline surface sediments of El-Djerid Chott, Tunisia. The isolate, designated as strain 6SANG, grew at NaCl concentrations ranging from 14 to 30%, with an optimum at 20–22%. Strain 6SANG was a non-spore-forming, non-motile, rod-shaped bacterium, appearing singly, in pairs, or occasionally as long chains (0.7–1 × 4–13 μm) and showed a Gram-negative-like cell wall pattern. It grew optimally at pH values between 7.2 and 7.4, but had a very broad pH range for growth (5.9–8.4). Optimum temperature for growth was 42°C (range 30–50°C). Strain 6SANG required yeast extract for growth on sugars. Glucose, sucrose, galactose, mannose, maltose, cellobiose, pyruvate, and starch were fermented. The end products from glucose fermentation were acetate, butyrate, lactate, H₂, and CO₂. The G + C ratio of the DNA was 34.3 mol%. Strain 6SANG exhibited 16S rRNA gene sequence similarity values of 91–92% with members of the genus Halobacteroides, H. halobius being its closest phylogenetic relative. Based on phenotypic and phylogenetic characteristics, we propose that this bacterium be classified as a novel species of a novel genus, Halanaerobaculum tunisiense gen. nov., sp. nov. The type strain is 6SANG^T (=DSM 19997^T = JCM 15060^T).     

Ilyobacter delafieldii sp. nov., a metabolically restricted anaerobic bacterium fermenting PHB

Enrichments from an estuarine sediment with crotonate as substrate resulted in the isolation of a motile, gram-negative, obligately anaerobic rod with pointed ends, designated strain 10cr1. The organism was asporogenous, did not reduce sulfur, sulfate, thiosulfate, nitrate, oxygen or fumarate, and had a mol %G+C ratio of 29. Strain 10cr1 was able to ferment crotonate, 3-hydroxybutyrate, lactate, pyruvate, and poly--hydroxybutyric acid (PHB). Acetate, propionate, butyrate, CO₂ and H₂ were the fermentation products. When grown on PHB there was accumulation of 3-hydroxybutyrate once growth had ceased, indicating degradation of PHB to the monomer. The 3-hydroxybutyrate formed during growth of the culture was fermented to acetate, butyrate and H₂. Experimental evidence suggested the production of an extracellular PHB depolymerase. The cells were not attached to the PHB granules. This is the first isolation of an anaerobic bacterium capable of degrading exogenous PHB. This strain is described as a new species, Ilyobacter delafieldii sp. nov., and strain 10cr1 (=DSM 5704) is designated as the type (and at present, only) strain.Abbreviations G+C guanine plus cytosine - OD optical density - PHB poly--hydroxybutyric acid - specific growth rate - HPLC high-performance liquid chromatography - YE yeast extract     

Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol-degrading bacterium isolated from seawater

A novel aerobic, Gram-negative bacterial strain, designated KU41E(T), which degrades p-n-nonylphenol, was isolated from seawater obtained from the coastal region of Ishigaki Island, Japan. Cells are motile, curved rods with a single polar flagellum. Strain KU41E(T) grew at 20-35 °C, pH 7.0-8.0, in the presence of 1.0-4.0% NaCl. The predominant respiratory lipoquinone was ubiquinone-8, and the major cellular fatty acids were summed feature 3 (C(15:0) iso 2OH and/or C(16:1) ω7c, 28.4%), C(18:1) ω7c (19.8%), and C(16:0) (17.0%). The DNA G + C content was 48.6 mol%. The 16S rRNA gene sequence analysis indicated that strain KU41E(T) is affiliated with the order Alteromonadales within the class Gammaproteobacteria and is most closely related to Pseudoteredinibacter isoporae SW-11(T) (93.6% similarity) and Teredinibacter turnerae T7902(T) (91.9% similarity). On the basis of physiological, chemotaxonomic, and phylogenetic data, strain KU41E(T) is suggested to represent a novel species of a new genus, for which the name Maricurvus nonylphenolicus gen. nov., sp. nov. is proposed. The type strain of M. nonylphenolicus is KU41E(T) (=JCM 17778(T)).     

Pigmentiphaga soli sp. nov., a bacterium isolated from soil

Strain BS12^T, a Gram-negative motile bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the family Alcaligenaceae in the class Betaproteobacteria. The highest degree of sequence similarities of strain BS12^T were found with Pigmentiphaga litoralis JSM 061001^T (98.3%), Pigmentiphaga daeguensis K110^T (98.2%), and Pigmentiphaga kullae K24^T (98.1%). Chemotaxonomic data revealed that strain BS12^T possessed ubiquinone-8, which is common in the family Alcaligenaceae, and the predominant fatty acids were C_16:0, C_17:0 cyclo, summed feature 3 (C_16:1 ω6c/ω7c), and summed feature 8 (C_18:1 ω6c/ω7c). The major polar lipids of strain BS12^T were phosphatidylethanolamine and phosphatidylglycerol. Based on these data, BS12^T (=KCTC 23577^T =JCM 17666^T =KEMB 9004-082^T) should be classified as a type strain of a novel species, for which the name Pigmentiphaga soli sp. nov. is proposed.