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     

Cetobacterium ceti gen. nov., sp. nov., a new Gram-negative obligate anaerobe from sea mammals

Phenotypic and phylogenetic studies were performed on a Gram-negative obligately anaerobic rod-shaped bacterium isolated from two sea mammals. 16S rRNA gene sequence analysis demonstrated the bacterium represents a hitherto unknown line of descent peripherally associated to the fusobacteria and low G + C relatives. Based on the result of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium should be assigned to a new genus, Cetobacterium ceti gen. nov., sp. nov. The type strain of Cetobacterium ceti sp. nov. is NCFB 3026.     

Propionispora vibrioides, nov. gen., nov. sp., a new gram-negative, spore-forming anaerobe that ferments sugar alcohols

Anaerobic enrichment cultures, with erythritol as substrate, resulted in the isolation of a strain with properties not yet found in an existing genus in this combination. The strain, FKBS1, was strictly anaerobic, stained gram-negative and formed spores. Cells were small motile vibrios with flagella inserted at the concave side of the cell. Spores were located terminally and caused only slight swelling of the cells if compared to related spore-forming genera. FKBS1 fermented fructose, mannitol, sorbitol, xylitol and erythritol to propionic acid, acetic acid, CO2 and small amounts of H2 to balance the difference in the oxidation-reduction value between substrate and cell mass. The 16S rDNA sequence revealed relationship to the Sporomusa-Pectinatus-Selenomonas group. However, the phylogenetic distance to any of its members was too great to allow it to be placed in one of the existing genera. Morphologically the strain resembled Sporomusa, which, however, performs an acetogenic type of fermentation. The propionic-acid-forming genera of the group are either not spore-formers or, in the case of Dendrosporobacter quercicolus (syn. Clostridium quercicolum), morphologically different. It is therefore proposed to classify strain FKBS1 as a new genus and species, Propionispora vibrioides.     

Slostridium homopropionicum sp. nov., a new strict anaerobe growing with 2-, 3-, or 4-hydroxybutyrate

From anoxic sewage sludge a new strictly anaerobic, spore-forming bacterium was isolated with 2-hydroxybutyrate as sole substrate. 2-, 3-, and 4-hydroxybutyrate, 4-chlorobutyrate, crotonate, vinylacetate, and pyruvate were fermented to acetate and butyrate. Fructose was converted to acetate, butyrate, butanol, and H₂. Lactate and acrylate were fermented to acetate and propionate. Cells pregrown with lactate fermented 2-hydroxybutyrate to butyrate, propionate and acetate. No inorganic electron acceptors were reduced. The DNA base ratio was 32.0±1.0 mol % and was similar to that of Clostridium propionicum, which was determined to be 35.3±0.5 mol %. Strain LuHBu1 is described as type strain of a new species, Clostridium homopropionicum sp. nov. Another isolate obtained from marine sediment degraded 2-and 3-hydroxybutyrate to acetate and butyrate and was in some respects similar to the known species Ilyobacter polytropus.     

Ultrastructural description of a new chytrid genus of caecum anaerobe, Caecomyces equi gen. nov., sp. nov., assigned to the Neocallimasticaceae

Vegetative and reproductive stages of Caecomyces equi gen. nov., sp. nov. isolated from the horse caecum were examined by light and electron microscopy. This organism, which is similar to isolates known as Sphaeromonas communis, produces uniflagellate, uninucleate zoospores whose perikinetosomal structures, i.e. circumflagellar ring, spur, struts and scoop, are similar in many respects to those described in species of Neocallimastix. Microtubular roots extend basally from the spur and associate with hydrogenosomes and the nucleus. Another group of microtubules radiates laterally in a fan-shaped array close to the plasmalemma. Zoospores encyst, shedding their flagella with basal bodies, and germinate to diglobular thalli. Either coralloid or bulbous rhizoids form in plant material, but only the latter in axenic culture. Incipient zoospores are produced from a multinucleate eucarpic thallus and devlop within cleavage vacuoles containing flagella. An isolate from the cow rumen was found to be similar to C. equi in morphology and zoospore ultrastructure. On the basis of zoospore ultrastructure, we assign the new genus to the Neocallimasticaceae of the order Spizellomycetales. Organisms previously described as Sphaeromonas communis and Piromonas communis are renamed Caecomyces communis and Piromyces communis and assigned to the same family.     

Selenihalanaerobacter shriftii gen. nov., sp. nov., a halophilic anaerobe from Dead Sea sediments that respires selenate

We isolated an obligately anaerobic halophilic bacterium from the Dead Sea that grew by respiration of selenate. The isolate, designated strain DSSe-1, was a gram-negative, non-motile rod. It oxidized glycerol or glucose to acetate + CO2 with concomitant reduction of selenate to selenite plus elemental selenium. Other electron acceptors that supported anaerobic growth on glycerol were nitrate and trimethylamine-N-oxide; nitrite, arsenate, fumarate, dimethylsulfoxide, thiosulfate, elemental sulfur, sulfite or sulfate could not serve as electron acceptors. Growth on glycerol in the presence of nitrate occurred over a salinity range from 100 to 240 g/l, with an optimum at 210 g/l. Analysis of the 16S rRNA gene sequence suggests that strain DSSe-1 belongs to the order Halanaerobiales, an order of halophilic anaerobes with a fermentative or homoacetogenic metabolism, in which anaerobic respiratory metabolism has never been documented. The highest 16S rRNA sequence similarity (90%) was found with Acetohalobium arabaticum (X89077). On the basis of physiological properties as well as the relatively low homology of 16S rRNA from strain DSSe-1 with known genera, classification in a new genus within the order Halanaerobiales, family Halobacteroidaceae is warranted. We propose the name Selenihalanaerobacter shriftii. Type strain is strain DSSe-1 (ATCC accession number BAA-73).     

Paraliobacillus ryukyuensis gen. nov., sp. nov., a new Gram-positive,slightly halophilic,extremely halotolerant,facultative anaerobe isolated from a decomposing marine alga

A slightly halophilic, extremely halotolerant, alkaliphilic, and facultatively anaerobic rod bacterium was isolated from a decomposing marine alga collected in Okinawa, Japan. The isolate, designated O15-7(T), was Gram-positive, endospore-forming, catalase-positive, menaquinone-7-possessing bacterium that is motile by peritrichous flagella. The isolate was an inhabitant of marine environments; the optimum NaCl concentration for growth was 0.75-3.0% (w/v) with a range of 0-22.0%, and the optimum pH was 7.0-8.5 with a range of 5.5-9.5. Catalase was produced in aerobic cultivation but not in anaerobic cultivation. Carbohydrate, sugar alcohol or a related carbon compound was required for growth. In aerobic cultivation, the isolate produced pyruvate, acetate and CO(2) from glucose, and in anaerobic cultivation, it produced lactate, formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1 for the last three products. No gas was produced anaerobically. Lactate yield per consumed glucose was markedly affected by the pH of the fermentation medium: 51% at pH 6.5 and 8% at pH 9.0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Phylogenetically, the isolate occupied an independent lineage within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1 with the highest 16S rRNA gene sequence similarity of 95.2% to the genus Gracilibacillus. For this isolate, Paraliobacillus ryukyuensis gen. nov., sp. nov. was proposed. The type strain, O15-7(T) (G+C535.6 mol%), has been deposited in the DSMZ, IAM, NBRC, and NRIC (DSM 15140(T)=IAM 15001(T)=NBRC 10001(T)=NRIC 0520(T)).     

Alkalobacter lublini gen. nov., sp. nov.

On the basis of phenotypic properties and G+C content of DNA, as well as competitive DNA-DNA hybridization and extracellular polymeric substance analysis it was shown that this strain was completely different from all other alkaliphilic bacteria. We hereby propose that this strain be designatedAlkalobacter lublini gen. nov., sp. nov.     

Blastobotrys nivea gen.nov., sp.nov.

Ohne Zusammenfassung     

A new fungus,Aureomyces mirabilis gen. et sp. nov., from pine-timber

Aureomyces gen. nov. with the type speciesAureomyces mirabilis sp. nov. isolated from a pine-timber,Pinus silvestris, in Finland is described and illustrated.

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Zusammenfassung Aureomyces gen. nov. wurde mit dem ArttypeAureomyces mirabilis sp. nov. vom Kiefernholz,Pinus sylvestris, in Finnland isoliert. Der Pilz ist beschrieben und illustriert.

     

Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.

On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).     

Perlabentimonas gracilis gen. nov., sp. nov., a gliding aerotolerant anaerobe of the order Bacteroidales,isolated from a terrestrial mud volcano

A novel anaerobic bacterium (strain M08_MB^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Gram-stain-negative cells were straight and slender rods with gliding motility, occasionally forming long filaments. The isolate was mesophilic, slightly halo- and alkaliphilic chemoorganoheterotroph, growing on carbohydrates (starch, dextrin, pectin, glucose, fructose, mannose, maltose, trehalose, lactose, sucrose) and proteinaceous compounds (peptone, tryptone, gelatin, casein and albumin). Strain M08_MB^T tolerated 3% oxygen in the gas phase while catalase negative. The dominant cellular fatty acids of strain M08_MB^T were C_15:0, C_15:1 and C_13:0 acids. 16S rRNA gene sequence analysis revealed that strain M08_MB^T belongs to the order Bacteroidales and only distantly related to other cultivated members of this order (85.12–90.01% 16S rRNA gene similarity). The genome of strain M08_MB^T had a size of 4.37 Mb with a DNA G + C content of 43.5 mol% (WGS). The genes involved in gliding motility, proteolysis, central carbon metabolism, and oxygen tolerance were listed in genome annotation. Based on the phenotypic and genotypic characteristics, strain M08_MB^T represents a novel species of a novel genus within family Tenuifilaceae, with proposed name Perlabentimonas gracilis gen. nov., sp. nov. The type strain is M08_ MB^T (=DSM 110720 ^T = VKM B-3471 ^T). This is the first representative of Bacteroidales isolated in pure culture from a mud volcano.     

Holophaga foetida gen. nov., sp. nov., a new,homoacetogenic bacterium degrading methoxylated aromatic compounds

A polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. Based on these results, the name Holophaga foetida gen. nov., sp. nov. is proposed. This microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. The only other compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol. The aromatic compounds were degraded to acetate. Although comparison of the signature nucleotide pattern of the five established subclasses of Proteobacteria with the 16S rDNA sequence of Holophaga foetida revealed a relationship to members of the -subclass, the phylogenetic position within the radiation of this class is so deep and dependent upon the number and selection of reference sequences that its affiliation to the Proteobacteria must be considered tentative. The type strain is H. foetida strain TMBS4 (DSM 6591).F. Bak died on 27 December 1992. A very promising and productive career thus ended much too early     

Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. Belong to the Family Microbacteriaceae

Two bacterial strains, KIS66-7^T and 5GH26-15^T, were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7^T had the highest similarities with those of Labedella gwakjiensis KSW2-17^T (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb^T (97.2%), Leifsonia naganoensis JCM 10592^T (97.0%), and Cryobacterium mesophilum MSL-15^T (97.0%). Strain 5GH26-15^T showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7^T exhibited 96.4% similarity with that from 5GH26-15^T. Strain KIS66-7^T contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C_15:0, ai-C_17:0, and i-C_16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C_15:0, i-C_16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7^T and 5GH26-15^T represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7^T=KACC 15515^T=NBRC 108724^T) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15^T=KACC 15524^T=NBRC 108755^T) within the family Microbacteriaceae.     

Wangella harbinensis gen. nov., sp. nov., a new member of the family Micromonosporaceae

A novel endophytic actinomycete, designated strain NEAU-J3^T, was isolated from soybean root (Glycine max (L.) Merr) and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain NEAU-J3^T fell within the family Micromonosporaceae. The strain was observed to form an extensively branched substrate mycelium, which carried non-motile oval spores with a smooth surface. The cell walls of strain NEAU-J3^T were determined to contain meso-diaminopimelic acid and galactose, ribose and glucose were detected as whole-cell sugars. The major menaquinones were determined to be MK-9(H₄) and MK-9(H₆). The phospholipids detected were phosphatidylcholine and phosphatidylethanolamine. The major cellular fatty acids were determined to be C_16:0, C_18:1 ω9c, C_18:0, C_17:0, C_17:1 ω7c, anteiso-C_17:0, C_16:1 ω7c and C_15:0. The DNA G + C content was 62.5 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J3^T is considered to represent a novel species of a new genus within the family Micromonosporaceae, for which the name Wangella harbinensis gen. nov., sp. nov. is proposed. The type strain of Wangella harbinensis is strain NEAU-J3^T (=CGMCC 4.7039^T = DSM 45747^T).     

Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture

Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3^T and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3^T and D11-58, and D1-19^T on two distinct branches within the alpha-3 proteobacterial Rhodobacteraceae, affiliated with, but clearly separate from, the genera Rhodobacter, Rhodovulum, and Rhodobaca. Based on morphological, physiological, and 16S rRNA-based phylogenetic characteristics, the isolated strains are proposed as new species of two novel genera, Defluviimonas denitrificans gen. nov., sp. nov. (type strain D9-3^T = DSM 18921^T = ATCC BAA-1447^T; additional strain D11-58 = DSM19039 = ATCC BAA-1448) and Pararhodobacter aggregans gen. nov., sp. nov (type strain D1-19^T = DSM 18938^T = ATCC BAA-1446^T).     

Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic,acetate-utilising,butyrate-producing bacterium from human faeces

Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two isolates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrated the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new subline within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic criteria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T).     

Kaistia adipata gen. nov., sp. nov., a novel alpha-proteobacterium

A taxonomic study was carried out on Chj404T, a bacterial strain isolated from a soil sample collected in an industrial stream near the Chung-Ju industrial complex in Korea. The strain was a gram-negative, aerobic, short rod to coccus-shaped bacterium. It grew well on nutrient agar medium and utilized a broad spectrum of carbon sources. The G+C content of the DNA was 67.4 mol% and the major composition of ubiquinone was Q-10. The major fatty acid was C18:1. Comparative 16S rDNA studies showed a clear affiliation of this bacterium to alpha-Proteobacteria. Comparison of phylogenetic data indicated that it was most closely related to Prosthecomicrobium pneumaticum (92.7% similarity in 16S rDNA sequence). Since strain Chj404 is clearly distinct from closely related species, we propose the name Kaistia adipata gen. nov., sp. nov. for this strain Chj404T (=IAM 15023T=KCTC 12095T).