- Volume 54, Issue 1, 2004

Five hydrogen-oxidizing, thermophilic, strictly chemolithoautotrophic, microaerophilic strains, with similar (99–100 %) 16S rRNA gene sequences were isolated from terrestrial hot springs at Furnas, São Miguel Island, Azores, Portugal. The strain, designated Az-Fu1T, was characterized. The motile, 0·9–2·0 μm rods were Gram-negative and non-sporulating. The temperature growth range was from 50 to 73 °C (optimum at 68 °C). The strains grew fastest in 0·1 % (w/v) NaCl and at pH 6, although growth was observed from pH 5·5 to 7·0. Az-Fu1T can use elemental sulfur, sulfite, thiosulfate, ferrous iron or hydrogen as electron donors, and oxygen (0·2–9·0 %, v/v) as electron acceptor. Az-Fu1T is also able to grow anaerobically, with elemental sulfur, arsenate and ferric iron as electron acceptors. The Az-Fu1T G+C content was 33·6 mol%. Maximum-likelihood analysis of the 16S rRNA phylogeny placed the isolate in a distinct lineage within the Aquificales, closely related to Sulfurihydrogenibium subterraneum (2·0 % distant). The 16S rRNA gene of Az-Fu1T is 7·7 % different from that of Persephonella marina and 6·8 % different from Hydrogenothermus marinus. Based on the phenotypic and phylogenetic characteristics presented here, it is proposed that Az-Fu1T belongs to the recently described genus Sulfurihydrogenibium. It is further proposed that Az-Fu1T represents a new species, Sulfurihydrogenibium azorense.

Two bacterial isolates from the Baltic Sea, BA1 and BA134T, were characterized for their physiological and biochemical features, fatty acid profiles and phylogenetic position based on 16S rRNA gene sequences. The strains were isolated from surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation to the family ‘Flexibacteriaceae’ and showed highest sequence similarity (91 %) to Cyclobacterium marinum. The G+C content of the DNA was 35·4 mol%. The strains were pink-coloured due to carotinoids, Gram-negative, rod-shaped and catalase- and oxidase-positive. Growth was observed at 0–6 % salinity, with good growth at 0–3 %. Temperature for growth was 4–37 °C, with an optimum around 25 °C. The fatty acid profiles were dominated by branched-chain fatty acids (70 %), with a high abundance of iso-C15 : 0 (29–33 %), iso-C17 : 1 ω9c (7–10 %) and C17 : 1 ω6c (5–10 %). According to their morphology, physiology, fatty acid composition, 16S rRNA gene sequences and DNA–DNA similarity, on one hand, the described bacteria are considered to be members of the same novel species; on the other hand, they are suggested as a novel genus of the family ‘Flexibacteriaceae’. To honour the late aquatic microbiologist Russell T. Bell, the name Belliella baltica gen. nov, sp. nov. is suggested for the Baltic Sea isolates, for which the type strain is BA134T (=DSM 15883T=LMG 21964T=CIP 108006T).

Taxonomic studies were performed on 36 strains that were isolated from microbial mats in Antarctic lakes of the Vestfold Hills, the Larsemann Hills and the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to members of the genus Flavobacterium; sequence similarity values with their nearest phylogenetic neighbours ranged from 96·8 to 98·5 %. Results of DNA–DNA hybridization and comparison of repetitive extragenic palindromic DNA-PCR fingerprinting patterns revealed that these strains are members of three distinct species. Genotypic results, together with phenotypic characteristics, allowed the differentiation of these species from related Flavobacterium species with validly published names. The isolates are Gram-negative, chemoheterotrophic, rod-shaped cells that are psychrophilic and moderately halotolerant; their DNA G+C contents range from 33·1 to 34·5 mol%. Their whole-cell fatty acid profiles are similar and include C15 : 0, anteiso-C15 : 0, iso-C15 : 0, C15 : 1 ω6c, iso-C16 : 0, iso-C16 : 0 3-OH and summed feature 3 (which comprises iso-C15 : 0 2-OH, C16 : 1 ω7c or both) as major fatty acid components. On the basis of these results, three novel species are proposed, namely Flavobacterium degerlachei sp. nov. (consisting of 14 strains, with LMG 21915T=DSM 15718T as the type strain), Flavobacterium micromati sp. nov. (consisting of three strains, with LMG 21919T=CIP 108161T as the type strain) and Flavobacterium frigoris sp. nov. (consisting of 19 strains, with LMG 21922T=DSM 15719T as the type strain).

Two heterotrophic, aerobic, Gram-negative, pigmented and non-motile marine bacteria that were isolated from the green alga Ulva fenestrata were studied by polyphasic taxonomic methods. 16S rDNA sequence analysis indicated that strain KMM 3912T formed a distinct lineage within the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacteria were classified as Ulvibacter litoralis gen. nov., sp. nov. The type strain is KMM 3912T (=KCTC 12104T=CCUG 47093T).

Three marine strains of the Cytophaga–Flavobacterium–Bacteroides group, designated JC2050T, JC2051T and JC2052T, were obtained from a single sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were not closely related to any validly published genera and that these strains were only distantly related to the genus Cyclobacterium (88·7–91·2 %). Phylogenetic analyses demonstrated that the three getbol isolates formed a distinct monophyletic clade within the family Cytophagaceae. Physiological, biochemical and chemotaxonomic data also indicated that these three getbol isolates differed significantly from members of other genera and were sufficiently different from each other to be recognized as separate species. On the basis of polyphasic evidence, a new genus, Hongiella gen. nov., is proposed, with three novel species, Hongiella mannitolivorans sp. nov. (type strain JC2050T=IMSNU 14012T=DSM 15301T), Hongiella halophila sp. nov. (type strain JC2051T=IMSNU 14013T=DSM 15292T) and Hongiella ornithinivorans sp. nov. (type strain JC2052T=IMSNU 14014T=DSM 15282T). Hongiella mannitolivorans is the type species of the genus.

A novel anaerobic, thermophilic, xylanolytic, motile rod-shaped bacterium with a sheath-like outer structure (toga) was isolated from a Mexican oil well in the Gulf of Mexico. Strain MET12T was a Gram-negative bacterium, reducing elemental sulfur, thiosulfate and sulfite to hydrogen sulfide. Its optimum growth conditions were 55 °C, pH 6·6, 3 % NaCl and 0·15 % MgCl2.6H2O. The DNA G+C content was 36·1 mol%. Phylogenetically, strain MET12T was related to members of genus Petrotoga, with similarities to Petrotoga mobilis, Petrotoga sibirica, Petrotoga miotherma and Petrotoga olearia varying from 97·6 to 98·8 %. However DNA–DNA relatedness values between these species and strain MET12T were lower than 70 %. As strain MET12T (=DSM 14811T=CIP 107371T) was genomically and phenotypically different from existing Petrotoga species, it is proposed as the type strain of a novel species, Petrotoga mexicana sp. nov.

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55–80 °C, with an optimum at 70 °C. The NaCl concentration range for growth was 10–35 g l−1, with an optimum at 25 g l−1. The pH range for growth was 6–6·7, with an optimum at approximately pH 6·25. H2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812T were similar to those of Thermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesulfobacteriaceae (similarity values of less than 90 %). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812T could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T (46·0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812T represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812T (=DSM 15286T=JCM 11887T).

A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 °C (optimum temperature, 55 °C; 70 min doubling time) and between pH 4·9 and 7·2 (optimum, pH 5·9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated ε-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

A novel moderately thermophilic, microaerobic to anaerobic, chemolithoautotrophic bacterium, designated strain CRT, was isolated from a deep-sea hydrothermal vent site at 36°N on the Mid-Atlantic Ridge. Cells were Gram-negative, non-motile rods. The organism grew at 45–65 °C and pH 6·5–7·4, with optimum growth at 55 °C and pH 6·9–7·1. The NaCl range for growth was 5–50 g l−1 (optimum 30 g l−1). Strain CRT was an obligate chemolithoautotroph, growing with H2 as energy source, sulfur, nitrate or oxygen as electron acceptors and CO2 as carbon source. Hydrogen sulfide and ammonium were the respective products of sulfur and nitrate reduction. The G+C content of the genomic DNA was 32·1 mol%. Based on 16S rRNA gene sequence analysis, this organism was most closely related to Caminibacter hydrogeniphilus (94·9 % similarity). On the basis of phenotypic and phylogenetic data, it is proposed that the isolate represents a novel species, Caminibacter profundus sp. nov. The type strain is CRT (=DSM 15016T=JCM 11957T). The phylogenetic data also correlate well with the significant phenotypic differences between the lineage encompassing the genera Nautilia and Caminibacter and other members of the class ‘Epsilonproteobacteria’. The lineage encompassing the genera Nautilia and Caminibacter is therefore proposed as a new order, Nautiliales ord. nov., represented by a single family, Nautiliaceae fam. nov.

A novel marine sulfate-reducing bacterium, strain CV2803T, which is able to oxidize aliphatic hydrocarbons, was isolated from a hydrocarbon-polluted marine sediment (Gulf of Fos, France). The cells were rod-shaped and slightly curved, measuring 0·6×2·2–5·5 μm. Strain CV2803T stained Gram-negative and was non-motile and non-spore-forming. Optimum growth occurred in the presence of 24 g NaCl l−1, at pH 7·5 and at a temperature between 28 and 35 °C. Strain CV2803T oxidized alkanes (from C13 to C18) and alkenes (from C7 to C23). The DNA G+C content was 41·4 mol%. Comparative sequence analyses of the 16S rRNA gene and dissimilatory sulfite reductase (dsrAB) gene and those of other sulfate-reducing bacteria, together with its phenotypic properties, indicated that strain CV2803T was a member of a distinct cluster that contained unnamed species. Therefore, strain CV2803T (=DSM 15576T=ATCC BAA-743T) is proposed as the type strain of a novel species in a new genus, Desulfatibacillum aliphaticivorans gen. nov., sp. nov.

Strain CJ2T, capable of growth on naphthalene as a sole carbon and energy source, was isolated from coal-tar-contaminated freshwater sediment. The Gram reaction of strain CJ2T was negative. The cells were non-spore-forming, non-motile cocci (without flagella). The isolate was found to be an aerobic heterotroph capable of utilizing glucose and other simple sugars. Growth was observed between 4 and 25 °C (optimum, 20 °C) and between pH 6·0 and 9·0 (optimum, pH 7·0–7·5). The G+C content of the genomic DNA was 61·5 mol% and the major quinone was ubiquinone-8. The peptidoglycan of strain CJ2T was determined as belonging to type A1-γ, meso-diaminopimelic acid. The major fatty acids of strain CJ2T were 16 : 1ω7c (67·0 %), 16 : 0 (19·6 %), 18 : 1ω7c (∼7·9 %) and 10 : 0 3-OH (∼2·5 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Mycolic acid and glycolipids could not be detected. Comparative 16S rDNA analysis indicated that strain CJ2T is related to the family Comamonadaceae and that the nearest phylogenetic relative was Polaromonas vacuolata 34-PT (97·1 % similarity). On the basis of the physiological and molecular properties, the naphthalene-degrading isolate was designated Polaromonas naphthalenivorans sp. nov. The type strain is CJ2T (=ATCC BAA-779T=DSM 15660T).

Strain K11T was isolated from activated sludge of a municipal wastewater-treatment plant. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it represents a distinct line of descent within the Comamonadaceae. The novel strain was a Gram-negative, catalase- and oxidase-positive, non-motile, straight to slightly curved rod. Polyhydroxyalkanoate granules were stored intracellularly as reserve material. Colonies on agar plates were small, regular and characterized by a water-insoluble yellow pigment. Unbranched fatty acids 16 : 1ω7c, 16 : 0 and 18 : 1ω7c dominated the cellular fatty acid pattern and ubiquinone-8 (Q-8) was the major component of the respiratory lipoquinones, both traits typical of members of the Comamonadaceae. A distinguishing characteristic was the presence of the two hydroxy fatty acids 10 : 0 3-OH and 12 : 0 2-OH, each in significant amounts. The G+C content of the DNA was 59 mol%. Strain K11T was capable of aerobic chemolithoheterotrophic growth using thiosulfate as an additional substrate, but could not grow autotrophically with thiosulfate or hydrogen. Facultative anaerobic growth was possible with nitrate and nitrite as electron acceptors, but not with ferric iron, sulfate or by fermentation. The sole end product of denitrification was N2O; nitrite accumulated only transiently in small amounts. Based upon phylogenetic and phenotypic evidence, it is proposed to establish the novel taxon Ottowia thiooxydans gen. nov., sp. nov., represented by the type strain K11T (=DSM 14619T=JCM 11629T). Aquaspirillum gracile was among the phylogenetically most closely related species to strain K11T. This species has been wrongly classified, and it is proposed to reclassify it as Hylemonella gracilis gen. nov., comb. nov. The type strain is ATCC 19624T (=DSM 9158T).

Bacterial canker of papaya (Carica papaya) emerged during the 1980s in different islands of the Caribbean. Nineteen strains of Gram-negative, rod-shaped, non-spore-forming bacteria isolated from papaya were compared to 38 reference and type strains of phytopathogenic Enterobacteriaceae and related bacteria. Phylogenetic analysis of 16S rRNA gene sequences showed that the papaya strains belonged to the genus Erwinia. The DNA G+C content of strain CFBP 5189T, 52·5 mol%, is in the range of the genus Erwinia. The 19 papaya strains were all pathogenic to papaya and were differentiated clearly from type or reference strains of phytopathogenic enterobacteria and related bacteria by phenotypic tests. The papaya strains constituted a discrete DNA hybridization group, indicating that they belonged to a unique genomic species. Thus, strains pathogenic to papaya belong to a novel species for which the name Erwinia papayae sp. nov. is proposed, with the type strain CFBP 5189T (=NCPPB 4294T).

An aerobic, heterotrophic, Gram-negative, curved bacterial strain, designated MIL-1T, was isolated by extinction dilution from an n-tetradecane enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Italy. In the primary enrichment, the isolate formed creamy-white, medium-sized colonies on the surface of the agar. The isolate did not grow in the absence of NaCl; growth was optimal at 2·7 % NaCl. Only a narrow spectrum of organic compounds, including aliphatic hydrocarbons (C7–C20), their oxidized derivatives and acetate, were used as growth substrates. The isolate was not able to grow under denitrifying conditions. The DNA G+C content and genome size of strain MIL-1T were estimated to be 53·2 mol% and 2·2 Mbp, respectively. The major cellular and phospholipid fatty acids were palmitoleic, palmitic and oleic acids (33·5, 29·5 and 11·0 % and 18, 32 and 31 %, respectively). 3-Hydroxy lauric acid was the only hydroxy fatty acid detected. Thirteen different compounds that belonged to two types of phospholipid (phosphatidylethylamine and phosphatidylglycerol) were identified. 16S rRNA gene sequence analysis revealed that this isolate represents a distinct phyletic lineage within the γ-Proteobacteria and has about 94·4 % sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80 % similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans.

In conformity with the nomenclature of the genus Rhizobium published by Young et al. (Int J Syst Evol Microbiol 51, 89–103, 2001 ), it is proposed that Agrobacterium larrymoorei be named as Rhizobium larrymoorei comb. nov.

A novel species, Methylocella tundrae, is proposed for three methanotrophic strains (T4T, TCh1 and TY1) isolated from acidic Sphagnum tundra peatlands. These strains are aerobic, Gram-negative, non-motile, dinitrogen-fixing rods that possess a soluble methane monooxygenase and utilize the serine pathway for carbon assimilation. Strains T4T, TCh1 and TY1 are moderately acidophilic organisms capable of growth between pH 4·2 and 7·5 (optimum 5·5–6·0) and between 5 and 30 °C (optimum 15 °C). The major phospholipid fatty acid is 18 : 1ω7c. The DNA G+C content of strain T4T is 63·3 mol%. The three strains possess almost identical 16S rRNA gene sequences and are most closely related to two previously identified species of Methylocella, Methylocella palustris (97 % similarity) and Methylocella silvestris (97·5 % similarity). DNA–DNA hybridization values of strain T4T with Methylocella palustris KT and Methylocella silvestris BL2T were respectively 27 and 36 %. Thus, the tundra strains represent a novel species, for which the name Methylocella tundrae sp. nov. is proposed. Strain T4T (=DSM 15673T=NCIMB 13949T) is the type strain.