16S rRNA Gene Sequence Identity Research Articles

Multilocus sequence analysis of Streptomyces griseus isolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential

Systematics can provide a fundamental framework for understanding the relationships and diversification of organisms. Multilocus sequence analysis (MLSA) has shown great promise for an elaborate taxonomic grouping of streptomycete diversity. To evaluate the practical significance of MLSA as a valuable systematic tool for streptomycetes, we examined six endophytic Streptomyces griseus isolates and two S. griseus reference strains possessing obvious antagonistic activities and identical 16S rRNA gene sequences, using both housekeeping genes and secondary metabolic genes. All the eight strains contained PKS-I and NRPS genes, but not PKS-II genes, and showed similar diversity in both the MLSA phylogeny based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) and fingerprinting of KS-AT genes. We also inferred a phylogeny based on concatenated amino acid sequences of representative KS-AT genes from the strains, which displayed a topology correlated well with those of housekeeping-gene MLSA and KS-AT fingerprinting. The good congruence observed between phylogenies based on the different datasets verified that the MLSA scheme provided robust resolution at intraspecific level and could predict the overall diversity of secondary metabolic potential within a Streptomyces species, despite somewhat of a discrepancy with antimicrobial data. It is therefore feasible to apply MLSA to dissecting natural diversity of streptomycetes for a better understanding of their evolution and ecology, as well as for facilitating their bioprospecting.

Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots

Facultatively anaerobic bacterial strains (A48(T), RR25 and RR54) were isolated from roots of living rice plants in an irrigated rice-field in Japan. The three strains had identical 16S rRNA gene sequences and showed almost the same phenotypic properties examined. Cells of the strains were Gram-negative, non-spore-forming rods. Reproduction of cells was by binary fission as well as by budding. Cells occurred singly or in pairs arranged angularly. Some cells, including dividing cells, were motile with a single polar flagellum. Cells developed a polar prostheca (stalk) with a holdfast-like structure and the cell with the stalk budded a daughter cell. The strains were chemoorganotrophs and utilized various sugars as growth substrates. The strains fermentatively produced acetate and lactate as well as small amounts of ethanol and H(2) from the substrates. Growth temperature and pH ranges for growth were 15-40 degrees C and pH 5.5-7.3 with optimum growth at 30-35 degrees C and pH 6.8. NaCl concentration range for growth was 0-1.0% (wt/vol) with an optimum at 0% (wt/vol). Catalase and oxidase activities were not detected. The strains reduced Fe(III) to Fe(II) in the presence of glucose, while they did not reduce nitrate, fumarate, malate or sulfate. The major cellular fatty acids of the strains were C18:1omega7, anteiso-C15:0, iso-C15:0, C16:0 and C18:0. Ubiquinone Q-10 was the major respiratory quinone and the genomic DNA G + C contents were 53.4-55.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains in the class Alphaproteobacteria and the strains formed a novel deep branch in the phylogenetic trees constructed. Based on the differences in 16S rRNA gene sequences and phenotypic properties of the novel strains from those of their relatives, we proposed that the strains be assigned in the novel genus and species as Rhizomicrobium palustre gen. nov., sp. nov. The type strain of the novel species is strain A48(T) (= JCM 14971(T) = DSM 19867(T)).

Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36(T) and Mesorhizobium temperatum SDW018(T) were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA-DNA relatedness values between the representative strain, CCNWYC 115(T), and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115(T) (=ACCC 14543(T) =HAMBI 3082(T)). Strain CCNWYC 115(T) can form effective nodules only on its original host.

Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia)

Twenty-one homofermentative lactic acid bacteria were isolated from fermented cummingcordia (pobuzihi), a traditional food in Taiwan. The isolates had identical 16S rRNA gene sequences that were distinct from those of other lactobacilli, and their closest neighbours in the 16S rRNA gene sequence phylogenetic tree were strains of Lactobacillus acidipiscis. Levels of DNA-DNA relatedness between representative pobuzihi isolates and strains of L. acidipiscis were 17% and below. Furthermore, the new isolates could be differentiated clearly from L. acidipiscis NBRC 102163T and NBRC 102164 in terms of acid production from L-arabinose, rhamnose, mannitol, lactose and 5-ketogluconate. It was concluded that the new isolates represent a single novel species of the genus Lactobacillus, for which the name Lactobacillus pobuzihii sp. nov. is proposed. The type strain is E100301T (=RIFY 6501T =NBRC 103219T =KCTC 13174T).

Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria

Bryobacter aggregatus gen. nov., sp. nov. is proposed to accommodate three strains of slowly growing, chemo-organotrophic bacteria isolated from acidic Sphagnum peat bogs. These bacteria were strictly aerobic, Gram-negative, colourless, non-motile coccoids or short rods that multiplied by normal cell division and formed irregularly shaped cell aggregates. Strains MPL3(T), MPL1011 and MOB76 were acidotolerant, mesophilic organisms capable of growth at pH 4.5-7.2 and between 4 and 33 degrees C (optimum growth at pH 5.5-6.5 and 22-28 degrees C). The preferred growth substrates were sugars, some heteropolysaccharides and galacturonic and glucuronic acids, which are released during decomposition of Sphagnum moss. The major fatty acids were iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c); the major quinones were MK-9 and MK-10. The DNA G+C content was 55.5-56.5 mol%. Strains MPL3(T), MPL1011 and MOB76 possessed nearly identical 16S rRNA gene sequences and belonged to the phylum Acidobacteria. They represent the first taxonomically characterized members of acidobacterial subdivision 3 and display only 81.7-86.7 % 16S rRNA gene sequence similarity to other members of the Acidobacteria with validly published names. Therefore, strains MPL3(T), MPL1011 and MOB76 are classified as representatives of a novel species in a new genus, for which the name Bryobacter aggregatus gen. nov., sp. nov. is proposed; strain MPL3(T) (=ATCC BAA-1390(T) =DSM 18758(T)) is the type strain of Bryobacter aggregatus.

Lactobacillus sucicola sp. nov., a motile lactic acid bacterium isolated from oak tree (Quercus sp.) sap

Three strains of rod-shaped and motile lactic acid bacteria, NRIC 0736(T), NRIC 0735 and NRIC 0737 were isolated from sap obtained from two different oak trees (Quercus sp.) on Awashima Island, Kagawa Prefecture, Japan. The three strains showed nearly identical 16S rRNA gene sequences (>99.7 % sequence similarity). The novel strains showed low 16S rRNA gene sequence similarities to recognized species of lactic acid bacteria. High gene sequence similarities were found between strain NRIC 0736(T) and Lactobacillus satsumensis NRIC 0604(T) (96.3 %), Lactobacillus mali DSM 20444(T) (95.3 %) and Lactobacillus vini DSM 20605(T) (95.3 %). DNA-DNA relatedness values revealed the genotypic separation of the three novel isolates from these recognized species. It is concluded that the three new isolates represent a novel species, for which the name Lactobacillus sucicola sp. nov. is proposed. The type strain is NRIC 0736(T) (=JCM 15457(T)=DSM 21376(T)).

Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlands

Three obligately aerobic, heterotrophic bacteria, designated strains WM1T, TPB606T and TPB621, were isolated from acidic Sphagnum-dominated tundra and Siberian wetlands in Russia. Cells of these isolates were Gram-negative, non-motile coccobacilli that occurred singly, in pairs or in chains, and were covered by large capsules. The novel strains were moderately acidophilic and psychrotolerant organisms capable of growth at pH 3.0-7.6 and 2-30 degrees C. Cells contained numerous intracellular poly-beta-hydroxybutyrate granules (3-4 per cell). The major cellular fatty acid was cyclo C19:0omega8c and the predominant quinone was Q-10. Strains TPB606T and TPB621, isolated from Siberian wetland, possessed almost identical 16S rRNA gene sequences and shared 97.2% sequence similarity with tundra strain WM1T. The three strains were shown to belong to the Alphaproteobacteria, but were related only distantly to the type strains of acidophilic bacteria Acidisphaera rubrifaciens (93.4-94.3% 16S rRNA gene sequence similarity), Rhodopila globiformis (92.2-93.3%), and members of the genera Acidiphilium (91.3-93%) and Acidocella (91.8-92.4%). The DNA G+C contents of the novel strains were 60.5-61.9 mol%. The low levels of DNA-DNA relatedness (37%) and a number of phenotypic differences between the Siberian strains TPB606T and TPB621 and the tundra strain WM1T indicated that they represent two separate species. As the three isolates are clearly distinct from all recognized acidophilic members of the Alphaproteobacteria, they are considered to represent two novel species of a new genus, for which the names Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov. are proposed. The type strain of Acidisoma sibiricum is TPB606T (=DSM 21000T=VKM B-2487T) and the type strain of Acidisoma tundrae is WM1T (=DSM 19999T=VKM B-2488T).

Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia

Biserrula pelecinus L. is a pasture legume that was introduced to Australia from the Mediterranean basin in 1993. Although the native rhizobial population could not nodulate B. pelecinus at the time of its introduction, recent research has shown the emergence of a diversity of strains (novel isolates) that are able to do so. Three novel isolates, WSM2073T, WSM2074 and WSM2076, had nearly identical 16S rRNA gene sequences, and clustered separately with all recognized species of the genus Mesorhizobium. Conversely, the novel isolate WSM2075T had >23 nt mismatches with the above three isolates. All four novel isolates shared 97-99% 16S rRNA gene sequence similarity with the type strains of all recognized Mesorhizobium species. However, strains WSM2073T, WSM2074 and WSM2076 showed <95.2% dnaK gene sequence similarity to the type strains of recognized Mesorhizobium species, and <92.9% to WSM2075T (which also shared <95.5% dnaK gene sequence similarity to the type strains of recognized Mesorhizobium species). Results for GSII gene sequencing were consistent with those for the dnaK gene. The fatty acid profiles of the novel isolates were diagnostic of root-nodule bacteria, but did not match those of recognized bacterial species. Strain WSM2075T had a significantly different fatty acid profile from the other three isolates. The above results indicated that strains WSM2073T, WSM2074 and WSM2076 represent the same species. Strain WSM2073T showed <45% DNA-DNA relatedness and WSM2075T<5% DNA-DNA relatedness with the type strains of recognized Mesorhizobium species; these two novel isolates shared 59% DNA-DNA relatedness. Collectively, these data indicate that strains WSM2073T, WSM2074 and WSM2076, and strain WSM2075T belong to two novel species of the genus Mesorhizobium, for which the names Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov. are proposed, respectively. The type strain of Mesorhizobium australicum sp. nov. is WSM2073T (=LMG 24608T=HAMBI 3006T) and the type strain of Mesorhizobium opportunistum sp. nov. is WSM2075T (=LMG 24607T=HAMBI 3007T).

Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA–DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens

The Streptomyces albidoflavus 16S rRNA gene clade contains 10 species and subspecies with identical 16S rRNA gene sequences and very similar numerical taxonomic data, including Streptomyces griseus subsp. solvifaciens. Type strains of this clade, as well as three CGMCC strains which were received as Streptomyces galilaeus, Streptomyces sioyaensis and Streptomyces vinaceus, respectively, that shared the same 16S rRNA gene sequences with the clade, were subjected to multilocus sequence analysis (MLSA), DNA–DNA hybridization (DDH) and phenotypic characterization for a comprehensive reevaluation. The 13 strains still formed a distinct, albeit loosely related, clade in the phylogenetic tree based on concatenated sequences of aptD, gyrB, recA, rpoB and trpB genes, supported by a high bootstrap value and different tree-making algorithms, with MLSA evolutionary distances ranging from 0 to 0.003. DDH values among these strains were well above the 70% cut-off point for species delineation. Based on the genotypic data of MLSA and DDH, combined with key phenotypic properties in common, it is proposed that the 10 species and subspecies of the S. albidoflavus clade, namely S. albidoflavus, S. canescens, S. champavatii, S. coelicolor, S. felleus, S. globisporus subsp. caucasicus, S. griseus subsp. solvifaciens, S. limosus, S. odorifer and S. sampsonii, should be merged into a single genomic species, for which the name S. albidoflavus is retained, and that the three strains S. galilaeus CGMCC 4.1320, S. sioyaensis CGMCC 4.1306 and S. vinaceus CGMCC 4.1305 should be assigned to S. albidoflavus as well. The results also indicated that MLSA could be the procedure of choice for distinguishing between species within Streptomyces 16S rRNA gene clades.

Phaselicystis flava gen. nov., sp. nov., an arachidonic acid-containing soil myxobacterium, and the description of Phaselicystidaceae fam. nov.

A bacterial strain designated SBKo001(T) was isolated from a forest soil sample from Mt Makiling in Laguna, Philippines. It shows the general characteristics associated with myxobacteria, such as swarming of Gram-negative, rod-shaped vegetative cells, fruiting body formation and bacteriolytic activity. The strain is mesophilic, strictly aerobic and chemoheterotrophic and also exhibits resistance to various antibiotics. Major fatty acids are iso-C(15 : 0), C(17 : 1) 2-OH and C(20 : 4) (arachidonic acid). The G+C content of the genomic DNA is 69.2 mol%. A reference strain, NOSO-1 (=DSM 53757), isolated from the Etosha Basin in Namibia, shares nearly the same characteristics with SBKo001(T). The identical 16S rRNA gene sequences of the two strains show 94 % identity to strains of the cellulose-degrading Byssovorax and Sorangium species. Phylogenetic analysis reveals a novel branch diverging from the Polyangiaceae, Sorangiineae, Myxococcales. Their uniqueness in morphological growth stages, unusual fatty acid profile, broad-spectrum antibiotic resistance and branch divergence from the Polyangiaceae imply that strains SBKo001(T) and NOSO-1 not only represent a novel genus and species, proposed here as Phaselicystis flava gen. nov., sp. nov., but also belong to a new family, Phaselicystidaceae fam. nov. The type strain of Phaselicystis flava is SBKo001(T) (=DSM 21295(T) =NCCB 100230(T)).

Pseudomonas cuatrocienegasensis sp. nov., isolated from an evaporating lagoon in the Cuatro Cienegas valley in Coahuila, Mexico

Nine Gram-negative, rod-shaped, non-spore-forming isolates with identical or very similar repetitive-sequence-based PCR profiles were recovered from an evaporative lagoon in Mexico. Two strains, designated 1N(T) and 3N, had virtually identical 16S rRNA gene sequences and, on the basis of these sequences, were identified as members of the genus Pseudomonas, with Pseudomonas peli R-20805(T) as the closest relative. All nine isolates had practically identical whole-cell protein profiles. The major fatty acids [C(16 : 0,) C(18 : 1)omega7c and summed feature a (C(16 : 1)omega7 and/or C(16 : 1)omega6c)] of strains 1N(T) and 3N supported their affiliation with the genus Pseudomonas. The DNA-DNA reassociation values with respect to P. peli LMG 23201(T) and other closely related Pseudomonas species were <15 %. Physiological and biochemical tests allowed phenotypic differentiation of the strains analysed, including strain 1N(T), from the five phylogenetically closest Pseudomonas species. On the basis of the data obtained by using this polyphasic taxonomic approach, the nine strains represent a novel species, for which the name Pseudomonas cuatrocienegasensis sp. nov. is proposed. The type strain is 1N(T) (=LMG 24676(T)=CIP 109853(T)).

Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) Oxidizing Representatives of a Globally Distributed Clade of alpha-Proteobacteria from the Order Rhizobiales

Several closely related Mn(II)-oxidizing alpha-Proteobacteria were isolated from very different marine environments: strain SI85-9A1 from the oxic/anoxic interface of a stratified Canadian fjord, strain HTCC 2156 from the surface waters off the Oregon coast, and strain AE01 from the dorsal surface of a hydrothermal vent tubeworm. 16S rRNA analysis reveals that these isolates are part of a tight phylogenetic cluster with previously characterized members of the genus Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface waters of the Arctic and Mediterranean seas, a deep-sea hydrothermal plume, and a Caribbean coral. Further analysis of all these strains revealed that many of them are capable of oxidizing dissolved Mn(II) and producing particulate Mn(III/IV) oxides. Strains SI85-9A1 and HTCC 2156 were characterized further. Despite sharing nearly identical 16S rRNA gene sequences with the previously described Aurantimonas coralicida, whole genome DNA-DNA hybridization indicated that their overall genomic similarity is low. Polyphasic phenotype characterization further supported distinguishing characteristics among these bacteria. Thus SI85-9A1 and HTCC 2156 are described as two new species within the family ‘Aurantimonadaceae’: Aurantimonas manganoxydans sp. nov. and Aurantimonas litoralis sp. nov. This clade of bacteria is widely distributed around the globe and may be important contributors to Mn cycling in many environments. Our results highlight the difficulty in utilizing 16S rRNA-based approaches to investigate the microbial ecology of Mn(II) oxidation.

Marinobacter mobilis sp. nov. and Marinobacter zhejiangensis sp. nov., halophilic bacteria isolated from the East China Sea

Three Gram-negative, aerobic, motile, halophilic, rod-shaped strains (CN46(T), CN71 and CN74(T)) were isolated from sediment of the East China Sea and subjected to a polyphasic taxonomic study. Strains CN46(T) and CN71 had identical 16S rRNA gene sequences and phenotypic characteristics. Strain CN46(T) was moderately halophilic. Growth of strain CN46(T) was observed between 0.5 and 10.0 % (w/v) NaCl (optimal growth at 3.0-5.0 %) and between pH 6.5 and 9.0. Strain CN74(T) grew over a wider range of pH (pH 6.0-9.5); the optimum NaCl concentration for growth was 1.0-3.0 %. The major fatty acids of strain CN46(T) were C(16 : 1)omega9c, C(16 : 0) and C(12 : 0), whereas strain CN74(T) contained C(16 : 0), C(16 : 1)omega9c, C(18 : 1)omega9c and C(12 : 0). The DNA G+C contents of the three isolates were between 58.0 and 58.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains CN46(T), CN71 and CN74(T) grouped together within the cluster of Marinobacter species. 16S rRNA gene sequence similarities of the three strains with the type strains of Marinobacter species ranged from 94.0 to 97.1 %. The DNA-DNA hybridization values of strain CN74(T) with strains CN46(T) and CN71 were 35.0 and 36.0 %, respectively. Levels of DNA-DNA relatedness between strains CN46(T) and CN74(T) and Marinobacter pelagius CGMCC 1.6775(T), Marinobacter gudaonensis CGMCC 1.6294(T) and Marinobacter koreensis DSM 17924(T) were 15.3-45.2 %. The results of DNA-DNA hybridizations, fatty acid analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Two novel species are proposed, named Marinobacter mobilis sp. nov. (type strain CN46(T) =CGMCC 1.7059(T) =JCM 15154(T)) and Marinobacter zhejiangensis sp. nov. (type strain CN74(T) =CGMCC 1.7061(T) =JCM 15156(T)).

Nosocomiicoccus ampullae gen. nov., sp. nov., isolated from the surface of bottles of saline solution used in wound cleansing

Strains TRF-1(T) and TC-9 were isolated from transfer spikes of two separate bottles containing 0.9 % NaCl (physiological saline) solution used repeatedly to wash wounds in hospital wards, months apart. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains TRF-1(T) and TC-9 formed a distinct branch within the family Bacillaceae most closely related to the members of the genus Jeotgalicoccus. The two strains, with identical 16S rRNA gene sequences, showed sequence similarities of 89.8-93.9 % with species of Jeotgalicoccus, 91.1-91.8 % with species of Salinicoccus and 89.1-89.7 % with species of Staphylococcus. Strains TRF-1(T) and TC-9 are Gram-positive, non-spore-forming and non-motile cocci, with an optimum growth temperature of about 37 degrees C. Strain TRF-1(T) grew optimally in medium containing 3 % (w/v) NaCl (maximum about 14 % NaCl), while strain TC-9 grew optimally in medium with 1 % (w/v) NaCl. Both strains produce a brown pigment when grown in the presence of NaCl. The cell-wall peptidoglycan is of the A3alpha type with a cross-linkage containing the peptide l-Lys-Gly(4)-l-Ser-Gly. The major respiratory quinones are menaquinone 7 (MK-7) and menaquinone 8 (MK-8), the major fatty acids are straight-chain C(14 : 0) and C(16 : 0) (more than 85 % of the total) and the major polar lipid is an unknown aminophospholipid. The DNA G+C content is 33.5 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, we are of the opinion that strains TRF-1(T) and TC-9 represent a novel species of a new genus, for which we propose the name Nosocomiicoccus ampullae gen. nov., sp. nov. The type strain of Nosocomiicoccus ampullae is strain TRF-1(T) (=LMG 24060(T) =CIP 109506(T)).

Genotypic and phenotypic diversity of Bacillus spp. isolated from steel plant waste.

BackgroundMolecular studies of Bacillus diversity in various environments have been reported. However, there have been few investigations concerning Bacillus in steel plant environments. In this study, genotypic and phenotypic diversity and phylogenetic relationships among 40 bacterial isolates recovered from steel plant waste were investigated using classical and molecular methods.Results16S rDNA partial sequencing assigned all the isolates to the Bacillus genus, with close genetic relatedness to the Bacillus subtilis and Bacillus cereus groups, and to the species Bacillus sphaericus. tDNA-intergenic spacer length polymorphisms and the 16S–23S intergenic transcribed spacer region failed to identify the isolates at the species level. Genomic diversity was investigated by molecular typing with rep (repetitive sequence) based PCR using the primer sets ERIC2 (enterobacterial repetitive intergenic consensus), (GTG)5, and BOXAIR. Genotypic fingerprinting of the isolates reflected high intraspecies and interspecies diversity. Clustering of the isolates using ERIC-PCR fingerprinting was similar to that obtained from the 16S rRNA gene phylogenetic tree, indicating the potential of the former technique as a simple and useful tool for examining relationships among unknown Bacillus spp. Physiological, biochemical and heavy metal susceptibility profiles also indicated considerable phenotypic diversity. Among the heavy metal compounds tested Zn, Pb and Cu were least toxic to the bacterial isolates, whereas Ag inhibited all isolates at 0.001 mM.ConclusionIsolates with identical 16S rRNA gene sequences had different genomic fingerprints and differed considerably in their physiological capabilities, so the high levels of phenotypic diversity found in this study are likely to have ecological relevance.

Lactobacillus hordei sp. nov., a bacteriocinogenic strain isolated from malted barley

A high-throughput screening effort, designed to isolate bacteriocin-producing lactic acid bacteria (LAB) from malted cereals, resulted in the isolation of four bacteriocin-producing strains that could not be assigned conclusively to recognized species. The four isolates (UCC128T, UCC125, UCC126 and UCC127) were found to share identical (100%) 16S rRNA gene sequences and were therefore deemed to belong to the same species. The strains were Gram-positive, catalase-negative, non-motile homofermentative LAB. The closest recognized relative to strain UCC128T identified based on comparative 16S rRNA gene sequence analysis was Lactobacillus mali DSM 20444T (97% similarity). The strains were characterized phenotypically to identify specific growth requirements. DNA-DNA hybridization between strain UCC128T and L. mali DSM 20444T revealed a level of relatedness of only 39.4%. This indicates that strain UCC128T does not belong to the species L. mali. The four bacteriocin-producing strains are therefore considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus hordei sp. nov. is proposed. The type strain is UCC128T (=DSM 19519T=LMG 24241T).

Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter

Three rod-shaped, Gram-negative, chemo-organotrophic, heterotrophic, strictly aerobic, gliding bacterial strains, KT02ds18-4, KT02ds18-5 and KT02ds18-6T, were isolated from North Sea surface waters near the island of Helgoland, Germany. Their taxonomic position was investigated by a polyphasic approach. The three strains were light yellow, oxidase- and catalase-positive, and grew optimally at 25 degrees C, at pH 7.5, and in the presence of 2.5 % (w/v) NaCl. The Chargaff's coefficient was 34.2-34.4 mol%. The three strains shared >90 % DNA-DNA relatedness and an identical 16S rRNA gene sequence. Comparative 16S rRNA gene sequence analysis allocated the three strains to the genus Maribacter in the family Flavobacteriaceae, with similarities of 97.0-97.4 % to five of the recognized Maribacter species. Their low level of DNA-DNA relatedness (<20 %) with these species and differentiating phenotypic characteristics demonstrated that they constitute a new Maribacter species for which the name Maribacter forsetii sp. nov. is proposed. Strain KT02ds18-6T (=CIP 109504T=DSM 18668T) is the type strain. An emended description of the genus Maribacter is also proposed.

Yersinia massiliensis sp. nov., isolated from fresh water

Two bacterial organisms, 50640T and 823, were isolated from fresh water in Marseilles, France, and were further identified as members of the genus Yersinia on the basis of their phenotypic characteristics and 16S rRNA gene sequencing. Their unique phenotypic profile differed from that of closely related species of Yersinia bercovieri and Yersinia mollaretii by exhibiting positive indole and inositol tests, and from that of Yersinia frederiksenii by lacking the ability to ferment l-rhamnose. A polyphasic approach, including almost complete 16S rRNA gene sequencing (1461 bp) and partial sequencing of hsp60 (683 bp), gyrB (662 bp), sodA (624 bp) and rpoB (1049 bp) showed that isolates 50640T and 823 exhibited 98.5, 93.5, 90.4, 92.4 and 96.6 % similarity with Y. mollaretii, 98.7, 93.0, 90.1, 89.1 and 96.2 % with Y. bercovieri, and 98.4, 93.2, 89.8, 88.9 and 95.2 % with Y. frederiksenii, respectively. Both isolates exhibited an identical 16S rRNA gene sequence and differed by one to five point mutations in housekeeping gene sequences. Phylogenetic reconstructions based on the combination of these four housekeeping genes indicated that the two isolates formed a unique branch supported by a bootstrap value of 93 %. Their unique phenotypic traits, 16S rRNA gene sequence, together with housekeeping gene sequences exhibiting <97 % similarity with closely related species, and phylogenetic analyses suggested that the two isolates represent a so far undescribed Yersinia species. The name Yersinia massiliensis sp. nov. is proposed for this new taxon (type strain 50640T=CIP 109351T=CCUG 53443T; isolate 823=CIP 109352=CCUG 53444).

Burkholderia sartisoli sp. nov., isolated from a polycyclic aromatic hydrocarbon-contaminated soil

A Gram-negative, rod-shaped, aerobic bacterium, designated strain RP007(T), was isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Two additional strains were recovered from a compost heap in Belgium (LMG 18808) and from the rhizosphere of maize in the Netherlands (LMG 24204). The three strains had virtually identical 16S rRNA gene sequences and whole-cell protein profiles, and they were identified as members of the genus Burkholderia, with Burkholderia phenazinium as their closest relative. Strain RP007(T) had a DNA G+C content of 63.5 mol% and could be distinguished from B. phenazinium based on a range of biochemical characteristics. Strain RP007(T) showed levels of DNA-DNA relatedness towards the type strain of B. phenazinium and those of other recognized Burkholderia species of less than 30 %. The results of 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments and physiological and biochemical tests allowed the differentiation of strain RP007(T) from all recognized species of the genus Burkholderia. Strains RP007(T), LMG 18808 and LMG 24204 are therefore considered to represent a single novel species of the genus Burkholderia, for which the name Burkholderia sartisoli sp. nov. is proposed. The type strain is RP007(T) (=LMG 24000(T) =CCUG 53604(T) =ICMP 13529(T)).

Bacteroides propionicifaciens sp. nov., isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms

Two strictly anaerobic bacterial strains (SV434(T) and S562) were isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. They had identical 16S rRNA gene sequences and showed almost the same phenotypic properties. The cells of both strains were Gram-negative, non-motile, non-spore-forming rods; extraordinarily long rods often occurred. Remarkable stimulation of growth occurred with the addition of haemin and cobalamin (vitamin B(12)) to the medium. The supplementary cobalamin and haemin could be replaced if autoclaved and clarified sludge fluid obtained from the reactor was added. Both strains utilized a range of growth substrates, including arabinose, fructose, galactose, glucose, mannose, cellobiose, maltose, glycogen, starch, dextrin, amygdalin, lactate and pyruvate. Both strains produced acetate and propionate with a small amount of succinate from these substrates in the presence of haemin and cobalamin. Both strains were slightly alkaliphilic, having a pH optimum at about 7.9. The temperature range for growth was 5-35 degrees C, the optimum being 30 degrees C. The NaCl concentration range for growth was 0-4 % (w/v). Catalase activity was not detected in cells cultivated without haemin, whereas cells cultivated with haemin usually had the enzyme activity. Oxidase and nitrate-reducing activities were not detected. Aesculin was hydrolysed, but gelatin was not hydrolysed. Both strains were sensitive to bile acids. The major cellular fatty acids of both strains were anteiso-C(15 : 0) and iso-C(15 : 0). Menaquinones MK-8(H(0)) and MK-9(H(0)) were the major respiratory quinones and the genomic DNA G+C contents were 46.2-47.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. Bacteroides coprosuis (isolated from swine-manure storage pits) was the species most closely related to both strains (95.9 % 16S rRNA gene sequence similarity to the type strain). On the basis of the phylogenetic, physiological and chemotaxonomic analyses, strains SV434(T) and S562 represent a novel species of the genus Bacteroides, for which the name Bacteroides propionicifaciens sp. nov. is proposed. The type strain is SV434(T) (=JCM 14649(T) =DSM 19291(T)).