Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

Bacillus nematocida sp. nov., a novel bacterial strain with nematotoxic activity isolated from soil in Yunnan, China

An endospore-forming bacterium, designated strain B-16T, was isolated from a forest soil sample in Yunnan, China. The isolate presented remarkable nematotoxic activity against nematode Panagrellus redivivus. The organism was strictly aerobic, motile, spore forming and rod shaped, catalase- and oxidase-positive. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acid profiles were anteiso-C15:0 (48.67%), iso-C15:0 (13.45%), C16:0 (9.06%) and anteiso-Cl7:0 (8.29%). The DNA G+C content was 46%. Phylogenetic analyses based on 16S rDNA sequence revealed that isolate belongs to the genus Bacillus. Strain B-16T exhibited high 16S rDNA similarity with its closest neighbors Bacillus vallismortis (99.79%), B. subtilis (99.43%), B. atrophaeus (99.43%), B. amyloliquefaciens (99.36%), B. licheniformis (98.0%) and less than 97.0% with all the other relative type strains in the genus Bacillus. The phenotypic and genotypic characteristics and DNA-DNA relatedness data indicate that strain B-16T should be distinguished from all the relative species of genus Bacillus. Therefore, on the basis of the polyphasic taxonomic data presented, a new species of the genus Bacillus, B. nematocida, with the type strain B-16T ( = CGMCC 1128T) is proposed. The GenBank accession number for the sequence reported in this paper is AY820954.     

Streptomyces pharetrae sp. nov., isolated from soil from the semi-arid Karoo region

An actinomycete, strain CZA14T, was isolated from Worcester in the Western Cape province of South Africa. Based on rapid genus identification, 16S-rDNA sequence similarities and chemotaxonomy, strain CZA14T was identified as a member of the genus Streptomyces. It exhibited weak antibiosis against Bacillus coagulans ATCC 7050T, Mycobacterium aurum A+ and Acinetobacter calcoaceticus C91. The results of physiological tests and analysis of the 16S-rDNA sequence allowed for the differentiation of strain CZA14T from other species of the genus Streptomyces. Strain CZA14T therefore represents a new species for which the name Streptomyces pharetrae is proposed, with the type strain CZA14T (= DSM 41856T = NRRL 24333T).     

Nakamurella panacisegetis sp. nov. and proposal for reclassification of Humicoccus flavidus Yoon et al., 2007 and Saxeibacter lacteus Lee et al., 2008 as Nakamurella flavida comb. nov. and Nakamurella lactea comb. nov

A novel actinobacterial strain, designated P4-7(T), was isolated from soil of a ginseng field located in Geumsan County, Korea. Cells of the strain were aerobic, Gram-stain-positive, non-motile, short rods. The isolate contained MK-8(H(4)) as the predominant menaquinone, iso-C(16:0), anteiso-C(15:0) and anteiso-C(17:0) as the major fatty acids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the major polar lipids, glucose, mannose, xylose, ribose and rhamnose as whole-cell sugars, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P4-7(T) belongs to the family Nakamurellaceae and is most closely related to Nakamurella multipartita, Humicoccus flavidus and Saxeibacter lacteus (96.3, 97.0 and 96.4% similarity to the respective type strains). Based on comparative analyses of the 16S rRNA and rpoB gene sequences and chemotaxonomic data, it is proposed that H. flavidus and S. lacteus be transferred to the genus Nakamurella. Combined genotypic and phenotypic data also suggested that strain P4-7(T) be placed in a novel species of the genus Nakamurella, for which the name Nakamurella panacisegetis sp. nov. is proposed; the type strain is P4-7(T) (=KCTC 19426(T)=CECT 7604(T)).     

Hansschlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants

A new genus, Hansschlegelia, and a new species, Hansschlegelia plantiphila, are proposed for three strains of methanol-utilizing bacteria isolated from lilac buds (strain S(1)(T)), linden buds (strain S(2)) and blue spruce needles (strain S(4)), which were selected in winter at -17 degrees C. These bacteria are aerobic, Gram-negative, colorless, non-motile short rods that multiply by binary fission and employ the ribulose bisphosphate (RuBP) and the serine pathways for C(1) assimilation. The strains have a limited number of growth substrates and use methanol, methylamine, formate, CO(2)/H(2) and glycerol as carbon and energy sources. Only strain S(1)(T) grows with ethanol and inulin. The strains are neutrophilic and mesophilic, and synthesize phytohormones (auxins and cytokinins) and vitamin B(12). Their major cellular fatty acids are saturated C(16:0), straight-chain, unsaturated C(18:1)(omega)(7) and cyclopropane C(19 cyc) acids. The main ubiquinone is ubiquinone-10 (Q-10). The dominant phospholipids are phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.5+/-0.2 mol%. The strains share almost identical 16S rRNA gene sequences, a high DNA-DNA hybridization value (72-86%) and represent a novel lineage of autotrophic methanol-utilizing bacteria within the Alphaproteobacteria. Collectively, these strains comprise a new genus and species H. plantiphila gen. nov., sp. nov., with strain S(1)(T) (VKM B-2347(T), NCIMB 14035(T)) as the type strain.     

Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries

Three Gram-positive, anaerobic, pleomorphic strains (PG10(T), PG18 and PG22), were selected among five strains isolated from pig slurries while searching for host specific bifidobacteria to track the source of fecal pollution in water. Analysis of the 16S rRNA gene sequence showed a maximum identity of 94% to various species of the family Bifidobacteriaceae. However, phylogenetic analyses of 16S rRNA and HSP60 gene sequences revealed a closer relationship of these strains to members of the recently described Aeriscardovia, Parascardovia and Scardovia genera, than to other Bifidobacterium species. The names Neoscardovia gen. nov. and Neoscardovia arbecensis sp. nov. are proposed for a new genus and for the first species belonging to this genus, respectively, and for which PG10(T) (CECT 8111(T), DSM 25737(T)) was designated as the type strain. This new species should be placed in the Bifidobacteriaceae family within the class Actinobacteria, with Aeriscardovia aeriphila being the closest relative. The prevailing cellular fatty acids were C(16:0) and C(18:1)ω9c, and the major polar lipids consisted of a variety of glycolipids, diphosphatidyl glycerol, two unidentified phospholipids, and phosphatidyl glycerol. The peptidoglycan structure was A1γmeso-Dpm-direct. The GenBank accession numbers for the 16S rRNA gene and HSP60 gene sequences of strains PG10(T), PG18 and PG22 are JF519691, JF519693, JQ767128 and JQ767130, JQ767131, JQ767133, respectively.     

Isolation and characterization of a new type of aerobic,oxalic acid utilizing bacteria,and proposal of Oxalicibacterium flavum gen. nov., sp. nov

A mesophilic, aerobic oxalic acid utilizing yellow-pigmented bacterium has been isolated from litter of oxalate producing plants in the region of Izmir (Turkey). It is motile by means of 1-3 polar flagella. Optimal growth occurred between 25-30 degrees C at pH 6.9. The G+C content of DNA is 62-64 mol % (Tm). Based on its morphological and biochemical features the organism belongs to the genus Pseudomonas, but differs from all the previously described species. The taxonomic relationships among strains described as or previously tentatively assigned to the genus Pseudomonas were investigated using numerical classification, DNA base composition and DNA-DNA hybridization. 16S rDNA sequences were determined for the strain TA17. On the basis of 16S rDNA sequence comparisons, physiological and biochemical characteristics, it is proposed to classify TA17T in a new genus and species for which the name Oxalicibacterium flavum gen. nov., sp. nov. is proposed. The type strain is TA17T (= NEU98T, = LMG 21571T).     

Sphingobacterium canadense sp. nov., an isolate from corn roots

A free-living Gram-negative bacterial strain CR11(T) was isolated from corn roots. Polyphasic taxonomy was performed, including API20 NE and API50 CH bacterial identification kits, Biolog analysis, lipids and fatty acid analysis, DNA-DNA hybridization, 16S rRNA and cpn60 gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain CR11(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium multivorum IFO 14947(T) (98% similarity) and Sphingobacterium. thalpophilum ATCC 43320(T) (97% similarity). DNA-DNA hybridization showed 11% and 13% DNA re-association with S. multivorum LMG 8342(T) and S. thalpophilum LMG 11520(T), respectively. Major fatty acids (16:0, 15:0 iso and 17:0 iso 3-OH) and the G+C content of the DNA (40.5 mol%), were also similar to those of the genus Sphingobacterium. The predominant respiratory quinone was MK-7. In all analyses, including phenotypic characterization, this isolate was found to be different from the closely related species, S. multivorum and S. thalpophilum. On the basis of these results, this strain represents a new species within the genus Sphingobacterium. The name Sphingobacterium canadense sp. nov. is suggested and the type strain is CR11(T) (=NCCB 100125(T)=LMG 23727(T)).     

Isolation and characterization of Bacillus thioparus sp. nov., chemolithoautotrophic, thiosulfate-oxidizing bacterium

A novel bacterium, strain BMP-1(T), was isolated from a continuous wastewater treatment culture system operating with a bacterial consortium. Cells of the isolate were Gram-variable, aerobic, moderately halotolerant, motile and endospore-forming rods. Strain BMP-1(T) grew chemolithoautotrophically by oxidation of thiosulfate to sulfate with a growth yield of 1.07 g protein mol(-1) of thiosulfate consumed. DNA G+C content was 43.8 mol%. Its cell wall had peptidoglycan based on m-diaminopimelic acid, and the major component of fatty acid was C(15 : 0). The 16S rRNA gene analysis showed that strain belongs to the genus Bacillus, sharing a 99.5% of sequence similarity with Bacillus jeotgali CCM 7133(T). DNA-DNA hybridization between the isolate of this study and this strain was 44%. Thus, the inclusion of strain BMP-1(T) in the genus Bacillus is suggested as a novel species and the name Bacillus thioparus sp. nov. (Type strain BMP-1(T)=BM-B-436(T)=CECT 7196(T)) is proposed. The sequence of the 16S rRNA gene has been deposited in GenBank with accession number DQ371431.     

Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout (Oncorhynchus mykiss)

Genotypic and phenotypic analyses were performed on five Gram-negative, catalase and oxidase-positive, rod-shaped bacteria isolated from the gill and liver of four rainbow trout. Studies based on comparative 16S rRNA gene sequence analysis showed that the five new isolates shared 99.8-100% sequence similarity and that they belong to the genus Chryseobacterium. The nearest phylogenetic neighbours of the strain 701B-08(T) were Chryseobacterium ureilyticum F-Fue-04IIIaaaa(T) (99.1% 16S rRNA gene sequence similarity) and Chryseobacterium joosteii LMG 18212(T) (98.6%). DNA-DNA hybridization values between the five isolates were 91-99% and ranged from 2 to 53% between strain 701B-08(T) and the type strains of phylogenetically closely related species of Chryseobacterium. Strain 701B-08(T) had a DNA G+C content of 36.3 mol%, the major fatty acids were iso-C(15:0), iso-C(17:1)ω9c, C(16:1)ω6c and iso-C(17:0) 3-OH and the predominant respiratory quinone was MK-6. The novel isolates were distinguished from related Chryseobacterium species by physiological and biochemical tests. The genotypic and phenotypic properties of the isolates from rainbow trout suggest their classification as representatives of a novel species of the genus Chryseobacterium, for which the name Chryseobacterium oncorhynchi sp. nov. is proposed. The type strain is 701B-08(T) (=CECT 7794(T)=CCUG 60105(T)).     

Tateyamaria omphalii gen. nov., sp. nov., an alpha-Proteobacterium isolated from a top shell Omphalius pfeifferi pfeifferi

A Gram-negative, strictly aerobic, coccoid to short rod-shaped marine bacterium strain MKT107(T) was isolated from the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MKT107(T) constitutes a new lineage in alpha-Proteobacteria related to the genera Nereida, Roseobacter, Staleya, Oceanibulbus and Sulfitobacter. Strain MKT107(T) was found to require salt for its growth and to be mesophilic. It contained 18:1omega7c and 16:0 as major cellular fatty acids and 3-OH 10:0 and 3-OH 12:0 as hydroxy fatty acids. The DNA base composition of the isolate was 61.6 mol% G+C. The major quinone was Q-10. Sufficient differences existed to distinguish this strain from currently recognized bacterial genera. Therefore, the isolate is classified as representing a new genus and species, Tateyamaria omphalii gen. nov., sp. nov. (type strain MKT107(T) =IAM 15108(T) =KCTC 12333(T); GenBank accession no. AB193438).     

Bradyrhizobium rifense sp. nov. isolated from effective nodules of Cytisus villosus grown in the Moroccan Rif

Two bradyrhizobial strains, CTAW71(T) and CTAW69, previously isolated from root nodules of Cytisus villosus, have been analysed using a polyphasic approach. These strains have identical 16S rRNA genes and their closest relative species is Bradyrhizobium cytisi, whose type strain CTAW11(T) presented 99.8% identity with respect to strain CTAW71(T). Despite the closeness of the 16S rRNA genes, the housekeeping genes recA, atpD and glnII harboured by strain CTAW71(T) were divergent to those from B. cytisi CTAW11(T), with identity values of 93%, 95% and 97%, respectively. These differences were congruent with DNA-DNA hybridization analysis that revealed an average of 37% relatedness between strain CTAW71(T) and B. cytisi CTAW11(T). Phenotypic characteristics were identical for strains CTAW71(T) and CTAW69, but differed from those of the described species from genus Bradyrhizobium. Based on the genotypic and phenotypic data obtained in this study, we propose that strains CTAW71(T) and CTAW69 should be classified into a new species for which the name Bradyrhizobium rifense sp. nov. is proposed (type strain CTAW71(T)=LMG 26781(T)=CECT 8066(T)).     

Taxonomic and phylogenetic studies on a new taxon of budding, hyphal Proteobacteria, Hirschia baltica gen. nov., sp. nov

Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16S rRNA of strain IFAM 1418T (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteria. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschia baltica is the type species of this genus, and the type strain of H. baltica is strain IFAM 1418 (= DSM 5838).     

Three new species of brevibacteria--Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov. and Brevibacterium permense sp. nov

This work deals with the taxonomic study of 12 orange-pigmented bacteria isolated from permafrost sediments, rice plots, and soils contaminated with wastes from the chemical and salt industries, which were assigned to the genus Brevibacterium on the basis of phenotypic characteristics, as well as of some strains described previously as Brevibacterium linens. The study revealed three genomic species, whose members and the type strains of the closest species of Brevibacterium had DNA similarity levels between 24 and 59%. The strains of the genomic species differed from each other and from the known species of Brevibacterium in some physiological and biochemical characteristics, as well as in the sugar and polyol composition of their teichoic acids. The 16S rDNA sequence analysis confirmed the assignment of the environmental isolates to the genus Brevibacterium and showed the phylogenetic distinction of the three genomic species. The results obtained in this study allow three new Brevibacterium species to be described: Brevibacterium antiquum (type strain VKM Ac-2118T = UCM Ac-411T), Brevibacterium aurantiacum (type strain VKM Ac-2111T = NCDO 739T = ATCC 9175T), and Brevibacterium permense (type strain VKM Ac-2280T = UCM Ac-413T).     

Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system

Three red-pink pigmented strains, designated A1-12(T), A2-50A(T) and A2-91(T), were recovered from two different sites in a uranium mine. For all strains, the optimum growth temperature was 25°C, the optimum pH was 6.0-6.5 and the DNA G+C contents were between 60 and 63.4 mol%. The major respiratory quinone was menaquinone 7 (MK-7) and the fatty acid profiles contained iso- and anteiso-branched C15 fatty acids, summed feature 3 (16:1 ω6c and/or ω7c and/or 15:0 iso 2-OH), summed feature 4 (17:1 anteiso B and/or iso I) and the unsaturated fatty acid 16:1 ω5c as the major components. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented three distinct branches within the family Flexibacteraceae most closely related to the members of the genus Hymenobacter. Strain A1-12(T) formed a distinct phylogenetic line along with H. rigui KCTC 12533(T) and they shared approximately 98.9% 16S rRNA gene sequence similarity. However, these two strains shared only 14.7% pairwise similarity in their genomic DNA. Strains A2-50A(T) and A2-91(T) formed two distinct lineages, related to the species H. soli KCTC 12607(T), sharing about 95.5% 16S rRNA gene sequence similarity between themselves, and 88.3 and 92.0% with other members of the genus Hymenobacter. Based on the phylogenetic analysis and physiological and biochemical characteristics, these isolates were considered to represent three novel species for which we propose the names Hymenobacter perfusus for strain A1-12(T) (=CIP 110166=LMG 26000), Hymenobacter flocculans for strain A2-50A(T) (=CIP 110139=LMG 25699) and Hymenobacter metalli for strain A2-91(T) (=CIP 110140=LMG 25700).     

Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside

Two anaerobic bacteria involved in the conversion of the plant lignan secoisolariciresinol diglucoside were isolated from faeces of a healthy male adult. The first isolate, strain SDG-Mt85-3Db, was a mesophilic strictly anaerobic Gram-positive helically coiled rod. Based on 16S r RNA gene sequence analysis, its nearest relatives were Clostridium cocleatum (96.7% similarity) and Clostridium ramosum (96.6%). In contrast to these species, the isolate was devoid of alpha-galactosidase and -glucosidase and did not grow on maltose, melibiose, raffinose, rhamnose and trehalose. The hypothesis that strain SDG-Mt85-3Db represents a new bacterial species of the Clostridium cluster XVIII was confirmed by DNA-DNA hybridisation experiments. The G+C content of DNA of strain SDG-Mt85-3Db (30.7+/-0.8 mol%) was comparable with that of Clostridium butyricum, the type species of the genus Clostridium. The name Clostridium saccharogumia is proposed for strain SDG-Mt85-3Db (=DSM 17460T=CCUG 51486T). The second isolate, strain ED-Mt61/PYG-s6, was a mesophilic strictly anaerobic Gram-positive regular rod. Based on 16S rRNA gene sequence analysis, its nearest relatives were Clostridium amygdalinum (93.3%), Clostridium saccharolyticum (93.1%) and Ruminococcus productus (93.0%). The isolate differed from these species in its ability to dehydrogenate enterodiol. It also possessed alpha-arabinosidase and -galactosidase and had a higher G+C content of DNA (48.0 mol%). According to these findings, it is proposed to create a novel genus, Lactonifactor, and a novel species, Lactonifactor longoviformis, to accommodate strain ED-Mt61/PYG-s6. The type strain is DSM 17459T (=CCUG 51487T).     

Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae

Timonella senegalensis strain JC301^T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301^T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301^T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301^T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels.