- Volume 61, Issue 4, 2011

A bacterial strain, designated SW6T, was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038T (97.9 % 16S rRNA gene sequence similarity). Strain SW6T required NaCl for growth and exhibited optimal growth at 25–30 °C and 3–4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6T ( = LMG 25377T = BCRC 80085T).

Two strains (JA480T and JA481) of phototrophic alphaproteobacteria were isolated from sediment samples collected from brackish water near Nagapattinam, India. They were Gram-negative, vibrioid cells containing bacteriochlorophyll a and rhodopin as major photosynthetic pigments. Most cells of both strains were non-flagellated; 1 % of cells showed two monopolar flagella. Cells showed positive phototaxis. Both strains showed chimeric intracellular photosynthetic membranes, where both lamellar stacks and vesicles were present together in a single cell. The major fatty acids were C18 : 1ω7c and C16 : 0 in both strains. The genomic G+C content was 67.2–68.8 mol% and the two strains were closely related (mean DNA–DNA hybridization >85 %). 16S rRNA gene sequence comparisons indicated that the isolates represent members of the Rhodospirillaceae within the class Alphaproteobacteria. According to the sequence comparison data, strain JA480T is positioned distinctly outside the group formed by the phototrophic genera Rhodospirillum, Rhodocista, Phaeospirillum, Rhodovibrio, Rhodospira and Roseospira, with only 80–92 % 16S rRNA gene sequence similarity. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeovibrio sulfidiphilus gen. nov., sp. nov. is proposed. The type strain of Phaeovibrio sulfidiphilus is JA480T ( = KCTC 5825T  = NBRC 106163T  = DSM 23193T).

A Gram-negative, rod-shaped, non-spore-forming bacterium (MH96T) was isolated from diseased larvae of the New Zealand grass grub, Costelytra zealandica (Coleoptera: Scarabaeidae). On the basis of 16S rRNA gene sequence similarity, strain MH96T is a member of the genus Yersinia, which is a member of the class Gammaproteobacteria. The most similar 16S rRNA gene sequence to that of MH96T is that of the type strain of Yersinia mollaretii (98.5 % similarity) followed by those of the type strains of Yersinia aldovae, Y. frederiksenii and Y. rohdei (all 98.4 % similarity). Multilocus sequence typing of five housekeeping genes (dnaJ, glnA, gyrB, groEL and recA) identified Yersinia ruckeri (81–92 % similarity) as the closest relative. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MH96T from the four most closely related Yersinia species with validly published names, including a Y. ruckeri isolate. Strain MH96T therefore represents a novel species, for which the name Yersinia entomophaga sp. nov. is proposed, with the type strain MH96T ( = DSM 22339T  = ATCC BAA-1678T).

A novel psychrotolerant bacterial strain, BCw111T, was isolated from seawater samples from the Chukchi Sea in the Arctic Ocean. Cells of strain BCw111T were Gram-negative, motile, facultatively anaerobic, curved rods and were able to grow at 0–30 °C (optimum 23–25 °C). Strain BCw111T had Q-8 as the major respiratory quinone and contained iso-C15 : 0 2-OH and/or C16 : 1ω7c (28.13 %), C16 : 0 (13.28 %) and C17 : 1 (12.90 %) as the major cellular fatty acids. The genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BCw11T formed a distinct lineage within the genus Colwellia and exhibited the highest 16S rRNA gene sequence similarity with Colwellia polaris 537T (97.8 %) and Colwellia aestuarii SMK-10T (97.1 %). Based on phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Colwellia chukchiensis sp. nov., is proposed. The type strain is BCw111T ( = CGMCC 1.9127T  = LMG 25329T  = DSM 22576T).

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1T, was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27T, Methylobacterium fujisawaense DSM 5686T, Methylobacterium radiotolerans JCM 2831T and Methylobacterium jeotgali S2R03-9T, with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA–DNA relatedness between strain JT1T and these and the type strains of other closely related species were lower than 70 %. Cells of JT1T stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm−2). Major fatty acids were C18 : 1ω7c and C16 : 0. Based on the morphological, physiological and biochemical data presented, strain JT1T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1T ( = DSM 21328T  = CCUG 56108T).

Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501T, D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HST) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strainsof Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575T, DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C16 : 1ω7, C16 : 0 and C18 : 1ω7 as the major fatty acids. The DNA–DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501T, D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575T. However, strains D-501T, D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575T by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501T, D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501T = DSM 22545T = VKM B-2573T) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575T. Strains D-380 and S. natans DSM 6575T were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575T = ATCC 13338T). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HST and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575T. Strain HST shared 99 % DNA–DNA relatedness with strain

DSM 565 and 48 % with S. natans DSM 6575T. The 16S rRNA, hsp60 and gyrB gene sequence similarities between strain DSM 566T and S. natans DSM 6575T were 97.5 %, 91.5 % and 87.0 %, respectively. Strain DSM 566T had 52 % DNA–DNA relatedness to S. natans DSM 6575T and shared 44 % DNA–DNA similarity with strain HST. The creation of two novel species is proposed, Sphaerotilus montanus sp. nov. for strains HST and DSM 565 (type strain HST = DSM 21226T = VKM B-2519T) and Sphaerotilus hippei sp. nov. for strain DSM 566T (type strain DSM 566T = ATCC 29330T). Emended descriptions of the genus Sphaerotilus and of Sphaerotilus natans are presented.

A Gram-negative, rod-shaped, non-spore-forming and nitrogen-fixing bacterium, designated ICB 89T, was isolated from stems of a Brazilian sugar cane variety widely used in organic farming. 16S rRNA gene sequence analysis revealed that strain ICB 89T belonged to the genus Stenotrophomonas and was most closely related to Stenotrophomonas maltophilia LMG 958T, Stenotrophomonas rhizophila LMG 22075T, Stenotrophomonas nitritireducens L2T, [Pseudomonas] geniculata ATCC 19374T, [Pseudomonas] hibiscicola ATCC 19867T and [Pseudomonas] beteli ATCC 19861T. DNA–DNA hybridization together with chemotaxonomic data and biochemical characteristics allowed the differentiation of strain ICB 89T from its nearest phylogenetic neighbours. Therefore, strain ICB 89T represents a novel species, for which the name Stenotrophomonas pavanii sp. nov. is proposed. The type strain is ICB 89T ( = CBMAI 564T  = LMG 25348T).

Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).

A novel halophilic bacterium of the genus Kangiella was isolated from a marine sponge collected from the Florida Keys, USA. Strain A79T, an aerobic, Gram-negative, non-motile, rod-shaped bacterium, grew in 2–15 % (w/v) NaCl, at a temperature of 10–49 °C and at pH 4.5–10. Phylogenetic analysis placed strain A79T in the family Alcanivoraceae in the class Gammaproteobacteria. Strain A79T showed 98.5 % 16S rRNA gene sequence similarity to Kangiella japonica KMM 3899T, 96.6 % similarity to Kangiella koreensis DSM 16069T and 95.6 % similarity to Kangiella aquimarina DSM 16071T. The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and the G+C content of the genomic DNA was 44.9 mol%. On the basis of physiological, chemotaxonomic and phylogenetic comparisons, strain A79T represents a novel species in the genus Kangiella, for which the name Kangiella spongicola sp. nov. is proposed. The type strain is A79T ( = ATCC BAA-2076T = DSM 23219T).

A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T  = LMG 25227T  = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T  = KCTC 22740T  = JCM 16344T).

Two strains of a novel yeast species were isolated from ectomycorrhizal Nothofagus pumilio rhizospheric soil in a native forest of Patagonia, Argentina. Analysis of the D1/D2 large-subunit rRNA gene sequences indicated that the novel species belongs to the recently described genus Lindnera. The name Lindnera rhizosphaerae sp. nov. is proposed to accommodate these isolates, and the type strain is CRUB 1796T ( = CBS 11400T  = JCM 16499T).

In the present work, a novel ascomycete species, Lachancea mirantina sp. nov., isolated from the fermentation process that produces cachaça, a Brazilian spirit, is proposed. Nucleotide sequence analysis of the 26S D1/D2 rDNA locus showed that L. mirantina sp. nov. was genetically related to Lachancea cidri and Lachancea fermentati, although some physiological traits showed remarkable differences. Analysis of the D1/D2 large-subunit rDNA molecular marker showed a clear distinction among all three species, confirming that L. mirantina sp. nov. belongs to a separate taxonomic species in the Lachancea clade. The type strain of Lachancea mirantina sp. nov. is URM 5925T ( = CLIB 1160T  = CBS 11717T).

Ten strains of a novel heterothallic yeast species were isolated from rotten wood collected at different locations in Hungary. Analysis of gene sequences for the D1/D2 domain of the large subunit rRNA, as well as analysis of concatenated gene sequences for the nearly complete nuclear large subunit rRNA, nuclear small subunit rRNA and translation elongation factor 1-α, placed the novel species in the family Trichomonascaceae, but showed that it was distinct from all currently recognized genera. The name Spencermartinsiella europaea gen. nov., sp. nov. is proposed to accommodate the new genus and novel species. The novel species could be distinguished from recognized species of neighbouring genera on the basis of standard phenotypic characteristics. The type and isotype strains of Spencermartinsiella europaea are NCAIM Y.01817T ( = NRRL Y-48265T =  CBS 11730T) and NCAIM Y.01819I ( = NRRL Y-48266I = CBS 11731I), respectively.