- Volume 59, Issue 9, 2009
Volume 59, Issue 9, 2009
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 6, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Streptomyces baliensis sp. nov., isolated from Balinese soil
The taxonomic positions of actinomycete strains ID03-0915T and ID03-0825, isolated from soil on the Indonesian island of Bali, were examined using a polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these organisms are typical of the genus Streptomyces. Phylogenetic analyses performed using almost-complete 16S rRNA gene sequences demonstrated that the strains were closely related to Streptomyces glauciniger and Streptomyces lilacinus. However, DNA–DNA hybridization and phenotypic characteristics revealed that the strains differed from known Streptomyces species. Therefore, we conclude that strains ID03-0915T and ID03-0825 (=BTCC B-563) represent a novel species of the genus Streptomyces, for which we propose the name Streptomyces baliensis sp. nov. The type strain is strain ID03-0915T (=BTCC B-608T =NBRC 104276T).
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Jiangella alba sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis
More LessA novel actinomycete strain, YIM 61503T, isolated from the stem of Maytenus austroyunnanensis, was characterized by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 61503T belonged to the genus Jiangella and exhibited 16S rRNA gene sequence similarities of 98.8 and 98.6 % to Jiangella alkaliphila D8-87T and Jiangella gansuensis YIM 002T. The chemotaxonomic properties of strain YIM 61503T were consistent with those of the genus Jiangella: the cell-wall peptidoglycan type was based on ll-diaminopimelic acid and MK-9(H4) was the predominant menaquinone. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0, C17 : 1 ω8c and anteiso-C17 : 0. The DNA G+C content was 71.9 mol%. Strain YIM 61503T was phenotypically distinct from recognized Jiangella species and was shown to belong to a separate genomic species based on DNA–DNA hybridization results. Thus, strain YIM 61503T is considered to represent a novel species of the genus Jiangella, for which the name Jiangella alba sp. nov. is proposed. The type strain is YIM 61503T (=DSM 45237T =CCTCC AA 208023T).
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Saccharopolyspora qijiaojingensis sp. nov., a halophilic actinomycete isolated from a salt lake
A halophilic actinomycete strain, designated YIM 91168T, was isolated from a salt lake in Xinjiang province, north-west China. The isolate grew at 20–40 °C, pH 5–8 and 6–22 % (w/v) NaCl; there was no growth in the absence of NaCl. The whole-cell hydrolysate contained meso-diaminopimelic acid, galactose and arabinose. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. MK-9(H4) was the predominant menaquinone and the genomic DNA G+C content was 70.1 mol%. These chemotaxonomic data, together with its morphological properties, were consistent with the assignment of strain YIM 91168T to the genus Saccharopolyspora. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 91168T had highest sequence similarity (95.4 %) with Saccharopolyspora gregorii NCIB 12823T, and showed lower 16S rRNA gene sequence similarity (93.0–95.1 %) with the other species of the genus Saccharopolyspora. On the basis of evidence from this polyphasic study, the novel species Saccharopolyspora qijiaojingensis sp. nov. is proposed. The type strain is YIM 91168T (=DSM 45088T =KCTC 19235T).
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Fodinibacter luteus gen. nov., sp. nov., an actinobacterium isolated from a salt mine
A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2–96.0 % similarity), Oryzihumus (95.6 %), Terrabacter (94.9–95.4 %), Janibacter (94.9–95.4 %), Kribbia (95.0 %), Lapillicoccus (95.0 %) and Phycicoccus (94.2–95.0 %) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18 : 1 ω9c and C16 : 0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T =CCTCC AA 208036T) as the type strain of Fodinibacter luteus.
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Actinopolymorpha alba sp. nov., isolated from a rhizosphere soil
More LessA Gram-positive, milk–white coloured, aerobic strain, YIM 48868T, was isolated from the rhizosphere soil of Maytenus hookeri Loes in Xishuangbanna, China. 16S rRNA gene sequence similarity studies showed that strain YIM 48868T was a member of the genus Actinopolymorpha, showing 96.8 % sequence similarity to Actinopolymorpha singaporensis IM 7744T and 97.0 % similarity to Actinopolymorpha rutila YIM 45725T. Chemotaxonomic data (peptidoglycan type I, ll-diaminopimelic acid; sugar pattern C, glucose, rhamnose and ribose; polar lipids PI, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannosides and phosphatidylinositol) were characteristic of the genus Actinopolymorpha. A phylogenetic tree based on 16S rRNA gene sequences showed that strain YIM 48868T formed a distinct phylogenetic lineage within the genus Actinopolymorpha. Strain YIM 48868T could be differentiated from recognized species by means of phenotypic properties and the predominant menaquinones [MK-9(H6), MK-9(H8), MK-10(H6), MK-10(H8)]. The DNA G+C content was 66.6 mol%. The DNA–DNA relatedness values between strain YIM 48868T and the type strains of A. singaporensis and A. rutila were 48.7 % and 53.1 %, respectively. These data, in combination with phenotypic and chemotaxonomic data, demonstrate that strain YIM 48868T represents a novel species in the genus Actinopolymorpha, for which the name Actinopolymorpha alba sp. nov. is proposed. The type strain is YIM 48868T (=CCTCC AA 208030T=DSM 45243T).
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Kineococcus rhizosphaerae sp. nov., isolated from rhizosphere soil
More LessAn orange-coloured actinomycete, designated strain RP-B16T, was isolated from a rhizosphere soil. Cells of strain RP-B16T were strictly aerobic, Gram-positive-staining, oxidase-negative, catalase-positive, motile cocci. A phylogenetic tree, based on 16S rRNA gene sequences, showed that members of the genus Kineococcus were divided into two independent clusters and that strain RP-B16T formed a coherent clade with the type strains of Kineococcus aurantiacus (99.5 % sequence similarity) and Kineococcus radiotolerans (99.1 %). Levels of 16S rRNA gene sequence similarity between strain RP-B16T and Kineococcus marinus KST3-3T and ‘Kineococcus tegulae’ T2A-S27 were lower than 97.0 %. Chemotaxonomic characteristics were typical of the genus Kineococcus in having meso-diaminopimelic acid as the diagnostic diamino acid, MK-9(H2) as the predominant menaquinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown phospholipids, anteiso-C15 : 0 as the predominant fatty acid and a DNA G+C content of 73.8 mol%. Strain RP-B16T showed levels of DNA–DNA relatedness of 34.6–37.3 % to Kineococcus aurantiacus DSM 7487T and 31.2–32.7 % to Kineococcus radiotolerans DSM 14245T. On the basis of phenotypic features and DNA–DNA hybridization data, strain RP-B16T is considered to represent a novel species of the genus Kineococcus, for which the name Kineococcus rhizosphaerae sp. nov. is proposed. The type strain is RP-B16T (=KCTC 19366T =DSM 19711T).
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Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample
A novel Gram-positive, aerobic, spore-forming actinobacterium, designated strain YIM 013T, was isolated from a mangrove sediment sample and subjected to a polyphasic taxonomic study. The peptidoglycan type was A1γ and the major whole-cell sugars contained glucose and xylose. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and some unknown phospholipids. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C15 : 0 and iso-C16 : 0. The genomic DNA G+C content was 69.3 mol%. blast search results based on an almost-complete 16S rRNA gene sequence showed that strain YIM 013T had the highest similarity with Verrucosispora gifhornensis DSM 44337T (98 %) and phylogenetic analysis revealed that strain YIM 013T should be assigned to the genus Verrucosispora. The mean level of DNA–DNA relatedness between strain YIM 013T and V. gifhornensis DSM 44337T was 38.2 %. Based on its phenotypic and genotypic characteristics, strain YIM 013T (=CCTCC AA207012T =KCTC 19195T) is proposed to be the type strain of a novel species, Verrucosispora lutea sp. nov.
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Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov.
The Mycobacterium avium complex (MAC) consists of four recognized species, Mycobacterium avium, Mycobacterium colombiense, Mycobacterium intracellulare and Mycobacterium chimaera, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous Mycobacterium species within the M. avium complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99 % similar to Mycobacterium colombiense, and the MAC-Q 16S–23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97 % similarity to M. avium. The rpoB gene sequence was 98 % similar to M. colombiense. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of M. avium and M. colombiense. Together, these findings supported a separate species status within the Mycobacterium avium complex. We propose elevation of scotochromogenic M. avium complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name Mycobacterium vulneris sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).
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Helcobacillus massiliensis gen. nov., sp. nov., a novel representative of the family Dermabacteraceae isolated from a patient with a cutaneous discharge
More LessGram-positive, non-spore-forming rods (strain 6401990T), isolated from a human cutaneous discharge were subjected to a polyphasic taxonomy study. The only respiratory quinone was MK-7 and the major fatty acids were anteiso-C15 : 0 (34.3 %), anteiso-C17 : 0 (18.7 %) and iso-C16 : 0 (18.6 %). Mycolic acids were not present. Polar lipids present were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified glycolipids. The isomer of diaminopimelic acid identified was meso-diaminopimelic acid, and the analysis of whole-cell sugars showed the presence of high amounts of galactose, ribose and some glucose. The G+C content of strain 6401990T was 68.6 %. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed 95.1 % similarity with Dermabacter hominis. On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain represents a novel species in a new genus of the family Dermabacteraceae, for which the name Helcobacillus massiliensis gen. nov., sp. nov. is proposed. The type strain is 6401990T (CSUR P17T=CIP 109418T=CCUG 53859T).
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- Archaea
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Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food
A novel red-pigmented halophilic archaeon, strain A29T, was isolated from shrimp jeotgal, a traditional salt-fermented food from Korea. This strain grows in the ranges 10–30 % (w/v) NaCl, 17–50 °C and pH 6.5–8.5, with optimal growth occurring at 15–20 % NaCl, 37–45 °C and pH 7.0–7.5. The isolate is Gram-negative and non-motile. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain A29T is associated with the genus Haloterrigena and closely related to the species Haloterrigena thermotolerans (99.0 % similarity). However, DNA–DNA hybridization experiments revealed that the level of hybridization between strain A29T and related strains of Haloterrigena is less than 70 %. The polar lipid fraction consists of phosphatidylglyerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and mannose-2,6-disulfate(1-2)-glucose glycerol diether (S2-DGD). The G+C content of genomic DNA of the type strain is 62.3 mol%. On the basis of this polyphasic taxonomic study, strain A29T should be placed in the genus Haloterrigena as a novel species, for which the name Haloterrigena jeotgali sp. nov. is proposed. The type strain of the new species is A29T (=KCTC 4020T=DSM 18794T=JCM 14585T=CECT 7218T).
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- Bacteroidetes
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Jejuia pallidilutea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater
An aerobic, pale-orange-pigmented, Gram-stain-negative bacterium, designated strain EM39T, was isolated from seawater from the eastern coast of Jeju Island, Korea, and its taxonomic status was established using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain EM39T formed a distinct lineage within the family Flavobacteriaceae and could be distinguished from strains of members of the related genera Gaetbulibacter, Mariniflexile and Tamlana by 16S rRNA gene sequence analysis (similarity values between strain EM39T and related strains were all less than 93.8 %). Cells of strain EM39T were non-gliding, catalase- and oxidase-positive rods that were devoid of flexirubin pigments. Growth was observed at 15–35 °C (optimum, 25–30 °C) and pH 6.5–9.0 (optimum, pH 7.0–8.5). The genomic DNA G+C content was 34.6 mol% and the major respiratory quinone was MK-6. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. On the basis of phenotypic and genotypic data, strain EM39T represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Jejuia pallidilutea gen. nov., sp. nov. is proposed. The type strain is EM39T (=KCTC 22298T=DSM 21165T).
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Winogradskyella rapida sp. nov., isolated from protein-enriched seawater
More LessFlavobacteria are emerging as an important group of organisms associated with the degradation of complex organic matter in aquatic environments. A novel Gram-reaction-negative, heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium, strain SCB36T, was isolated from a protein-enriched seawater sample, collected at Scripps Pier, Southern California Bight (Eastern Pacific). Analysis of the 16S rRNA gene sequence showed that the bacterium was related to members of the genus Winogradskyella within the family Flavobacteriaceae, phylum Bacteroidetes. 16S rRNA gene sequence similarity to the other Winogradskyella species was 94.5–97.1 %. DNA–DNA relatedness between strain SCB36T and Winogradskyella thalassocola KMM 3907T, its closest relative in terms of 16S rRNA gene sequence similarity, was 20 %. On the basis of the phylogenetic and phenotypic data, strain SCB36T represents a novel species of the genus Winogradskyella, for which the name Winogradskyella rapida sp. nov. is proposed. The type strain is SCB36T (=CECT 7392T =CCUG 56098T).
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Phocaeicola abscessus gen. nov., sp. nov., an anaerobic bacterium isolated from a human brain abscess sample
More LessA strictly anaerobic bacterial strain, 7401987T, was isolated from a human brain abscess sample. Cells were Gram-negative, non-spore-forming, coccoid to rod-shaped and motile by flagella in a lophotrichous arrangement. The isolate was asaccharolytic and the major cellular fatty acids were anteiso-C15 : 0 (28.2 %), C16 : 0 (18.0 %), iso-C15 : 0 (12.3 %) and iso-C17 : 0 3-OH (11.7 %). 16S rRNA gene sequence comparisons showed that the isolate was distantly related to members of the genera Bacteroides (<83.6 % similarity), Parabacteroides (<79.9 % similarity), Tannerella (<79.8 % similarity), Dysgonomonas (<79.6 % similarity), Porphyromonas (<79.3 % similarity) and Prevotella (<78.9 % similarity). The low 16S rRNA gene sequence similarity values and physiological and biochemical characteristics differentiated strain 7401987T from all known species and indicate that our isolate represents a novel species in a new genus within the phylum Bacteroidetes. The name Phocaeicola abscessus gen. nov., sp. nov. is proposed; the type strain of Phocaeicola abscessus is 7401987T (=CCUG 55929T =CSUR P22T =DSM 21584T).
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Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov.
More LessThe genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0 % similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T =JCM 12381T =IMSNU 14040T =KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T =JCM 12382T =IMSNU 14049T =KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T =KCCM 42689T =NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data.
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Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment
More LessA facultatively anaerobic, moderately halophilic, Gram-negative, filamentous bacterium, designated JC2469T, was isolated from tidal flat sediment in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the phylum Bacteroidetes and its closest taxonomic relative was Cytophaga fermentans NCIMB 2218T (89.6 % sequence similarity). Cells appeared as filaments during exponential growth, but became fragmented to rods at stationary phase. Spherical cells were also observed in aged cultures. Strain JC2469T contained iso-C15 : 0 (56.2 %) and MK-7 as the predominant fatty acid and respiratory quinone, respectively. On the basis of evidence from this polyphasic study, the isolate showed substantial differences from other genera. The phylogenetic and physiological data of the present study strongly suggest that the isolate represents a novel genus and species, for which the name Marinifilum fragile gen. nov., sp. nov. is proposed. The type strain of Marinifilum fragile is JC2469T (=IMSNU 14138T =KCTC 22488T =JCM 15579T).
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- Firmicutes And Related Organisms
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Lactobacillus aquaticus sp. nov., isolated from a Korean freshwater pond
More LessA Lactobacillus strain, IMCC1736T, was isolated recently from a Korean freshwater pond following an extensive study of the microbial community in this ecosystem. Its 16S rRNA gene was sequenced and phylogenetic analysis placed this strain within the Lactobacillus salivarius group, closely related to Lactobacillus satsumensis NRIC 0604T, with 97.9 % sequence similarity. In the present work, the taxonomic status of strain IMCC1736T has been re-evaluated. It was characterized phylogenetically, genotypically and phenotypically and, based on DNA–DNA hybridization values, this strain represents a novel Lactobacillus species. Strain IMCC1736T can be differentiated genotypically from its closest relatives by randomly amplified polymorphic DNA analysis and ribotyping patterns; phenotypically, it can be distinguished by its inability to grow in 5 % NaCl and at pH 3.3 and by certain carbohydrate fermentations. Strain IMCC1736T is Gram-positive, catalase-negative and microaerophilic. Cells are motile rods and show homofermentative metabolism. The name Lactobacillus aquaticus sp. nov. is proposed, with strain IMCC1736T (=CECT 7355T =DSM 21051T) as the type strain.
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Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic
More LessA novel, moderately halophilic, endospore-forming bacterial strain, designated Hal 1T, was isolated from a permafrost core collected from the Canadian high Arctic. The temperature for growth of strain Hal 1T was 0–30 °C with no growth observed at either −5 or 37 °C (optimum growth at about 25 °C). Strain Hal 1T was able to grow at NaCl concentrations of 0–20 % (w/v) and did not have an absolute NaCl requirement for growth; optimal growth was at 5 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain Hal 1T and the type strains of Virgibacillus carmonensis and Virgibacillus necropolis was 98.2 %; values with respect to the type strains of other recognized Virgibacillus species were below 96.0 %. The DNA G+C content of strain Hal 1T was 38.2 mol%. Levels of DNA–DNA relatedness between strain Hal 1T and the type strains of V. carmonensis and V. necropolis were 14.0 and 21.0 %, respectively. The major fatty acid of strain Hal 1T was anteiso-C15 : 0, consistent with species of the genus Virgibacillus. The cell-wall peptidoglycan of strain Hal 1T was type A1α and the major respiratory quinone was MK-7. On the basis of genotypic and physiological results, strain Hal 1T (=DSM 19574T=JCM 14839T) is proposed as the type strain of a novel species of the genus Virgibacillus, namely Virgibacillus arcticus sp. nov.
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Bacillus acidiproducens sp. nov., vineyard soil isolates that produce lactic acid
More LessTwo novel spore-forming lactic acid bacteria, strains SL213T and SL1213, were isolated from vineyard soils in Korea. Cells of both isolates were rod-shaped bacilli and contained subterminal, ellipsoidal spores. Strains were facultatively anaerobic, catalase-positive, oxidase-negative and motile with single flagella. meso-Diaminopimelic acid, glucose and galactose were detected in whole-cell hydrolysates. Major fatty acids found in the strains were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The G+C contents of the DNA were 46.1 and 46.3 mol%. 16S rRNA gene sequences from the two strains were almost identical (99.9 %) and placed them in the genus Bacillus, according to phylogenetic analysis. The type strains most closely related to SL213T were Bacillus coagulans ATCC 7050T and Bacillus badius ATCC 14574T, with 16S rRNA gene sequence similarities of 96.9 and 95.9 %, respectively. Levels of DNA–DNA relatedness between strain SL213T and strain SL1213, B. coagulans ATCC 7050T and B. badius ATCC 14574T were 92.5, 49.0 and 27.5 %, respectively. On the basis of 16S rRNA gene sequences and chemotaxonomic and phenotypic evidence given in this study, we report that SL213T represents a novel species, for which the name Bacillus acidiproducens sp. nov. is proposed. The type strain is SL213T (=KCTC 13078T =JCM 14638T).
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Oceanobacillus kapialis sp. nov., from fermented shrimp paste in Thailand
More LessA Gram-positive, rod-shaped, strictly aerobic, spore-forming, moderately halophilic bacterium, designated strain SSK2-2T, was isolated from fermented shrimp paste (ka-pi) produced in Thailand. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The isolate grew at 8–43 °C, pH 6–9 and in 0.5–24 % (w/v) NaCl (optimum, 6–14 % NaCl). The major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. Phosphatidylglycerol and diphosphatidylglycerol were the major polar lipid components. The DNA G+C content was 39.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SSK2-2T was most closely related to Oceanobacillus picturae KCTC 3821T with 98.7 % sequence similarity. Based on phenotypic and molecular features combined with DNA–DNA hybridization results (≤24.9 % with O. picturae KCTC 3821T), this strain represents a novel species of the genus Oceanobacillus for which the name Oceanobacillus kapialis sp. nov. is proposed; the type strain is SSK2-2T (=KCTC 13177T=PCU 300T=TISTR 1858T).
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Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano
A novel, obligately anaerobic, psychrotolerant bacterium, designated strain PPP2T, was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Chilean Patagonia. Cells were Gram-stain-positive, spore-forming, straight rods (0.7–0.8×3.0–5.0 μm) that were motile by means of peritrichous flagella. Growth was observed at pH 6.7−9.7 (optimum pH 8.3) and 2–37 °C (optimum 29 °C). Growth was observed between 0 and 4 % (w/v) NaCl with optimum growth at 0.5 % (w/v). Strain PPP2T was a catalase-negative chemo-organoheterotroph that was capable of fermentative metabolism. Peptone, bacto-tryptone, Casamino acids, oxalate, starch, chitin and yeast extract were utilized as substrates. The major metabolic products were acetate, butyrate and ethanol. Strain PPP2T was resistant to ampicillin, but sensitive to tetracycline, chloramphenicol, rifampicin, kanamycin, vancomycin and gentamicin. The DNA G+C content of strain PPP2T was 39.5 mol%. Phylogenetic analysis revealed that strain PPP2T was related most closely to Clostridium sticklandii SR (∼90 % 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic characteristics, strain PPP2T is considered to represent a novel species of a new genus, for which the name Proteocatella sphenisci gen. nov., sp. nov. is proposed. The type strain of Proteocatella sphenisci is PPP2T (=ATCC BAA-755T =JCM 12175T =CIP 108034T).
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Bacillus persepolensis sp. nov., a moderately halophilic bacterium from a hypersaline lake
More LessA Gram-positive, moderately halophilic, endospore-forming bacterium, designated strain HS136T, was isolated from the hypersaline lake Howz-Soltan in Iran. Cells were motile rods, producing ellipsoidal endospores at a central–subterminal position in non-swollen sporangia. Strain HS136T, a strictly aerobic bacterium, grew between pH 7.0 and 10.0 (optimal growth at pH 8.0–8.5), between 25 and 45 °C (optimal growth at 40 °C) and at salinities of 5–20 % (w/v) NaCl, growing optimally at 10 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain HS136T was shown to belong to the genus Bacillus within the phylum Firmicutes and showed closest phylogenetic similarity to Bacillus salarius BH169T (95.2 %) and Bacillus qingdaonensis CM1T (94.5 %). The DNA G+C content of this new isolate was 37.1 mol%. The major cellular fatty acids of strain HS136T were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and its polar lipid pattern consisted of phosphatidylglycerol and diphosphatidylglycerol. The isoprenoid quinone was MK-7. The peptidoglycan type is A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic evidence from this study, Bacillus persepolensis sp. nov. is proposed, with strain HS136T (=CCM 7595T=DSM 21632T=JCM 15720T=LMG 25222T) as the type strain.
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- Proteobacteria
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Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba
More LessA reductively dehalogenating, strictly anaerobic, sulfate-reducing bacterium, designated strain AA1T, was isolated from the marine sponge Aplysina aerophoba collected in the Mediterranean Sea and was characterized phenotypically and phylogenetically. Cells of strain AA1T were Gram-negative, short, curved rods. Growth of strain AA1T was observed between 20 and 37 °C (optimally at 28 °C) at pH 7–8. NaCl was required for growth; optimum growth occurred in the presence of 25 g NaCl l–1. Growth occurred with lactate, propionate, pyruvate, succinate, benzoate, glucose and sodium citrate as electron donors and carbon sources and either sulfate or 2-bromophenol as electron acceptors, but not with acetate or butyrate. Strain AA1T was able to dehalogenate several different bromophenols, and 2- and 3-iodophenol, but not monochlorinated or fluorinated phenols. Lactate, pyruvate, fumarate and malate were not utilized without an electron acceptor. The G+C content of the genomic DNA was 58.5 mol%. The predominant cellular fatty acids were C14 : 0, iso-C14 : 0, C14 : 0 3-OH, anteiso-C15 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons placed the novel strain within the class Deltaproteobacteria. Strain AA1T was related most closely to the type strains of Desulfoluna butyratoxydans (96 % 16S rRNA gene sequence similarity), Desulfofrigus oceanense (95 %) and Desulfofrigus fragile (95 %). Based on its phenotypic, physiological and phylogenetic characteristics, strain AA1T is considered to represent a novel species of the genus Desulfoluna, for which the name Desulfoluna spongiiphila sp. nov. is proposed. The type strain is AA1T (=DSM 17682T =ATCC BAA-1256T).
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Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia
More LessBiserrula 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 <50 % 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).
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Rhodoplanes pokkaliisoli sp. nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil
More LessA Gram-negative, rod-shaped, purple non-sulfur bacterial strain, designated JA415T, was isolated from the mud of a pokkali rice field located on Vypeen Island, Ernakulam, Kerala, India. Strain JA415T was motile by means of a single polar flagellum. Photo- and chemo-organoheterotrophic growth was observed using organic compounds as carbon sources and electron donors. Photo- and chemolithoautotrophic growth using thiosulfate as electron donor did not occur. Fermentative growth could not be demonstrated. Intracellular photosynthetic membranes were lamellar stacks parallel to the cytoplasmic membrane. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series were present as photosynthetic pigments. Niacin, pantothenate and p-aminobenzoate were required as growth factors. C18 : 1 ω7c was the predominant cellular fatty acid component. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA415T clustered with members of the genus Rhodoplanes in the class Alphaproteobacteria. On the basis of phenotypic and molecular genetic evidence, it is proposed that strain JA415T be classified as a representative of a novel species of the genus Rhodoplanes, family Hyphomicrobiaceae, with the name Rhodoplanes pokkaliisoli sp. nov. The type strain is JA415T (=KCTC 5711T =NBRC 104972T).
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Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium
A novel aerobic, obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium, S10T, was isolated from hot-spring sediment samples collected from Atri, Bhubaneswar, India. The cells of this isolate stained Gram-negative and were strictly aerobic, non-sporulating, rod-shaped and motile with a single polar flagellum. Strain S10T was positive for oxidase and catalase activities. It was capable of utilizing thiosulfate under mixotrophic growth conditions. Mixotrophic growth was observed at pH 6.0–8.5 and 25–45 °C; optimum growth occurred at pH 7.5–8.0 and 30–37 °C. The major cellular fatty acids were C12 : 0 3-OH, C16 : 1 ω7c, C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain S10T was 64.8 mol%. 16S rRNA gene sequence analysis indicated that the bacterium clustered within the radiation of the genus Thiomonas and showed 98.0 % similarity with Thiomonas perometabolis ATCC 23370T and Thiomonas intermedia ATCC 15466T. However, DNA–DNA reassociation values of strain S10T with Thiomonas perometabolis JCM 20426T and Thiomonas intermedia JCM 20425T, its nearest phylogenetic relatives, were 46 and 39 %, respectively. On the basis of phenotypic, physiological and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain S10T represents a novel species of the genus Thiomonas, Thiomonas bhubaneswarensis sp. nov.; the type strain is S10T (=DSM 18181T =JCM 14806T).
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Spongiibacter tropicus sp. nov., isolated from a Synechococcus culture
More LessTwo Gram-staining-negative, rod-shaped and non-motile strains, designated CL-CB221T and CL-CB467, were isolated from a Synechococcus culture derived from tropical surface water of the Pacific Ocean. The 16S rRNA gene sequences of the two strains were identical, and it was found that they belonged to the class Gammaproteobacteria, with Spongiibacter marinus HAL40bT as their closest relative (similarity of 96.3 %). Both strains grew optimally at 30–35 °C and pH 7–8 in the presence of 3–4 % (w/v) NaCl. The major cellular fatty acids were C18 : 1 ω7c, C17 : 1 ω8c, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C contents were 57.7 and 57.8 mol%, respectively. DNA–DNA hybridization experiments revealed high values (97±2 %) for relatedness between strains CL-CB221T and CL-CB467, which suggested that these two strains belong to a single species. Based on the phylogenetic, chemotaxonomic and phenotypic data presented, it is proposed that strains CL-CB221T and CL-CB467 represent a novel species of the genus Spongiibacter, for which the name Spongiibacter tropicus sp. nov. is proposed. The type strain is CL-CB221T (=KCCM 90065T =DSM 19543T).
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Castellaniella ginsengisoli sp. nov., a β-glucosidase-producing bacterium
More LessA Gram-negative, motile bacterium, designated DCY36T, was isolated from soil of a ginseng field in South Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain DCY36T belongs to genus Castellaniella in the family Alcaligenaceae of the class Betaproteobacteria. The 16S rRNA gene sequence similarities between strain DCY36T and the three recognized representatives of the genus, Castellaniella caeni Ho-11T, Castellaniella defragrans 54PinT and Castellaniella denitrificans NKNTAUT, were 98.4, 97.5 and 98.1 %, respectively. Strain DCY36T exhibited relatively low levels of DNA–DNA relatedness with respect to these three species. The G+C content of the genomic DNA was 63.7 mol%. Strain DCY36T contained ubiquinone Q-8. The major fatty acids were C16 : 0 (27.4 %), C18 : 1 ω7c (16.9 %) and summed feature 4 (C16 : 1 ω7c and C15 : 0 iso 2-OH, 32.5 %). On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain DCY36T (=KCTC 22398T=JCM 15515T) should be classified in the genus Castellaniella as the type strain of a novel species, for which the name Castellaniella ginsengisoli sp. nov. is proposed.
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Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium
More LessExtracellular peptidoglycan is commonly found in natural environments, yet little is known about its biodegradation in nature. We here describe a novel peptidoglycan-degrading bacterium, designated strain 332T, isolated from mesotrophic lake water in Denmark. The strain was a Gram-negative-staining, motile rod. It had chitinase and lysozyme activities, which are relevant to peptidoglycan degradation, and was capable of utilizing several mono- and disaccharides, amino acids and organic acids. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 332T belonged to the genus Delftia. Fatty acids of the strain included C8 : 0 and C10 : 0, which are characteristic of the genus Delftia. The DNA G+C content of the strain was 65.3 mol%. A DNA–DNA hybridization value of 66.2 % was found between strain 332T and Delftia tsuruhatensis DSM 17581T. Based on differences in physiological and biochemical characteristics, the strain is considered to represent a novel species, for which the name Delftia lacustris sp. nov. is proposed. The type strain is 332T (=DSM 21246T =LMG 24775T). An emended description of Delftia tsuruhatensis is also presented.
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Desulfovibrio idahonensis sp. nov., sulfate-reducing bacteria isolated from a metal(loid)-contaminated freshwater sediment
Two novel sulfate-reducing bacteria, strains CY1T and CY2, were isolated from heavy-metal-contaminated sediments of Lake Coeur d'Alene, Idaho, USA. Strains CY1T and CY2 were found to contain c-type cytochromes and to reduce sulfate, sulfite, thiosulfate, elemental sulfur, DMSO, anthraquinone disulfonate and fumarate using lactate as an electron donor. In a comparison of 16S rRNA gene sequences, CY1T and CY2 were found to be 100 % identical, but only 97 and 92.4 % similar, respectively, to the type strains of Desulfovibrio mexicanus and Desulfovibrio aminophilus. Unlike these species, however, CY1T was neither able to disproportionate thiosulfate nor able to use yeast extract or amino acids as electron donors. These data, considered in conjunction with differences among strain CY1T and the two related type strains in chemotaxonomy, riboprint patterns, temperature and pH optima, support recognition of a distinct and novel species within the genus Desulfovibrio, Desulfovibrio idahonensis sp. nov., with the type strain CY1T (=DSM 15450T =JCM 14124T).
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Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae
More LessA Gram-negative, aerobic, neutrophilic, coccoid bacterium, strain E4A9T, was isolated from a deep-sea sediment sample collected from the East Pacific polymetallic nodule region. 16S rRNA gene sequence analysis showed that the isolate was related to the type strain of Altererythrobacter epoxidivorans (96.0 % sequence similarity). Lower 16S rRNA gene sequence similarities were observed with other members of the genera Altererythrobacter (94.7 %), Erythrobacter (94.0–95.4 %), Erythromicrobium (94.8 %) and Porphyrobacter (94.6–95.1 %) of the family Erythrobacteraceae. Phylogenetic analysis including all described species of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a distinct phylogenetic lineage with the family Erythrobacteraceae. Chemotaxonomic analysis revealed ubiquinone-10 as the predominant respiratory quinone, anteiso-C15 : 0, iso-C14 : 0 and iso-C15 : 0 as major fatty acids, and phosphatidylglycerol as the major polar lipid. The DNA G+C content was 71.5 mol%. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic and genotypic data presented in this study, strain E4A9T represents a novel species in a new genus in the family Erythrobacteraceae for which the name Croceicoccus marinus gen. nov., sp. nov. is proposed; the type strain is E4A9T (=CGMCC 1.6776T=JCM 14846T).
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Marinimicrobium locisalis sp. nov., isolated from a marine solar saltern, and emended description of the genus Marinimicrobium
More LessA Gram-negative, motile and rod-shaped bacterial strain, designated ISL-43T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-43T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of approximately 2 % NaCl. It contained Q-8 as the predominant ubiquinone and C16 : 0, C19 : 0 ω8c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 58.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ISL-43T fell within the genus Marinimicrobium, clustering with Marinimicrobium agarilyticum M18T with a bootstrap value of 100 %. Strain ISL-43T exhibited 16S rRNA gene sequence similarity values of 98.1 and 95.5 % to M. agarilyticum M18T and Marinimicrobium koreense M9T, respectively. Strain ISL-43T exhibited DNA–DNA relatedness values of 17 and 10 % to M. agarilyticum KCTC 12357T and M. koreense KCTC 12356T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-43T represents a novel species within the genus Marinimicrobium, for which the name Marinimicrobium locisalis sp. nov. is proposed. The type strain is ISL-43T (=KCTC 22484T=CCUG 56757T).
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Hirschia maritima sp. nov., isolated from seawater
More LessA Gram-negative, aerobic, orange-coloured bacterium, designated strain GSW-2T, was isolated from seawater sampled at a beach and its taxonomic status was established by using a polyphasic approach. Vegetative cells produced a prostheca and reproduced by budding. Mature vegetative cells were spherical, oval- or rod-shaped (0.6–1.1×1.2–1.3 μm) and both vegetative cells and buds produced one or more flagella. Cells grew well at 30 °C and at pH 8.1–9.1, and produced a non-diffusible pigment. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSW-2T was most closely related to the type strain of Hirschia baltica (97.5 % similarity), a member of the family Hyphomonadaceae, class Alphaproteobacteria. Chemotaxonomic characteristics supported the assignment of strain GSW-2T to the genus Hirschia, including the dominant cellular fatty acids (summed feature 7 and C16 : 0), isoprenoid quinone (mainly Q-10) and DNA G+C content (44.5 mol%). Levels of DNA–DNA relatedness between strain GSW-2T and Hirschia baltica DSM 5838T were 8.8–13.6 %. On the basis of phenotypic features and DNA–DNA hybridization data, strain GSW-2T is considered to represent a novel species of the genus Hirschia, for which the name Hirschia maritima sp. nov. is proposed. The type strain is GSW-2T (=DSM 19733T=JCM 14974T).
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‘Candidatus Liberibacter solanacearum’, associated with plants in the family Solanaceae
More LessA liberibacter (isolate NZ082226) was detected in a symptomatic tomato plant and subsequently in five other members of the family Solanaceae: capsicum, potato, tamarillo, cape gooseberry and chilli. Phylogenetic analyses of the 16S rRNA gene sequence, the deduced amino acid sequence of the rplJ gene and a partial nucleotide sequence of the β operon indicated that isolate NZ082226 represents a novel candidate species of ‘Candidatus Liberibacter’, for which the name ‘Candidatus Liberibacter solanacearum’ is proposed.
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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 °C. Cells contained numerous intracellular poly-β-hydroxybutyrate granules (3–4 per cell). The major cellular fatty acid was cyclo C19 : 0 ω8c 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).
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Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil
More LessThe taxonomic position of a yellow-pigmented bacterial strain, designated DS20T, isolated from a hexachlorocyclohexane dump site at Lucknow, India was determined based on a polyphasic taxonomic characterization. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain DS20T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity with ‘Pseudomonas abikonensis’ IAM 12404 (98.8 %), followed by Sphingobium rhizovicinum CC-FH12-1T (97.4 %) and Sphingobium olei IMMIB HF-1T (97.2 %). Therefore, the taxonomic characterization of ‘P. abikonensis’ NBRC 16140 was also undertaken. Phylogenetic, chemotaxonomic and morphological analyses, based on signature sequences, DNA–DNA hybridizations, fatty acid profiles, physiological characterizations and polar lipid profiles confirmed that both strains DS20T and ‘P. abikonensis’ NBRC 16140 represent two distinct species of the genus Sphingobium. Therefore, two novel Sphingobium species are proposed, Sphingobium lactosutens sp. nov. (type strain, DS20T=CCM 7540T=MTCC 9471T) and Sphingobium abikonense sp. nov. (type strain, NBRC 16140T=IAM 12404T=KCTC 2864T).
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Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater
A Gram-negative, pale-yellow, non-spore-forming bacterium, motile with single polar flagella, strain E6T, was isolated from coastal seawater collected from Tianjin, China, and its taxonomic position was investigated using a polyphasic approach. Strain E6T requires NaCl for growth and grows optimally at pH 8.2 and 36 °C and in the presence of 2.0 % (w/v) NaCl. It is positive for catalase and oxidase, and reduces nitrate to nitrite. The major fatty acids (>10 %) are C18 : 1 ω7c (64.71 %) and 11-methyl C18 : 1 ω7c (12.38 %), the ubiquinone system is Q-10 and the DNA G+C content is 53.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain E6T represented a new lineage in the Alphaproteobacteria and is related to genera Cucumibacter, Devosia, Ochrobactrum and Ahrensia. Strain E6T shows highest 16S rRNA gene sequence similarity (93.3 %) to Cucumibacter marinus CL-GR60T and less than 92.2 % similarity to other relatives. It can be differentiated from its closest phylogenetic neighbours on the basis of several phenotypic features, including nitrate reduction, assimilation of d-glucose, l-arabinose, d-mannose, mannitol and maltose and major fatty acid composition. A polyphasic analysis supported the conclusion that strain E6T represents a novel genus and species of the family Hyphomicrobiaceae, for which the name Zhangella mobilis gen. nov., sp. nov. is proposed. The type strain of Zhangella mobilis is E6T (=CGMCC 1.7002T =JCM 15144T).
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Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil
A yellow-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain KIS3-4T, was isolated from soil collected on Daechung Island in the West Sea of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KIS3-4T in a distinct lineage in the family Xanthomonadaceae. Strain KIS3-4T shared 87.3–93.7 % sequence similarity with members of the family Xanthomonadaceae, and was related most closely to the genera Dyella and Dokdonella. In its biochemical characteristics, strain KIS3-4T was clearly separable from other genera within the family Xanthomonadaceae on the basis of the hydrolysis of cellulose and urea, high G+C content (64 mol%) and fatty acid profile. Major fatty acids (>10 % of the total fatty acids) were iso-C17 : 1 ω9c (32.8 %), iso-C17 : 0 (18.0 %) and iso-C16 : 0 (12.7 %). Q-8 was the predominant respiratory quinone. Phosphatidylethanolamine and several unidentified aminophospholipids and phospholipids were present. Based on its unique phenotypic, genotypic and phylogenetic features, strain KIS3-4T represents a novel genus and species, for which the name Rudaea cellulosilytica gen. nov., sp. nov. is proposed. The type strain of Rudaea cellulosilytica is KIS3-4T (=KACC 12734T =JCM 15422T).
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Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella
A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 °C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values <70 % (42.6 and 14.8 % with A. aestuarii B11T and A. fetalis CCUG 30811T, respectively). Genotypic, physiological and biochemical analyses allowed the differentiation of strain MS1T from type strains of species belonging to the genus Alishewanella. Therefore, we propose that strain MS1T (=KCTC 22429T =JCM 15561T) is assigned to a novel species, Alishewanella jeotgali sp. nov.
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Identification of Beijerinckia fluminensis strains CIP 106281T and UQM 1685T as Rhizobium radiobacter strains, and proposal of Beijerinckia doebereinerae sp. nov. to accommodate Beijerinckia fluminensis LMG 2819
More LessDuring the course of a research project with free-living, nitrogen-fixing bacteria, we determined the 16S rRNA gene sequence of Beijerinckia fluminensis strains UQM 1685T and CIP 106281T and discovered that they were only 90.6–91.2 % similar to the sequences of strains of other Beijerinckia species and subspecies. Moreover, the highest similarity to these sequences (99.7 %) corresponded to strains of Rhizobium radiobacter (including Agrobacterium tumefaciens). Other diagnostic features confirmed that the two strains have the same origin but do not descend from the nomenclatural type. At the same time, B. fluminensis LMG 2819 was characterized and it was found that its properties also do not agree with the original description of the species, although it can be considered a member of the genus. Further characterization, including chemotaxonomic and other phenotypic traits, allows us to propose (i) the identification of B. fluminensis strains CIP 106281T and UQM 1685T as strains of Rhizobium radiobacter and (ii) the designation of strain LMG 2819T (=CECT 7311T) as the type strain of a novel species, Beijerinckia doebereinerae sp. nov.
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Marinospirillum celere sp. nov., a novel haloalkaliphilic, helical bacterium isolated from Mono Lake
Two strains of a Gram-negative, helical, haloalkaliphilic bacterium were isolated from Mono Lake (USA). Both strains were mesophilic and grew between 13 and 55 °C, with optimum growth at 35–45 °C. The optimum pH for growth was 9.5. Growth was observed at NaCl concentrations of 0.5–12 % (w/v), with optimum growth at 2 % NaCl. Both isolates were motile by means of bipolar tuft flagella, coccoid body-forming and strictly aerobic. It was concluded that they belong to the same species, based on DNA–DNA hybridization values (95 % DNA relatedness). DNA G+C contents of the novel strains were 52.1 and 52.3 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were shown to be related closely to the members of the genus Marinospirillum (family Oceanospirillaceae, class Gammaproteobacteria). Sequence similarity of strain v1c_Sn-redT to the type strains of Marinospirillum alkaliphilum, Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum insulare was 95.0, 92.7, 91.8 and 91.8 %, respectively. Chemotaxonomic data [major ubiquinone, Q8; major fatty acids, C18 : 1(n-7) and C16 : 0] and physiological and biochemical tests supported the affiliation of the novel strains to the genus Marinospirillum as members of a novel species, for which the name Marinospirillum celere sp. nov. is proposed, with the type strain v1c_Sn-redT (=LMG 24610T=VKM 2416T).
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Thiohalocapsa marina sp. nov., from an Indian marine aquaculture pond
More LessA spherical-shaped, phototrophic, purple sulfur bacterium was isolated in pure culture from anoxic sediment in a marine aquaculture pond near Bheemli (India). Strain JA142T is Gram-negative and non-motile. It has a requirement for NaCl (optimum of 2 % and maximum of 6 % w/v NaCl). Intracellular photosynthetic membranes are of the vesicular type. In vivo absorption spectra indicate the presence of bacteriochlorophyll a and carotenoids of the okenone series as photosynthetic pigments. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA142T is related to halophilic purple sulfur bacteria of the genera Thiohalocapsa and Halochromatium, with the highest sequence similarity to Thiohalocapsa halophila DSM 6210T (97.5 %). Morphological and physiological characteristics differentiate strain JA142T from other species of the genera Halochromatium and Thiohalocapsa. Strain JA142T is sufficiently different from Thiohalocapsa halophila based on 16S rRNA gene sequence analysis and morphological and physiological characteristics to allow the proposal of a novel species, Thiohalocapsa marina sp. nov., with the type strain JA142T (=JCM 14780T =DSM 19078T).
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Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.
Bacteria isolated from eucalyptus leaves and shoots showing symptoms of blight and die-back collected in Uganda, Uruguay and Argentina and from maize displaying brown stalk rot symptoms in South Africa were tentatively placed in the genus Pantoea on the basis of phenotypic and biochemical tests. These isolates, together with two strains (LMG 2558 and LMG 2560) previously assigned to Pantoea agglomerans based on protein electrophoregrams but later excluded from this species, were further investigated using molecular techniques. 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) revealed that the strains were phylogenetically closely related to Pantoea agglomerans, Pantoea stewartii and Pantoea ananatis. MLSA and amplified fragment length polymorphism analysis placed the strains into four separate clusters, not containing any of the type strains of species of the genus Pantoea. DNA–DNA hybridization confirmed the classification of the isolates into four novel species, for which the names Pantoea vagans sp. nov. (type strain R-21566T =LMG 24199T =BCC 105T =BD 765T), Pantoea eucalypti sp. nov. (type strain R-25678T =LMG 24197T =BCC 076T =BD 769T), Pantoea deleyi sp. nov. (type strain R-31523T =LMG 24200T =BCC 109T =BD 767T) and Pantoea anthophila sp. nov. (type strain LMG 2558T =BD 871T =NCPPB 1682T) are proposed.
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Campylobacter avium sp. nov., a hippurate-positive species isolated from poultry
More LessThree strains of an unusual hippurate-positive Campylobacter species were isolated at 37 °C from caecal contents of broiler chickens and a turkey. All strains were initially identified as Campylobacter by means of genus-specific PCR, but none was further identified using specific PCRs for known thermophilic species. Phylogenetic analyses based on 16S rRNA, rpoB and groEL gene sequences revealed that these strains formed a robust clade distinct from other Campylobacter species. Amplified fragment length polymorphism analysis and whole-cell protein electrophoresis were subsequently carried out and confirmed the divergence between the avian strains and other taxa. These data indicate that the unidentified Campylobacter strains belong to a novel taxon which could be distinguished from other campylobacters through its phenotypic and genotypic characteristics. The name Campylobacter avium sp. nov., is proposed for the novel species, with the type strain 86/06T (=LMG 24591T =CCUG 56292T).
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- Eukaryotic Micro-Organisms
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Geotrichum bryndzae sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces
More LessTen strains of an asexual arthroconidial yeast species were isolated from Bryndza, a traditional Slovak artisanal sheep cheese, which was manufactured from raw milk during a 4-month summer production period at two Slovakian sites (the northern Ružomberok and the central-southern Tisovec areas). Sequence comparison of the D1/D2 domains of the large-subunit rRNA gene revealed that this yeast represents a novel species of the genus Geotrichum, which contains anamorphs of the ascogenous genus Galactomyces, for which the name Geotrichum bryndzae sp. nov. is proposed (type culture CCY 16-2-1T =NRRL Y-48450T =CBS 11176T). The novel species is most closely related to Geotrichum silvicola NRRL Y-27641T, although yeasts with identical or very similar sequences have been found throughout the world.
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Cryptococcus ibericus sp. nov., Cryptococcus aciditolerans sp. nov. and Cryptococcus metallitolerans sp. nov., a new ecoclade of anamorphic basidiomycetous yeast species from an extreme environment associated with acid rock drainage in São Domingos pyrite mine, Portugal
More LessIn this report, we describe three novel asexual basidiomycetous yeast species, Cryptococcus aciditolerans sp. nov. (type strain CBS 10872T =SDY 081T), Cryptococcus ibericus sp. nov. (type strain CBS 10871T=SDY 022T) and Cryptococcus metallitolerans sp. nov. (type strain CBS 10873T =SDY 190T), which were isolated from acid rock drainage collected at the São Domingos mine in southern Portugal. Phylogenetic analysis of molecular sequence data indicated that the novel species belong to the order Filobasidiales of the class Tremellomycetes and form a well-separated clade, next to Cryptococcus gastricus and Cryptococcus gilvescens. Since the novel species also share a peculiar ecology, being able to thrive under extreme environmental conditions characterized by very low pH and high concentrations of heavy metals, we designate this combination of phylogenetic and ecological characteristics as an ecoclade.
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- Evolution, Phylogeny And Biodiversity
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Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus
More LessPhylogenetic analysis and species identification of members of the genus Streptococcus were carried out using partial sequence comparison of the 16S rRNA gene (1468–1478 bp), rpoB, encoding the β subunit of RNA polymerase (659–680 bp), sodA, encoding the manganese-dependent superoxide dismutase (435–462 bp), groEL, encoding the 60 kDa heat-shock protein (757 bp), and gyrB, encoding the Β subunit of DNA gyrase (458–461 bp). For the first time, most species within the genus Streptococcus were represented in the study (65 strains, representing 58 species and nine subspecies). Phylogenies inferred from rpoB, sodA, gyrB and groEL sequence comparisons were more discriminative than those inferred from 16S rRNA gene sequence comparison, and showed common clusters. The minimal interspecies divergence was 0.3, 2.7, 0, 2.5 and 3.4 % for the 16S rRNA gene, rpoB, sodA, gyrB and groEL, respectively. In general, groEL partial gene sequence comparison represented the best tool for identifying species and subspecies and for phylogenetic analysis.
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