- Volume 58, Issue 9, 2008
Volume 58, Issue 9, 2008
- 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 (i.e. documents certifying deposition and availability of type strains). 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 and in the volume author index. 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 58, 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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Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field
More LessStrain Gsoil 098T, a Gram-positive, non-spore-forming, non-motile coccus, was isolated from soil from a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Gsoil 098T belongs to the family Nocardioidaceae, and the highest degrees of sequence similarity were found with Aeromicrobium marinum T2T (99.0 %), A. panaciterrae Gsoil 161T (98.9 %), A. alkaliterrae KSL-107T (98.4 %), A. fastidiosum KCTC 9576T (98.1 %) and A. erythreum NRRL B-3381T (97.5 %). Chemotaxonomic analysis revealed that strain Gsoil 098T possesses menaquinone MK-9(H4) and predominant fatty acids C16 : 0, 10-methyl C18 : 0 and C18 : 0. DNA–DNA hybridization results and physiological and biochemical tests clearly demonstrated that strain Gsoil 098T represents a distinct species. Based on these data, Gsoil 098T (=KCTC 19207T =JCM 14732T =GBS 39T) should be classified as the type strain of a novel Aeromicrobium species, for which the name Aeromicrobium ginsengisoli sp. nov. is proposed.
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Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton
More LessA rod-shaped marine bacterium, designated CL-Z59T, was isolated from seawater enriched with zooplankton. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CL-Z59T belongs to the genus Nocardioides, the highest level of sequence similarity (99.2 %) being found with respect to Nocardioides marinisabuli KCCM 42681T. However, DNA–DNA hybridization experiments between strain CL-Z59T and N. marinisabuli KCCM 42681T revealed a mean relatedness value of 33 %. Cells were Gram-positive, strictly aerobic and non-motile. Strain CL-Z59T grew optimally at pH 6–7 and 25–30 °C and at a NaCl concentration of 3 %. The isolate was characterized chemotaxonomically as having ll-diaminopimelic acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the predominant cellular fatty acid was iso-C16 : 0. The DNA G+C content was 73.3 mol%. On the basis of phylogenetic, genotypic and phenotypic data, strain CL-Z59T represents a novel species of the genus Nocardioides, for which the name Nocardioides salarius sp. nov. is proposed. The type strain is CL-Z59T (=KCCM 42320T=DSM 18239T).
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Haloactinospora alba gen. nov., sp. nov., a halophilic filamentous actinomycete of the family Nocardiopsaceae
A novel halophilic, filamentous, actinomycete strain, designated YIM 90648T, was isolated from a salt lake in Xinjiang Province, north-west China, and subjected to a polyphasic taxonomic study. Optimal growth occurred at 37 °C, pH 7.0–8.0 and 15 % (w/v) NaCl. The aerial mycelium of strain YIM 90648T formed long chains of spores at maturity and the spores were cylindrical with smooth surfaces. Spore chains with pseudosporangia at the end were borne on the substrate mycelium and most spores had wrinkled surfaces. Strain YIM 90648T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and ribose as the major whole-cell components. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol mannoside. MK-10(H8), MK-11(H4), MK-11(H6) and MK-11(H8) were the predominant menaquinones. The major fatty acids were i-C16 : 0 and ai-C17 : 0. The DNA G+C content was 68 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 90648T formed a distinct lineage within the family Nocardiopsaceae and showed 16S rRNA gene sequence similarity of 93.3–95.0 % with members of the family Nocardiopsaceae. On the basis of the polyphasic evidence, a novel genus and species, Haloactinospora alba gen. nov., sp. nov., is proposed to accommodate this isolate. The type strain of Haloactinospora alba is YIM 90648T (=DSM 45015T =CCTCC AA 206008T).
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Pseudonocardia ailaonensis sp. nov., isolated from soil in China
More LessA Gram-positive, aerobic actinomycete, designated strain YIM 45505T, was isolated from a soil sample collected from Yunnan province, south-west China. Cells exhibited cream–white aerial mycelium and orange–yellow to yellow–brown substrate mycelium. The substrate mycelium fragmented into rod-shaped elements, and the aerial mycelium formed long chains of spores. 16S rRNA gene sequence analysis revealed that strain YIM 45505T was related most closely to Pseudonocardia oroxyli DSM 44984T (98.5 % similarity) and Pseudonocardia halophobica IMSNU 21327T (97.5 %). The G+C content of the DNA of strain YIM 45505T was 74.1 mol%. Combined with results of DNA–DNA hybridization and phenotypic tests, these data revealed that strain YIM 45505T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia ailaonensis sp. nov. is proposed. The type strain is YIM 45505T (=KCTC 19315T =DSM 44979T).
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Kribbella catacumbae sp. nov. and Kribbella sancticallisti sp. nov., isolated from whitish-grey patinas in the catacombs of St Callistus in Rome, Italy
More LessSeveral nocardioform actinomycetes were isolated from tufaceous surfaces with whitish-grey patinas in the catacombs of St Callistus in Rome, Italy. The morphology of the isolates and their chemotaxonomic characteristics such as ll-diaminopimelic acid in the cell-wall peptidoglycan, the major menaquinone of MK-9(H4), phosphatidylinositol, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids, as well as complex cellular fatty acid patterns with anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0 as predominating components, were in agreement with their classification as members of the genus Kribbella by 16S rRNA gene sequence analysis. The isolates fell into two clusters as revealed by their ribosomal intergenic spacer, RiboPrint and cellular fatty acid patterns and by their MALDI-TOF mass spectra. The two clusters were represented by the strains BC631T and BC633T which shared 97.9 % 16S rRNA gene sequence similarity. Strain BC631T represented a cluster of yellow pigmented strains and was a phylogenetic neighbour of Kribbella koreensis DSM 17837T (gene sequence similarity 98.0 %), while strain BC633T was related to Kribbella flavida DSM 17836T and Kribbella karoonensis DSM 17344T (gene sequence similarities of 98.8 % and 98.6 %, respectively). Strains BC631T and BC633T could be differentiated from each other and from their closest phylogenetic neighbours by phenotypic characteristics and DNA–DNA relatedness values far below 70 %. It is concluded that the two new strains represent two novel species, for which the names Kribbella catacumbae sp. nov. (type strain BC631T=DSM 19601T=JCM 14968T) and Kribbella sancticallisti sp. nov. (type strain BC633T=DSM 19602T=JCM 14969T) are proposed.
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Devriesea agamarum gen. nov., sp. nov., a novel actinobacterium associated with dermatitis and septicaemia in agamid lizards
More LessFive bacterial isolates were recovered from dermatitis or organ lesions of five agamid lizards. Three strains were recovered from Uromastyx species with dermatitis or septicaemia. All five isolates were Gram-positive small rods that could not be identified using conventional phenotypic systems. They grew on sheep blood agar as small haemolytic colonies after 24 h of incubation at temperatures between 25 and 42 °C under aerobic, microaerophilic or anaerobic conditions. They were catalase-positive and non-motile. Comparative analysis of 16S rRNA gene sequences revealed that the strains represent a new taxon within the class Actinobacteria. Their nearest phylogenetic neighbours were determined as Brachybacterium faecium LMG 19847T (95.9 % 16S rRNA gene sequence similarity) and Dermabacter hominis NCIMB 13131T (95.3 % similarity). The DNA G+C content of one of the novel isolates, strain IMP2T, was 61 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of coryneform bacteria, it is proposed that this novel taxon be classified as Devriesea agamarum gen. nov., sp. nov. The type strain is IMP2T (=LMG 24257T=CCUG 55056T).
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Nocardia altamirensis sp. nov., isolated from Altamira cave, Cantabria, Spain
A novel actinomycete strain, OFN S17T, was isolated from a sample collected from Altamira Cave, Cantabria, Spain. This strain was identified by using a polyphasic taxonomic approach. The 16S rRNA, hsp65 and sod gene sequences of the strain were determined and compared with those of representative Nocardia species. The results showed that strain OFN S17T should be assigned to the genus Nocardia. Phylogenetic analysis indicated that strain OFN S17T was most closely related to the type strain of Nocardia tenerifensis (98.6, 96.2 and 96 % similarity, respectively, for the 16S rRNA, hsp65 and sod gene sequences). The DNA G+C content was 64.4 mol%. DNA–DNA hybridization analyses revealed 29 % relative reassociation between the DNA of strain OFN S17T and N. tenerifensis DSM 44704T. The phenotypic and genotypic data show that strain OFN S17T merits recognition as a representative of a novel species of the genus Nocardia, for which the name Nocardia altamirensis sp. nov. is proposed. The type strain is OFN S17T (=CIP 109606T =DSM 44997T).
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Leifsonia pindariensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas, and emended description of the genus Leifsonia
More LessStrain PON10T is a yellow-pigmented, Gram-positive, aerobic, motile, rod-shaped bacterium isolated from the Pindari glacier of the Indian Himalayas. The cell-wall peptidoglycan contained dl-diaminobutyric acid as the diamino acid. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 and the major isoprenoid quinones were MK-10 and MK-11. Based on the above characteristics, strain PON10T was assigned to the genus Leifsonia. blast sequence similarity results indicated that Leifsonia ginsengi and Leifsonia poae were the nearest relatives, with 16S rRNA gene sequence similarity of 97.0 and 96.8 % to the respective type strains. A difference of 3 % in the 16S rRNA gene sequence indicated that PON10T represents a novel species of the genus Leifsonia, and therefore DNA–DNA hybridization was not done. In addition, PON10T showed a number of differences from Leifsonia ginsengi and Leifsonia poae with respect to phenotypic and chemotaxonomic characteristics. Thus, based on the differences it exhibited from Leifsonia ginsengi and Leifsonia poae, strain PON10T was identified as representing a novel species named Leifsonia pindariensis sp. nov. The type strain is PON10T (=LMG 24222T =MTCC9128T). An emended description of the genus Leifsonia is also presented.
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- Archaea
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Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake
A Gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain BG-1T, was isolated from a salt lake, Lake Bagaejinnor, in Inner Mongolia, China. Strain BG-1T was able to grow at 25–55 °C, required at least 2.5 M NaCl for growth (with an optimum at 3.4 M NaCl) and grew at pH 6.0–9.0 (with an optimum at pH 7.5). Hypotonic treatment with less than 2.0 M NaCl caused cell lysis. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence positioned the isolate within the genus Halorubrum in the family Halobacteriaceae. Strain BG-1T was most closely related to Halorubrum aidingense 31-hongT (98.8 % sequence similarity), Halorubrum saccharovorum NCIMB 2081T (98.6 %), Halorubrum lacusprofundi ACAM 34T (98.6 %) and Halorubrum lipolyticum 9-3T (98.4 %). However, values for DNA–DNA hybridization between strain BG-1T and the most closely related members of the genus Halorubrum were below 40 %. Analysis of the polar lipids of strain BG-1T revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid found in neutrophilic species of the genus Halorubrum. The G+C content of the genomic DNA was 69.4 mol% (T m). Comparison of the phenotypic characteristics of the strain with those of Halorubrum species supported the conclusion that BG-1T represents a novel species within this genus, for which the name Halorubrum kocurii sp. nov. is proposed. The type strain is BG-1T (=CECT 7322T =CGMCC 1.7018T =JCM 14978T).
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Halobacterium piscisalsi sp. nov., from fermented fish (pla-ra) in Thailand
A Gram-negative, motile, rod-shaped, extremely halophilic archaeon, designated strain HPC1-2T, was isolated from pla-ra, a salt-fermented fish product of Thailand. Strain HPC1-2T was able to grow at 20–60 °C (optimum at 37–40 °C), at 2.6–5.1 M NaCl (optimum at 3.4–4.3 M NaCl) and at pH 5.0–8.0 (optimum at pH 7.0–7.5). Hypotonic treatment with less than 1.7 M NaCl caused cell lysis. The major polar lipids of the isolate were C20C20 derivatives of phosphatidylglycerol, methylated phosphatidylglycerol phosphate, phosphatidylglycerol sulfate, triglycosyl diether, sulfated triglycosyl diether and sulfated tetraglycosyl diether. The G+C content of the DNA was 65.5 mol%. 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Halobacterium in the family Halobacteriaceae. Based on 16S rRNA gene sequence similarity, strain HPC1-2T was related most closely to Halobacterium salinarum DSM 3754T (99.2 %) and Halobacterium jilantaiense JCM 13558T (97.8 %). However, low levels of DNA–DNA relatedness suggested that strain HPC1-2T was genotypically different from these closely related type strains. Strain HPC1-2T could also be differentiated based on physiological and biochemical characteristics. Therefore, strain HPC1-2T is considered to represent a novel species of the genus Halobacterium, for which the name Halobacterium piscisalsi sp. nov. is proposed. The type strain is HPC1-2T (=BCC 24372T=JCM 14661T=PCU 302T).
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- Bacteroidetes
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Mucilaginibacter kameinonensis sp., nov., isolated from garden soil
More LessAn extracellular polysaccharide-producing bacterium, strain SCKT, was isolated from a soil sample taken from Kameino, Fujisawa, Japan. The isolate was Gram-negative and cells were non-motile, irregular-shaped rods that grew optimally at 25 °C and grew between pH 5 and 8. Strain SCKT contained MK-7 as the major isoprenoid quinone, iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids and sphingolipids, with d-17 : 0 as the main dihydrosphingosine. Flexirubin-type pigments were also present. The DNA G+C content was 43.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain SCKT was shown to belong to the genus Mucilaginibacter. The 16S rRNA gene sequence similarity between strain SCKT and the two type strains of Mucilaginibacter was 93 %. The results of physiological and biochemical tests allowed phenotypic differentiation of the strain from published Mucilaginibacter species. Therefore, strain SCKT represents a novel species, for which the name Mucilaginibacter kameinonensis sp. nov. is proposed. The type strain is SCKT (=NBRC 102645T =KCTC 22227T).
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Sphingobacterium anhuiense sp. nov., isolated from forest soil
Wei Wei, Yu Zhou, Xu Wang, Xing Huang and Ren LaiA Gram-negative bacterium, designated strain CW 186T, was isolated from forest soil in Anhui province, China. Cells of strain CW 186T were strictly aerobic, non-motile and rod-shaped. The strain grew optimally at 25–30 °C and pH 6.0–8.0. The major cellular fatty acids of strain CW 186T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (9.8 %) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 33.7 %). The predominant isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 36.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain CW 186T formed a monophyletic cluster with Sphingobacterium daejeonense LMG 23402T, Sphingobacterium composti LMG 23401T, Sphingobacterium composti DSM 18850T, Sphingobacterium mizutaii ATCC 33299T and Sphingobacterium spiritivorum ATCC 33861T. Sequence similarities were less than 94 % (the maximal similarity was about 93.9 % to S. composti LMG 23401T) to Sphingobacterium species with validly published names. A polyphasic taxonomic study including chemotaxonomic and phylogenetic analyses demonstrated that strain CW 186T should be classified as representing a novel species of the genus Sphingobacterium, for which the name Sphingobacterium anhuiense sp. nov. is proposed. The type strain is CW 186T (=KCTC 22209T=CCTCC AB 207197T).
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Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae
More LessA rod-shaped, Gram-negative, chemo-organotrophic, heterotrophic, strictly aerobic, gliding bacterial strain, SW5T, capable of degrading sulphated fucans from brown algae was isolated from a water-treatment facility that recycles the effluent of an alginate-extraction plant in Landerneau (Brittany, France). Its taxonomic position was investigated by a polyphasic approach. Strain SW5T formed dark-yellow colonies, was oxidase-negative and catalase-positive and grew optimally at 25 °C and pH 7.5 and in the presence of 2.5 % (w/v) NaCl. The DNA G+C content was 34.5 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene allocated strain SW5T to the genus Mariniflexile in the family Flavobacteriaceae, with a similarity of 98.4 % to the type strain of Mariniflexile gromovii, the only recognized Mariniflexile species. Its low level of DNA–DNA relatedness (<25 %) with the type strain of this species and differentiating phenotypic characteristics demonstrated that strain SW5T constitutes a novel Mariniflexile species, for which the name Mariniflexile fucanivorans sp. nov. is proposed. Strain SW5T (=CIP 109502T =DSM 18792T) is the type strain.
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Aestuariicola saemankumensis gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from tidal flat sediment
More LessA Gram-negative, non-motile, pleomorphic bacterial strain, designated SMK-142T, was isolated from a tidal flat of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain SMK-142T grew optimally at pH 7.0–8.0, 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SMK-142T clustered with Lutibacter litoralis with which it exhibited a 16S rRNA gene sequence similarity value of 91.2 %. This cluster joined the clade comprising the genera Tenacibaculum and Polaribacter at a high bootstrap resampling value. Strain SMK-142T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 37.2 mol%. Strain SMK-142T was differentiated from three phylogenetically related genera, Lutibacter, Tenacibaculum and Polaribacter, on the basis of low 16S rRNA gene sequence similarity values and differences in fatty acid profiles and in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SMK-142T represents a novel genus and species for which the name Aestuariicola saemankumensis gen. nov., sp. nov. is proposed (phylum Bacteroidetes, family Flavobacteriaceae). The type strain of the type species, Aestuariicola saemankumensis sp. nov., is SMK-142T (=KCTC 22171T=CCUG 55329T).
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Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir
More LessA Gram-negative, rod-shaped, yellow pigmented bacterium, strain NJ-26T, was isolated from sediment of the eutrophicated Guanting Reservoir in Beijing, China. A phylogenetic analysis based on 16S rRNA gene sequences placed strain NJ-26T within the genus Flavobacterium in the family Flavobacteriaceae. The highest sequence similarity was found with Flavobacterium cucumis R2A45-3T (97.7 %). The major fatty acids (>5 %) of the isolate were iso-C15 : 0, iso-C17 : 1 ω9c, C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. The G+C content of the genomic DNA was 40.6 mol%. The DNA–DNA relatedness value with F. cucumis R2A45-3T was 5.4 %. Molecular and phenotypic data suggest that strain NJ-26T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium cheniae sp. nov. is proposed. The type strain is NJ-26T (=CGMCC 1.6844T =NBRC 103934T).
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Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir
More LessStrain NJ-44T, isolated from sediment of the eutrophic Guanting Reservoir in Beijing (China), was subjected to a taxonomic study using a polyphasic approach. The strain was aerobic, with salmon-pink-pigmented colonies on R2A agar. Cells were single, Gram-negative rods, motile by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NJ-44T belonged to the phylum Bacteroidetes, with Terrimonas ferruginea ATCC 13524T (90.8 % similarity), Terrimonas lutea DYT (90.5 %) and Niabella aurantiaca R2A15-11T (89.1 %) as its closest relatives. Strain NJ-44T was clearly differentiated from members of the genera Terrimonas and Niabella in its DNA G+C content (40.6 mol%) and its major fatty acids, iso-C15 : 1 G, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 1 A and iso-C15 : 0 3-OH. It is proposed that strain NJ-44T represents a novel genus and species, named Sediminibacterium salmoneum gen. nov., sp. nov. The type strain of Sediminibacterium salmoneum is strain NJ-44T (=CGMCC 1.6845T =NBRC 103935T).
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- Other Bacteria
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Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum ‘Synergistetes’, isolated from an anaerobic sludge digester
A novel anaerobic, mesophilic, amino-acid-utilizing bacterium, strain 158T, was isolated from an anaerobic digester of a wastewater treatment plant. Cells of strain 158T were non-motile, rod-shaped (2.0–3.0 × 0.8–1.0 μm) and stained Gram-negative. Optimal growth occurred at 37 °C and pH 7.0 in an anaerobic basal medium containing 1 % Casamino acids. Strain 158T fermented arginine, histidine, lysine and serine and showed growth on yeast extract, brain-heart infusion (BHI) medium and tryptone, but not on carbohydrates, organic acids or alcohols. The end products of degradation were: acetate, butyrate, H2 and CO2 from arginine; acetate, propionate, butyrate, H2 and CO2 from lysine; and acetate, propionate, butyrate, valerate, H2 and CO2 from histidine, serine, BHI medium, Casamino acids and tryptone. The DNA G+C content was 55.8 mol%. The 16S rRNA gene sequence of strain 158T showed only 92.6 % sequence similarity with that of Synergistes jonesii, the only described species of the ‘Synergistes’ group. The major cellular fatty acids were iso-C15 : 0 (16.63 %), iso-C15 : 0 3-OH (12.41 %) and C17 : 1 ω6c (9.46 %) and the polar fatty acids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylamine; these fatty acid profiles did not resemble those of any recognized bacterial species. Due to the considerable differences in genotypic, phenotypic and phylogenetic characteristics between strain 158T and those of its nearest relative, it is proposed that strain 158T represents a novel species in a new genus, Cloacibacillus evryensis gen. nov., sp. nov., in the phylum ‘Synergistetes’. The type strain is 158T (=DSM 19522T=JCM 14828T).
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- Proteobacteria
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Description of Ancylobacter oerskovii sp. nov. and two additional strains of Ancylobacter polymorphus
More LessA Gram-negative, pleomorphic, rod-shaped, non-spore-forming bacterium, designated strain NS05T, was isolated from soil after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS05T was shown to be phylogenetically related to the genera Ancylobacter, Starkeya and Angulomicrobium (96.3–98.1 % sequence similarity), class Alphaproteobacteria. Strain NS05T was most closely related to Ancylobacter rudongensis AS 1.1761T (98.1 % sequence similarity). The whole-cell fatty acid pattern of strain NS05T was typical of those found in members of the genus Ancylobacter. Its main components were C18 : 1 ω7c (60.4 %), C19 : 0 ω8c cyclo (28.3 %) and C16 : 0 (7.4 %) and hydroxylated compounds were absent. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS05T with respect to the four Ancylobacter species with validly published names. Therefore, it is concluded that NS05T represents a novel species of the genus Ancylobacter, for which the name Ancylobacter oerskovii sp. nov. is proposed. The type strain is NS05T (=DSM 18746T =CCM 7435T). Two other oxalate-utilizing strains, NS03 and NS04, isolated from paper-mill effluents, were shown by 16S rRNA gene sequence analysis to be affiliated to the species Ancylobacter polymorphus. The study of their physiological properties extends the knowledge of the physiological variability within this species.
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Pseudoalteromonas arctica sp. nov., an aerobic, psychrotolerant, marine bacterium isolated from Spitzbergen
More LessA novel aerobic, psychrotolerant marine bacterium was isolated at 4 °C from seawater samples collected from Spitzbergen in the Arctic. The strain was a polar-flagellated, Gram-negative bacterium that grew optimally at 10–15 °C and pH 7–8 in media containing 2–3 % NaCl (w/v), using various carbohydrates and organic acids as substrates. The main fatty acid components included 16 : 0 (12.7 % of total fatty acids), straight-chain saturated fatty acid methyl ester (FAME) and 16 : 1ω7c (40.2 %) monounsaturated FAME. Phylogenetic analysis revealed a close relationship (99 % 16S rRNA gene sequence similarity) between the novel isolate and Pseudoalteromonas elyakovii KMM 162T and some other species of the genus Pseudoalteromonas. The DNA G+C content of the novel strain was 39 mol%. DNA–DNA hybridization showed only 47.6 % DNA–DNA relatedness with P. elyakovii KMM 162T, 44.2 % with Pseudoalteromonas distincta KMM 638T and 22.6 % with Pseudoalteromonas nigrifaciens NCIMB 8614T. Based on phylogenetic and phenotypic characteristics, this isolate represents a novel species of the genus Pseudoalteromonas for which the name Pseudoalteromonas arctica is proposed; the type strain is A 37-1-2T (=LMG 23753T=DSM 18437T).
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Microbulbifer halophilus sp. nov., a moderately halophilic bacterium from north-west China
A Gram-negative, rod-shaped, moderately halophilic bacterium, designated strain YIM 91118T, motile with a single polar flagellum, was isolated from Xinjiang province in north-west China and subjected to a polyphasic taxonomic study. Strain YIM 91118T grew optimally at 37 °C, pH 7.0–8.0 and 10 % NaCl (w/v). Its major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, C16 : 0 and iso-C17 : 1 ω9c. The predominant lipoquinone was Q-8. The DNA G+C content was 63.2 mol%. All of these chemotaxonomic data supported the assignment of the new isolate to the genus Microbulbifer. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 91118T belongs to the genus Microbulbifer and it formed a distinct subclade with Microbulbifer maritimus KCCM 41774T. The levels of 16S rRNA gene sequence similarity to the type strains of Microbulbifer species were in the range 93.5–95.0 %. The mean level of DNA–DNA relatedness between strain YIM 91118T and M. maritimus KCCM 41774T was 45.8 %. On the basis of phenotypic properties, phylogeny and genomic data, strain YIM 91118T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer halophilus sp. nov. is proposed. The type strain is YIM 91118T (=CCTCC AB 206094T =KCTC 12848T). Furthermore, it is necessary to emend the description of the genus Microbulbifer.
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Luteimonas aquatica sp. nov., isolated from fresh water from Southern Taiwan
More LessA yellow-pigmented bacterial strain, designated RIB1-20T, isolated from fresh water was investigated by means of a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses with the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Luteimonas, its two closest neighbours being Luteimonas composti CC-YY255T (96.1 % sequence similarity) and Luteimonas mephitis B1953/27.1T (95.8 %). Strain RIB1-20T was clearly distinguished from both of those type strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain RIB1-20T represents a novel species of the genus Luteimonas, for which the name Luteimonas aquatica sp. nov. is proposed. The type strain is RIB1-20T (=BCRC 17731T =LMG 24212T).
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Halomonas lutea sp. nov., a moderately halophilic bacterium isolated from a salt lake
More LessA Gram-negative, moderately halophilic bacterium, designated YIM 91125T, was isolated from a salt lake in Xinjiang province, north-west China. The isolate grew at salinities in the range 1–20 % (w/v) and at 4–45 °C. Optimal growth occurred at 37 °C, pH 7.5 and 5–10 % (w/v) NaCl. Cells were short rods motile by means of single polar flagella. The major fatty acids were C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c and C12 : 0 3-OH. The DNA G+C content was 60.8 mol%. The predominant respiratory quinone was Q-9. A comparison of 16S rRNA gene sequences revealed its relationship to Halomonas species, its closest neighbours being Halomonas pantelleriensis (95.9 % similarity to the type strain) and Halomonas muralis (95.4 % similarity). On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain YIM 91125T represents a novel member of the genus Halomonas, for which the name Halomonas lutea sp. nov. is proposed. The type strain is YIM 91125T (=KCTC 12847T =CCTCC AB 206093T).
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Roseomonas vinacea sp. nov., a Gram-negative coccobacillus isolated from a soil sample
Strain CPCC 100056T, which was isolated from a soil sample collected from the Qinghai–Tibet plateau, China, was subjected to a polyphasic taxonomic study. The organism was coccobacillus-shaped, non-motile and formed vinaceous colonies on ISP2 agar medium. The respiratory quinone was ubiquinone-10. The major fatty acids were C18 : 1 ω7c and C16 : 1 ω7c and/or C16 : 1 ω6c. The G+C content of the genomic DNA was 67.3 mol%. A comparison of sequences in GenBank revealed that strain CPCC 100056T exhibited highest 16S rRNA gene sequence similarity (84.5–95.5 %) with Roseomonas species. Strain CPCC 100056T could be distinguished from all Roseomonas species with validly published names by differences in phenotypic and genotypic properties. In view of the combined phenotypic, chemotaxonomic and phylogenetic data, strain CPCC 100056T should be classified as a representative of a novel species in the genus Roseomonas, Roseomonas vinacea sp. nov.; the type strain is CPCC 100056T (=KCTC 22045T =CCM 7468T).
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Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea
More LessA Gram-negative, strictly aerobic, non-motile, club-shaped bacterial strain, designated CL-ES2T, was isolated from coastal water from the east coast of Korea. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain CL-ES2T was related to the genera Phaeobacter (95.0–96.6 % similarity to the type strains), Leisingera (96.1 %) and Marinovum (95.6 %) in the family Rhodobacteraceae. However, strain CL-ES2T did not form a robust clade with any species of the Roseobacter clade, instead forming a distinct subline. The optimum temperature and pH for growth were 25 °C and pH 7. Strain CL-ES2T was able to grow with sea salts at concentrations in the range 2–6 %, with optimum growth occurring at 3–4 %. The major fatty acid was C18 : 1 ω7c (75.2 %). The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and three unidentified lipids. The isoprenoid quinone was Q-10. The G+C content of the DNA was 47.0 mol%. On the basis of the data from the polyphasic analysis, strain CL-ES2T represents a novel genus and species, for which the name Pelagicola litoralis gen. nov., sp. nov. is proposed. The type strain of Pelagicola litoralis is CL-ES2T (=KCCM 42274T =DSM 18290T).
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Tranquillimonas alkanivorans gen. nov., sp. nov., an alkane-degrading bacterium isolated from Semarang Port in Indonesia
More LessStrain A34T, an obligately halophilic, Gram-negative, non-motile, rod-shaped bacterium, was isolated from seawater obtained from Semarang Port in Indonesia. It possesses a pink pigment and degrades short-chain alkanes. It is positive for catalase and oxidase and reduces nitrate to nitrite. Analyses of 16S rRNA gene sequences revealed a clear affiliation of this strain with the family ‘Rhodobacteraceae’ in the class Alphaproteobacteria, with its closest relatives being Salipiger mucosus A3T (94.9 % sequence similarity) and Palleronia marisminoris B33T (93.4 %). The DNA G+C content was 69.1 mol%. The major cellular fatty acids of strain A34T were C18 : 1 ω7c (56.2 %), C19 : 0 cyclo ω8c (26.0 %) and C16 : 0 (9.1 %), while the predominant respiratory lipoquinone was ubiquinone-10. Based on the physiological and phylogenetic data, it is proposed that strain A34T should be classified in a new genus and species, for which the name Tranquillimonas alkanivorans gen. nov., sp. nov. is proposed. The type strain of Tranquillimonas alkanivorans is strain A34T (=JCM 14836T =DSM 19547T).
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Oceaniserpentilla haliotis gen. nov., sp. nov., a marine bacterium isolated from haemolymph serum of blacklip abalone
More LessAn aerobic, Gram-negative bacterial isolate, strain DSM 19503T, was isolated from haemolymph serum of the blacklip abalone Haliotis rubra. Cells of strain DSM 19503T were vibrioid to spiral, motile and were able to pass through sterile filters with a pore size of 0.2 μm, indicating the small width of the bacterium. The isolate was psychrophilic, with the ability to grow at 2–8 °C. Oxidase activity was present, whereas catalase activity was absent. The nearly complete 16S rRNA gene sequence of strain DSM 19503T was obtained and phylogenetic sequence analysis showed that it formed a distinct genus in the family Oceanospirillaceae with highest sequence similarity of 92.9 % to Oleispira antarctica RB-8T. The cellular fatty acid composition was dependent on the growth medium used for cultivation. During growth on seawater agar, the fatty acid composition was most similar to that of Oleispira antarctica DSM 14852T, with mainly C16 : 0 (90.3 %). In contrast, Columbia blood agar/NaCl-grown cells exhibited mainly C10 : 0 3-OH (11.8 %), C12 : 1 cis5 (8.2 %), C16 : 1 cis9 (29.6 %), C16 : 0 (19.3 %) and C18 : 1 cis9 (13.1 %) fatty acids. On the basis of phenotypic, chemotaxonomic and genotypic data, strain DSM 19503T is considered to represent a novel species in a new genus for which the name Oceaniserpentilla haliotis gen. nov., sp. nov. is proposed. The type strain of Oceaniserpentilla haliotis is DSM 19503T (=LMG 24225T).
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Castellaniella caeni sp. nov., a denitrifying bacterium isolated from sludge of a leachate treatment plant
More LessA Gram-negative, non-motile, facultatively anaerobic, denitrifying bacterial strain, designated Ho-11T, was isolated from sludge of a leachate treatment plant and was characterized taxonomically by using a polyphasic approach. The G+C content of the genomic DNA was 63.5 mol%. Strain Ho-11T contained ubiquinone Q-8 as the major respiratory lipoquinone and putrescine as the predominant polyamine. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 29.3 %), C16 : 0 (28.0 %) and summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t; 19.8 %). Comparative 16S rRNA gene sequence analysis showed that strain Ho-11T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. 16S rRNA gene sequence similarities between strain Ho-11T and the type strains of the two recognized species of the genus, Castellaniella denitrificans DSM 11046T and Castellaniella defragrans DSM 12141T, were 97.8 and 97.4 %, respectively. Levels of similarity between strain Ho-11T and all other recognized species of the family Alcaligenaceae were below 95.6 %. Strain Ho-11T exhibited relatively low levels of DNA–DNA relatedness with respect to C. denitrificans DSM 11046T (33 %) and C. defragrans DSM 12141T (28 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain Ho-11T (=KCTC 12197T=LMG 23411T) should be classified in the genus Castellaniella as the type strain of a novel species, for which the name Castellaniella caeni sp. nov. is proposed.
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Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny)
More LessA Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm Eisenia foetida. Comparisons of 16S rRNA gene sequences indicated its relatedness to the betaproteobacterial genus Acidovorax and the novel isolates shared 92–94 % sequence similarity with recognized species of this genus. Gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and independent clade. The DNA G+C content was 67.0±0.2 mol%. Major fatty acids were C16 : 0, C16 : 1 ω7c and C17 : 0 cyclo. While capable of growing in fully aerated media, all isolates favoured low oxygen concentrations and all required biotin or a mix of amino acids in order to grow on defined mineral media. Based on phylogenies inferred from three housekeeping gene sequences (gap, recA and rpoC), DNA–DNA hybridization values, the unique ecology and the distinct physiology of the novel strains, the new genus Verminephrobacter gen. nov. is proposed for the earthworm nephridial symbionts. The name Verminephrobacter eiseniae sp. nov. is proposed for the type species with strain EF01-2T (=ATCC BAA-1489T=DSM 19286T) as the type strain of the type species.
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Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta
More LessDuring a study of endophytic nitrogen-fixing bacteria present in the wild rice species Oryza alta, eight novel isolates were obtained from surface-sterilized roots and classified in the genus Rhizobium on the basis of almost-complete 16S rRNA gene sequence analysis. These strains can nodulate Phaseolus vulgaris and Glycine max. The highly similar protein patterns, DNA fingerprint patterns of insertion sequence-based PCR (IS-PCR) and DNA–DNA hybridizations showed that these novel isolates were members of the same species. The closest phylogenetic relatives of the representative strain Alt 505T of the novel group were Rhizobium etli CFN 42T and Rhizobium indigoferae CCBAU 71714T, with 96.2 and 96.0 % 16S rRNA gene sequence similarity, respectively. Low DNA–DNA relatedness with the type strains of R. etli, R. indigoferae, Rhizobium hainanense, Rhizobium mongolense and Rhizobium galegae and differences in IS-PCR fingerprinting patterns, SDS-PAGE of proteins, antibiotic resistance, phenotypic tests and comparison of cellular fatty acids with Rhizobium species indicated that the novel group of isolates were distinct from previously described species. Based on these results, we propose to place them in a novel species, as Rhizobium oryzae sp. nov. The type strain is Alt 505T (=LMG 24253T =CGMCC 1.7048T).
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Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia
Two rhizobial strains, Br3407T and Br3405, were isolated from nitrogen-fixing nodules on the roots of Mimosa caesalpiniifolia, a legume tree native to Brazil. On the basis of 16S rRNA gene sequence similarities, both strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA hybridizations, pulsed-field gel electrophoresis of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia sabiae sp. nov. is proposed. The type strain is strain Br3407T (=LMG 24235T =BCRC 17587T).
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Acetobacter fabarum sp. nov., an acetic acid bacterium from a Ghanaian cocoa bean heap fermentation
More LessSix acetic acid bacterial isolates, obtained during a study of the microbial diversity of spontaneous fermentations of Ghanaian cocoa beans, were subjected to a polyphasic taxonomic study. (GTG)5-PCR fingerprinting grouped the isolates together, but they could not be identified using this method. Phylogenetic analysis based on 16S rRNA gene sequences allocated the isolates to the genus Acetobacter and revealed Acetobacter lovaniensis, Acetobacter ghanensis and Acetobacter syzygii to be nearest neighbours. DNA–DNA hybridizations demonstrated that the isolates belonged to a single novel genospecies that could be differentiated from its phylogenetically nearest neighbours by the following phenotypic characteristics: no production of 2-keto-d-gluconic acid from d-glucose; growth on methanol and d-xylose, but not on maltose, as sole carbon sources; no growth on yeast extract with 30 % d-glucose; and weak growth at 37 °C. The DNA G+C contents of four selected strains were 56.8–58.0 mol%. The results obtained prove that the isolates should be classified as representatives of a novel Acetobacter species, for which the name Acetobacter fabarum sp. nov. is proposed. The type strain is strain 985T (=R-36330T =LMG 24244T =DSM 19596T).
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Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium
A denitrifying bacterium, designated strain FST, was isolated from anoxic digested sludge on oestradiol [17β-oestra-1,3,5(10)-triene-3,17-diol] or testosterone (17β-hydroxyandrost-4-en-3-one) as the sole source of carbon and energy with nitrate as the electron acceptor. Strain FST represents the first known bacterium to grow anaerobically on both oestradiol (C-18) and testosterone (C-19). Steroidal hormones were degraded completely by nitrate reduction to dinitrogen monoxide, which was further reduced to dinitrogen in stationary-phase cultures. Gram-negative cells were slightly curved rods, 0.3–0.5×0.6–1.6 μm in size, motile, non-fermentative, non-spore-forming and catalase- and oxidase-positive, showing optimal growth at pH 7.0, 28 °C and 0.1 % (w/v) NaCl. Beside steroidal hormones, the bacterium utilized only a narrow range of organic substrates with nitrate as the electron acceptor, including several fatty acids and glutamate. No aerobic or anaerobic growth occurred on liquid or solid complex media. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain FST has no known close relatives and represents a distinct lineage within the Gammaproteobacteria. Together with the genera Nevskia, Hydrocarboniphaga, Solimonas and Sinobacter (less than 88 % 16S rRNA gene sequence similarity to strain FST), it forms a phylogenetic cluster separated from the families Chromatiaceae, Ectothiorhodospiraceae and Xanthomonadaceae. The quinone system of strain FST consisted exclusively of ubiquinone Q-8. The dominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Spermidine in combination with putrescine and traces of sym-homospermidine were the basic polyamines. The major fatty acids detected in testosterone- or heptanoate-grown cells were C15 : 0 and C17 : 1 ω8c, minor hydroxylated fatty acids were C11 : 0 3-OH and C12 : 0 3-OH. The G+C content of the DNA was 61.9 mol%. Based on the high 16S rRNA gene sequence divergence and different phenotypic properties from previously described gammaproteobacteria in combination with chemotaxonomic data, strain FST is considered to represent a new genus and species, for which the name Steroidobacter denitrificans gen. nov., sp. nov. is proposed. The type strain of Steroidobacter denitrificans is FST (=DSM 18526T =JCM 14622T).
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Chelatococcus daeguensis sp. nov., isolated from wastewater of a textile dye works, and emended description of the genus Chelatococcus
More LessA Gram-negative, non-spore-forming, rod-shaped bacterial strain, K106T, was isolated from wastewater collected from a textile dye works in Korea. Strain K106T grew optimally at pH 7.0–7.5 and 30–37 °C in the presence of 0–1.0 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed that strain K106T joined the type strain of Chelatococcus asaccharovorans with a bootstrap resampling value of 99.9 %. The predominant ubiquinone of strain K106T was Q-10. The fatty acid profile of strain K106T was similar to that of C. asaccharovorans DSM 6462T. Major polar lipids of strain K106T and C. asaccharovorans DSM 6462T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two aminolipids and two unidentified phospholipids. sym-Homospermidine, spermidine and putrescine were major polyamines. The DNA G+C content was 68.3 mol%. Strain K106T exhibited 16S rRNA gene sequence similarity of 96.6 % to the type strain of C. asaccharovorans. DNA–DNA relatedness data and differential phenotypic properties, particularly differences in cell morphology and the ability to utilize nitrilotriacetate, demonstrated that strain K106T can be differentiated from C. asaccharovorans. On the basis of phenotypic, phylogenetic and genetic data, strain K106T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus daeguensis sp. nov. is proposed. The type strain is K106T (=KCTC 12979T =CCUG 54519T).
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Pseudoxanthomonas sacheonensis sp. nov., isolated from BTEX-contaminated soil in Korea, transfer of Stenotrophomonas dokdonensis Yoon et al. 2006 to the genus Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and emended description of the genus Pseudoxanthomonas
A Gram-negative, strictly aerobic, rod-shaped bacterium, designated strain BD-c54T, was isolated from BTEX (benzene, toluene, ethylbenzene and xylenes)-contaminated soil in Sacheon, Korea. Growth of strain BD-c54T was observed at 15–35 °C (optimum 25–30 °C) and pH 6.0–9.5 (optimum pH 7.0–8.0). The predominant fatty acids were iso-C15 : 0, iso-C17 : 1 ω9c, iso-C11 : 0 3-OH, iso-C16 : 0, iso-C11 : 0 and iso-C17 : 0. The strain contained large amounts of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and a small amount of an unknown amino-group-containing polar lipid as polar lipids. The major quinone was ubiquinone-8 (Q-8) and the G+C content of the genomic DNA was 67.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain BD-c54T formed a tight phylogenetic lineage with Pseudoxanthomonas yeongjuensis GR12-1T within the genus Pseudoxanthomonas and was most closely related to P. yeongjuensis GR12-1T and [Stenotrophomonas] dokdonensis DS-16T, with 98.3 and 96.6 % 16S rRNA gene sequence similarity, respectively. The DNA–DNA relatedness between strain BD-c54T and P. yeongjuensis GR12-1T was 24.5 %. On the basis of chemotaxonomic data and molecular properties, strain BD-c54T represents a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas sacheonensis sp. nov. is proposed. The type strain is BD-c54T (=KCTC 22080T =DSM 19373T). In addition, the transfer of Stenotrophomonas dokdonensis to Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and an emended description of the genus Pseudoxanthomonas are proposed.
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- Eukaryotic Micro-Organisms
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Metschnikowia shivogae sp. nov., a yeast species associated with insects of morning glory flowers in East Africa
More LessThe novel species Metschnikowia shivogae is described to accommodate three isolates recovered from insects of morning glory flowers at two localities in East Africa. The isolates differ slightly in rDNA ITS and D1/D2 large-subunit sequences and one isolate featured a two-base heterogeneity that might be the result of recombination between two variant rDNAs. M. shivogae is a sister species to Metschnikowia aberdeeniae and shares the same habitat. The reproductive boundaries of M. aberdeeniae, which were not clear in the past, have now been elucidated further. The type strain of Metschnikowia shivogae sp. nov. is strain SUB 04-310.1T (h +; =CBS 10292T =NRRL Y-27924T) and the allotype is strain UWOPS 07-203.2 (h −; =CBS 10770 =NRRL Y-48447).
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- Other Gram-Positive Bacteria
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Lactobacillus hordei sp. nov., a bacteriocinogenic strain isolated from malted barley
More LessA high-throughput screening effort, designed to isolate bacteriocin-producing lactic acid bacteria (LAB) from malted cereals, resulted in the isolation of four bacteriocin-producing strains that could not be assigned conclusively to recognized species. The four isolates (UCC128T, UCC125, UCC126 and UCC127) were found to share identical (100 %) 16S rRNA gene sequences and were therefore deemed to belong to the same species. The strains were Gram-positive, catalase-negative, non-motile homofermentative LAB. The closest recognized relative to strain UCC128T identified based on comparative 16S rRNA gene sequence analysis was Lactobacillus mali DSM 20444T (97 % similarity). The strains were characterized phenotypically to identify specific growth requirements. DNA–DNA hybridization between strain UCC128T and L. mali DSM 20444T revealed a level of relatedness of only 39.4 %. This indicates that strain UCC128T does not belong to the species L. mali. The four bacteriocin-producing strains are therefore considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus hordei sp. nov. is proposed. The type strain is UCC128T (=DSM 19519T=LMG 24241T).
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Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium
It is proposed that Clostridium proteoclasticum be reclassified as Butyrivibrio proteoclasticus comb. nov. on the basis of phylogenetic position, DNA G+C content and physiological traits. Phylogenetic analyses based on 16S rRNA gene sequences from an extensive range of taxa within clostridial rRNA subcluster XIVa grouped C. proteoclasticum together with isolates of the genus Butyrivibrio, though this species was genetically distinct from the extant Butyrivibrio species examined. The DNA G+C content of C. proteoclasticum was originally erroneously reported as 28 mol%. However the genome sequence of the type strain of C. proteoclasticum, strain B316T, and HPLC analysis estimate the DNA G+C content as 40 mol%, which is within the range reported for strains of Butyrivibrio. C. proteoclasticum was distinguishable from other species of the genus Butyrivibrio as the 16S rRNA gene from strain B316T shared less than 97 % sequence similarity with sequences from the type strains of Butyrivibrio species. C. proteoclasticum was also able to convert linoleic acid to stearic acid, in contrast to other species of Butyrivibrio. Physiological characteristics, including carbon source utilization, volatile fatty acid production and proteinase activities, were assessed for a panel of representative strains of the genera Butyrivibrio and Pseudobutyrivibrio and C. proteoclasticum. These data, together with the phylogenetic analyses, support the reclassification of Clostridium proteoclasticum as a separate species within the genus Butyrivibrio, Butyrivibrio proteoclasticus comb. nov. (type strain B316T=ATCC 51982T=DSM 14932T).
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Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China
More LessA Gram-positive, rod-shaped, motile, spore-forming bacterium, strain SA-7-6T, was isolated from desert soil in China and was subjected to a polyphasic taxonomic study. The strain grew optimally at pH 7.5 and 37 °C. The G+C content of the genomic DNA of strain SA-7-6T was 53.7 mol%. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Strain SA-7-6T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. 16S rRNA gene sequence analysis showed that the new isolate shared highest similarity with Paenibacillus glycanilyticus JCM 11221T (96.6 %) and Paenibacillus daejeonensis KCTC 3745T (96.6 %). Based on morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain SA-7-6T is considered to represent a novel species of the genus Paenibaillus, for which the name Paenibacillus tarimensis sp. nov. is proposed. The type strain is SA-7-6T (=CCTCC AB 206108T=DSM 19409T).
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Sporosarcina antarctica sp. nov., a psychrophilic bacterium isolated from the Antarctic
A Gram-positive, psychrophilic, rod-shaped bacterium, designated strain N-05T, was isolated from soil samples collected off King George Island, west Antarctica (6 ° 13′ 31″ S 5 ° 57′ 08″ W). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N-05T was related to members of the genus Sporosarcina and had highest 16S rRNA gene sequence similarity with the type strain of Sporosarcina macmurdoensis (98.0 %). The temperature range for growth of strain N-05T was 0–23 °C, with optimum growth occurring at 17–18 °C and approximately pH 6.0–8.0. Strain N-05T had MK-7 as the major menaquinone and anteiso-C15 : 0 and C16 : 1 ω7c alcohol as major fatty acids. The genomic DNA G+C content was 39.2 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain N-05T is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina antarctica is proposed. The type strain is N-05T (=CGMCC 1.6503T=JCM 14646T).
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Clostridium amylolyticum sp. nov., isolated from H2-producing UASB granules
Lei Song and Xiuzhu DongA Gram-stain-positive, strictly anaerobic, mesophilic, amylolytic, rod-shaped bacterium, designated strain SW408T, was isolated from a laboratory-scale H2-producing upflow anaerobic sludge blanket reactor. The strain grew at 24–45 °C (no growth at or below 22 °C or at or above 47 °C), with optimum growth at 37 °C. The pH range for growth was 4.0–9.0 (no growth at or below pH 3.6 or at or above pH 9.3), with optimum growth at pH 7.0. Starch, cellobiose, glucose, fructose, galactose, lactose, maltose, mannose, ribose and sucrose supported growth. The major end products from glucose fermentation were ethanol, acetate, hydrogen and carbon dioxide. Abundant H2 was produced from starch fermentation. The DNA G+C content was 33.1 mol% (T m method). Phylogenetic analysis based on 16S rRNA gene sequence analysis showed that the bacterium represents a previously unrecognized species within Clostridium rRNA cluster I and is most closely related to the type strain of Clostridium frigidicarnis (94.9 % similarity). On the basis of phenotypic, genotypic and phylogenetic characteristics, strain SW408T was identified as a representative of a novel species of the genus Clostridium, for which the name Clostridium amylolyticum sp. nov. is proposed. The type strain is SW408T (=JCM 14823T=AS 1.5069T=CGMCC 1.5069T).
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Paenibacillus konsidensis sp. nov., isolated from a patient
A Gram-positive, rod-shaped bacterium, designated strain LBYT, was isolated from the blood of a Korean patient. The organism could not be identified based on conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that it belonged to the genus Paenibacillus, but was distinct from recognized Paenibacillus species. Strain LBYT was related most closely to the type strains of Paenibacillus macerans and Paenibacillus popilliae, with 16S rRNA gene sequence similarities of 96.2 and 95.4 %, respectively. The major fatty acids of strain LBYT were anteiso-C15 : 0 (43.8 %), C16 : 0 (10.4 %), iso-C16 : 0 (10.3 %), iso-C15 : 0 (9.2 %) and anteiso-C17 : 0 (8.3 %). On the basis of biochemical characteristics, fatty acid composition and comparative 16S rRNA gene sequence analysis, strain LBYT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus konsidensis sp. nov. is proposed. The type strain is LBYT (=ABB-ID-KSY9T=KCTC 13165T=JCM 14798T).
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Halolactibacillus alkaliphilus sp. nov., a moderately alkaliphilic and halophilic bacterium isolated from a soda lake in Inner Mongolia, China, and emended description of the genus Halolactibacillus
More LessA moderately alkaliphilic and halophilic bacterium was isolated from sediment of Xiarinaoer soda lake located in the Inner Mongolia municipality. This bacterium, designated strain H-5T, was a facultative anaerobe, Gram-positive, rod-shaped and non-motile. Strain H-5T grew in complex medium with 0.5–30 % (w/v) NaCl and at pH 7.5–13. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinones found in this strain were MK-9H4 and MK-9H2, and the major cellular fatty acids were C16 : 0 and anteiso-C13 : 0. The DNA G+C content of strain H-5T was 38.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H-5T was located in the genus Halolactibacillus. The 16S rRNA gene sequence similarities between strain H-5T and the type strains of the two recognized species of the genus Halolactibacillus were 98.6 and 98.0 %. The DNA–DNA relatedness values between strain H-5T and the two type strains were 19 and 5 %. Based on the phenotypic and chemotaxonomic data, the phylogenetic analysis and genomic distinctiveness, strain H-5T is considered to represent a novel species of the genus Halolactibacillus, for which the name Halolactibacillus alkaliphilus is proposed. The type strain is H-5T (=CGMCC AS 1.6843T=NBRC 103919T).
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Reclassification of the genus Leuconostoc and proposals of Fructobacillus fructosus gen. nov., comb. nov., Fructobacillus durionis comb. nov., Fructobacillus ficulneus comb. nov. and Fructobacillus pseudoficulneus comb. nov.
More LessA taxonomic study was made of the genus Leuconostoc. The species in the genus were divided into three subclusters by phylogenetic analysis based on the 16S rRNA gene sequences. The three subclusters were the Leuconostoc mesenteroides subcluster (comprising L. carnosum, L. citreum, L. gasicomitatum, L. gelidum, L. inhae, L. kimchii, L. lactis, L. mesenteroides and L. pseudomesenteroides), the L. fructosum subcluster (L. durionis, L. ficulneum, L. fructosum and L. pseudoficulneum) and the L. fallax subcluster (L. fallax). Phylogenetic trees based on the sequences of the 16S–23S rRNA gene intergenic spacer region, the rpoC gene or the recA gene indicated a good correlation with the phylogenetic tree based on 16S rRNA gene sequences. The species in the L. fructosum subcluster were morphologically distinguishable from the species in the L. mesenteroides subcluster and L. fallax as species in the L. fructosum subcluster had rod-shaped cells. In addition, the four species in the L. fructosum subcluster needed an electron acceptor for the dissimilation of d-glucose and produced acetic acid from d-glucose rather than ethanol. On the basis of evidence presented in this study, it is proposed that the four species in the L. fructosum subcluster, Leuconostoc durionis, Leuconostoc ficulneum, Leuconostoc fructosum and Leuconostoc pseudoficulneum, should be transferred to a novel genus, Fructobacillus gen. nov., as Fructobacillus durionis comb. nov. (type strain D-24T=LMG 22556T=CCUG 49949T), Fructobacillus ficulneus comb. nov. (type strain FS-1T=DSM 13613T=JCM 12225T), Fructobacillus fructosus comb. nov. (type strain IFO 3516T=DSM 20349T=JCM 1119T=NRIC 1058T) and Fructobacillus pseudoficulneus comb. nov. (type strain LC-51T=DSM 15468T=CECT 5759T). The type species of the genus Fructobacillus is Fructobacillus fructosus gen. nov., comb. nov.. No significant physiological and biochemical differences were found between the species in the L. mesenteroides subcluster and L. fallax in the present study and thus L. fallax remains as a member of the genus Leuconostoc.
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- International Committee On Systematics Of Prokaryotes
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- Taxonomic Note
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Nomenclature and taxonomy of halophilic archaea – comments on the proposal by DasSarma and DasSarma for nomenclatural changes within the order Halobacteriales
More LessP. DasSarma & S. DasSarma [Saline Systems 4 (2008), 5] have proposed far-reaching changes in the nomenclature and taxonomy of the halophilic archaea of the order Halobacteriales, family Halobacteriaceae. While re-evaluation of the taxonomic classification of strains within the group is to be encouraged, the nomenclatural changes proposed are in violation of the General Considerations, Principles and Rules of the International Code of Nomenclature of Bacteria.
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