- Volume 65, Issue Pt_2, 2015
Volume 65, Issue Pt_2, 2015
- Notification List
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 64, part 11, of the IJSEM
More LessThis listing of names of prokaryotes 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).
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- New Taxa
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- Archaea
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Metallosphaera tengchongensis sp. nov., an acidothermophilic archaeon isolated from a hot spring
More LessTwo novel acidothermophilic archaea, strains Ric-AT and Ric-F, were isolated from muddy water samples of a sulfuric hot spring located in Tengchong County, Yunnan Province, PR China. The strains were aerobic and facultatively chemolithoautotrophic. Both strains could oxidize S0 and K2S4O6 for autotrophic growth, and could use organic materials for heterotrophic growth. Growth was observed at 55–75 °C and pH 1.5–6.5. The strains could oxidize metal sulfide ores, showing their potential in bioleaching. The DNA G+C contents of strains Ric-AT and Ric-F were 41.8 and 41.6 mol%, respectively. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but <97 % to other known species of the genus Metallosphaera . DNA–DNA hybridization indicated that the isolates were different strains of a novel species of the genus Metallosphaera . Strains Ric-AT and Ric-F also shared a number of physiological and biochemical characteristics that distinguished them from recognized species of the genus Metallosphaera . On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their closest relatives, it was concluded that strains Ric-AT and Ric-F represent a novel species of the genus Metallosphaera , for which the name Metallosphaera tengchongensis sp. nov. is proposed. The type strain is Ric-AT ( = NBRC 109472T = CGMCC 1.12287T).
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Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil
Qin Liu, Min Ren and Li-Li ZhangTwo halophilic archaeal strains, TRM20010T and TRM20345T, were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010T and TRM20345T were able to grow at 30–62 °C (optimum 37 °C), 0.9–5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0–10.0 (optimum pH 7.0−7.5) and neither strain required Mg2+ for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB′ genes revealed that strains TRM20010T and TRM20345T clustered together and formed a distinct clade separated from the related genera Halovivax , Haloterrigena , Halostagnicola , Natronolimnobius and Natrinema . The DNA G+C contents of strains TRM20010T and TRM20345T were 63.9 and 63.8 mol%, respectively. The DNA–DNA hybridization value between strain TRM20010T and strain TRM20345T was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010T and TRM20345T represent two novel species in a new genus within the family Halobacteriaceae , for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010T = CCTCC AB2013112T = NRRL B-59996T) and Natribaculum longum sp. nov. (type strain TRM20345T = CCTCC AB2013113T = NRRL B-59997T) are proposed.
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- Actinobacteria
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Arthrobacter nanjingensis sp. nov., a mineral-weathering bacterium isolated from forest soil
More LessA Gram-stain-positive, non-motile, rod- or coccoid-shaped actinobacterium, designated strain A33T, was isolated from a forest soil sample from Nanjing, Jiangsu Province, PR China. The strain grew optimally at 30 °C, pH 7.0 and with 3 % NaCl (w/v). Phylogenetic analysis of the strain, based on 16S rRNA gene sequences, showed that it was most closely related to Arthrobacter woluwensis (98.4 % sequence similarity), Arthrobacter humicola (97.5 %), Arthrobacter globiformis (97.4 %), Arthrobacter oryzae (97.3 %) and Arthrobacter cupressi (97.0 %). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0; MK-9(H2) was the predominant respiratory quinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and three glycolipids. Cell-wall analysis revealed that the peptidoglycan type was A3α, based on l-lysine-l-alanine; the cell-wall sugars were galactose and mannose. The genomic G+C content of strain A33T was 66.8 mol%. The low DNA–DNA relatedness values between strain A33T and recognized species of the genus Arthrobacter and many phenotypic properties supported the classification of strain A33T as a representative of a novel species of the genus Arthrobacter , for which the name Arthrobacter nanjingensis sp. nov. is proposed. The type strain is A33T ( = CCTCC AB 2014069T = DSM 28237T).
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Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater
C. Y. Hwang, I. Lee, Y. Cho, Y. M. Lee, K. Baek, Y.-J. Jung, Y. Y. Yang, T. Lee, T. S. Rhee and H. K. LeeA Gram-stain-positive, rod-shaped and non-motile strain, designated PAMC 27367T, was isolated from rainwater collected on the Bering Sea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Rhodococcus . Phylogenetic analyses revealed that strain PAMC 27367T formed a robust clade with the type strains of Rhodococcus rhodnii , Rhodococcus aetherivorans and Rhodococcus ruber with 16S rRNA gene sequence similarities of 96.3 %, 95.8 % and 95.5 %, respectively. Cells of the strain grew optimally at 25 °C and at pH 6.5–7.0 in the presence of 0–2 % (w/v) sea salts. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and three unknown phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Cell wall analysis showed that strain PAMC 27367T contained meso-diaminopimelic acid. The genomic DNA G+C content was 77.1 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Rhodococcus aerolatus sp. nov., with PAMC 27367T ( = KCTC 29240T = JCM 19485T) as the type strain.
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Description of Kribbella italica sp. nov., isolated from a Roman catacomb
More LessA novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).
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Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens
Abdolrazagh Hashemi Shahraki, Cengiz Çavuşoğlu, Emanuele Borroni, Parvin Heidarieh, Orhan Kaya Koksalan, Andrea Maurizio Cabibbe, Mohamad Hashemzadeh, Alessandro Mariottini, Ehsan Mostafavi, Davide Cittaro, Mohamad Mehdi Feizabadi, Dejan Lazarevic, Farhad Yaghmaei, Gian Lorenzo Molinari, Anna Camaggi and Enrico TortoliSix strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).
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Nesterenkonia alkaliphila sp. nov., an alkaliphilic, halotolerant actinobacteria isolated from the western Pacific Ocean
More LessA Gram-staining-positive, aerobic, motile and non-spore-forming actinobacteria, designated strain F10T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Nesterenkonia . Strain F10T shared highest 16S rRNA gene sequence similarity of 96.8 % with Nesterenkonia aethiopica DSM 17733T, followed by Nesterenkonia xinjiangensis YIM 70097T (96.7 %) and Nesterenkonia alba CAAS 252T (96.6 %). The organism grew at 4–50 °C, at pH 7.0–12.0 and in the presence of 0–12 % (w/v) NaCl, with optimal growth occurring at 40 °C, at pH 9.0 and in the presence of 1 % (w/v) NaCl. The peptidoglycan type was A4(alpha), l-Lys–Gly–l-Glu. The polar lipid profile of strain F10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and two unknown lipids. The isolate contained MK-9 (92 %) and MK-8 (5.8 %) as the major components of the menaquinone system, and anteiso-C17 : 0 (50.9 %) and anteiso-C15 : 0 (29.8 %) as the predominant fatty acids. The G+C content of the genomic DNA of strain F10T was 66.2 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain F10T represents a novel species of the genus Nesterenkonia for which the name Nesterenkonia alkaliphila sp. nov. is proposed. The type strain is F10T ( = LMG 28112T = CGMCC 1.12781T = JCM 19766T = MCCC 1A09946T).
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Corynebacterium atrinae sp. nov., isolated from the gastrointestinal tract of a pen shell, Atrina pectinata
More LessA novel Gram-stain-positive, non-motile, facultatively anaerobic and rod-shaped bacterium, strain PSPT56T, was isolated from the gastrointestinal tract of a pen shell (Atrina pectinata). Optimal growth of strain PSPT56T was ascertained to occur at 30 °C, pH 8.0 and in the presence of 1–2 % (w/v) NaCl. The strain was catalase-positive and oxidase-negative. The major cellular fatty acids were C18 : 1ω9c, C16 : 0, C17 : 1ω8c and C17 : 0. Tuberculostearic acid was not present. The major cell-wall sugars were ribose, galactose, glucose and arabinose. Peptidoglycan amino acids were meso-diaminopimelic acid, alanine and glutamic acid. The predominant isoprenoid quinone was MK-8(H2). Strain PSPT56T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified lipids and two unidentified amino-lipids. Mycolic acids were detected as constitutive components of the cell wall. A phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain PSPT56T was most closely related to Corynebacterium testudinoris M935/96/4T and Corynebacterium felinum M714/95/5T with 98.69 % and 97.01 % similarity, respectively. DNA–DNA hybridization experiments indicated less than 29.9 % relatedness to the phylogenetically closest species. The G+C content of genomic DNA was 67.6 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain PSPT56T represents a novel species within the genus Corynebacterium , for which the name Corynebacterium atrinae is proposed. The type strain is PSPT56T ( = KACC 17525T = JCM 19266T).
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Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species
More LessThe remarkable host specificity of the species of the genus Actinobaculum led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus Actinobaculum . The proposals of this study include the reclassification of Actinobaculum schaalii and Actinobaculum urinale as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541T = CCUG 27420T) and Actinotignum urinale comb. nov. (type strain DSM 15805T = CCUG 46093T), respectively. Emended descriptions of the genus Actinobaculum and Actinomyces suis are also provided. The results of 16S rRNA gene sequence analysis and DNA–DNA hybridization also indicated that the type strain of Actinobaculum massiliense deposited as CCUG 47753T ( = DSM 19118T) should in fact be considered a member of the species Actinobaculum schaalii . In addition, comparative 16S rRNA gene sequencing and DNA–DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199T ( = DSM 26039T = CCUG 64068T).
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Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.
Ana R. Fusco da Costa, Tarcisio Fedrizzi, Maria L. Lopes, Monica Pecorari, Wana L. Oliveira da Costa, Elisabetta Giacobazzi, Jeann R. da Costa Bahia, Veronica De Sanctis, Karla V. Batista Lima, Roberto Bertorelli, Antonella Grottola, Anna Fabio, Alessandro Mariottini, Pamela Ferretti, Francesca Di Leva, Giulia Fregni Serpini, Sara Tagliazucchi, Fabio Rumpianesi, Olivier Jousson, Nicola Segata and Enrico TortoliFourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic approach. Thorough genetic investigation, including whole-genome sequencing, demonstrated that the strains belong to the M. simiae complex, being most closely related to Mycobacterium interjectum . For 14 of the strains, evidence emerged supporting their inclusion in a previously unreported species of the genus Mycobacterium , for which the name Mycobacterium paraense sp. nov. is proposed (type strain, IEC26T = DSM 46749T = CCUG 66121T). The novel species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and a HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions, high sequence microheterogeneity was detected.
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- Firmicutes and Related Organisms
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Compostibacillus humi gen. nov., sp. nov., a member of the family Bacillaceae, isolated from sludge compost
More LessTwo novel Gram-staining-positive, rod-shaped, endospore-forming and moderately thermophilic bacteria, designated strains DX-3T and GIESS002, were isolated from sludge composts from Guangdong Province, China. Analysis of 16S rRNA gene sequences revealed that the isolates were closely related to each other with extremely high similarity (99.6 %), and were members of the family Bacillaceae . However, these two isolates formed a novel phylogenetic branch within this family. Their closest relatives were the members of the genera Ornithinibacillus , Oceanobacillus and Virgibacillus . Cells of both strains were facultatively anaerobic and catalase- and oxidase-positive. The cell-wall peptidoglycan type was A1γ (meso-diaminopimelic acid direct). The predominant isoprenoid quinone was MK-7. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acid was iso-C15 : 0. The DNA G+C content was 43.2–43.7 mol%. The results of a polyphasic taxonomic study indicated that strains DX-3T and GIESS002 represent a novel species in a new genus in the family Bacillaceae , order Bacillales , for which the name Compostibacillus humi gen. nov., sp. nov. is proposed. The type strain is DX-3T ( = KCTC 33104T = CGMCC 1.12360T).
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Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil
More LessA Gram-stain-positive, moderately halophilic bacterium, designated BH043T, was isolated from saltern soil of Gomso in Korea. Cells were motile rods, producing ellipsoidal endospores at a terminal position in swollen sporangia. Strain BH043T was strictly aerobic, grew at pH 6.0–10.0 (optimal growth at pH 7.5), at 10–55 °C (optimal growth at 30 °C) and at salinities of 1–20 % (w/v) NaCl, growing optimally with 7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BH043T belongs to the family Bacillaceae and was most closely related to the type strains of the five recognized species of the genus Pontibacillus , showing sequence similarity to Pontibacillus yanchengensis Y32T (97.5 % similarity), Pontibacillus marinus BH030004T (97.4 %), Pontibacillus chungwhensis BH030062T (97.0 %), Pontibacillus litoralis JSM 072002T (96.4 %) and Pontibacillus halophilus JSM 076056T (96.2 %). The major cellular fatty acids of strain BH043T were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 42.5 mol%. The major isoprenoid quinone was MK-7 and meso-diaminopimelic acid was present in the cell-wall peptidoglycan as the diagnostic diamino acid. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. DNA–DNA relatedness between strain BH043T and the type strains of other species of the genus Pontibacillus , P. yanchengensis CGMCC 1.10680T and P. marinus KCTC 3917T and P. chungwhensis KCTC 3890T, was 35, 24 and 18 %, respectively. On the basis of polyphasic analysis from this study, strain BH043T represents a novel species of the genus Pontibacillus for which the name Pontibacillus salicampi sp. nov. is proposed. The type strain is BH043T ( = KACC 17607T = NBRC 109831T = NCAIM B.02529T).
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Reappraisal of the taxonomy of Streptococcus suis serotypes 20, 22 and 26: Streptococcus parasuis sp. nov.
More LessIn order to clarify the taxonomic position of serotypes 20, 22 and 26 of Streptococcus suis , biochemical and molecular genetic studies were performed on isolates (SUT-7, SUT-286T, SUT-319, SUT-328 and SUT-380) reacted with specific antisera of serotypes 20, 22 or 26 from the saliva of healthy pigs as well as reference strains of serotypes 20, 22 and 26. Comparative recN gene sequencing showed high genetic relatedness among our isolates, but marked differences from the type strain S. suis NCTC 10234T, i.e. 74.8–75.7 % sequence similarity. The genomic relatedness between the isolates and other strains of species of the genus Streptococcus , including S. suis, was calculated using the average nucleotide identity values of whole genome sequences, which indicated that serotypes 20, 22 and 26 should be removed taxonomically from S. suis and treated as a novel genomic species. Comparative sequence analysis revealed 99.0–100 % sequence similarities for the 16S rRNA genes between the reference strains of serotypes 20, 22 and 26, and our isolates. Isolate STU-286T had relatively high 16S rRNA gene sequence similarity with S. suis NCTC 10234T (98.8 %). SUT-286T could be distinguished from S. suis and other closely related species of the genus Streptococcus using biochemical tests. Due to its phylogenetic and phenotypic similarities to S. suis we propose naming the novel species Streptococcus parasuis sp. nov., with SUT-286T ( = JCM 30273T = DSM 29126T) as the type strain.
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Characterization of Sporohalobacter salinus sp. nov., an anaerobic, halophilic, fermentative bacterium isolated from a hypersaline lake
Halophilic, obligately anaerobic, Gram-stain-negative bacterial strains were isolated from a sediment sample taken from under the salt crust of El-Jerid hypersaline lake in southern Tunisia by using tryptone or glucose as the substrate. One strain, CEJFT1BT, was characterized phenotypically and phylogenetically. Cells were non-motile, non-spore-forming, short rods. Strain CEJFT1BT was able to grow in the presence of 5–30 % (w/v) NaCl (optimum 20 %) and at 30–60 °C (optimum 45 °C). It grew at pH 5.5–7.8 and the optimum pH for growth was 6.8. The isolate required yeast extract for growth. Substrates utilized by strain CEJFT1BT as the sole carbon source included glucose, fructose, sucrose, pyruvate, Casamino acids and starch. Individual amino acids such as glutamate, lysine, methionine, serine, tyrosine, and amino acid mixtures formed by the Stickland reaction such as alanine-glycine, valine-proline, leucine-proline, isoleucine-proline were also utilized. Products of glucose fermentation were acetate (major product), butyrate, H2 and CO2. The genomic DNA G+C content of strain CEJFT1BT was 32.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFT1BT should be assigned to the genus Sporohalobacter . The sequence similarity between strain CEJFT1BT and Sporohalobacter lortetii was 98.5 %, but DNA–DNA hybridization between the two strains revealed a relatedness value of 56.4 %, indicating that they are not related at the species level. The combination of phylogenetic analysis, DNA–DNA hybridization data, and differences in substrate utilization support the view that strain CEJFT1BT represents a novel species of the genus Sporohalobacter , for which the name Sporohalobacter salinus sp. nov. is proposed. The type strain is CEJFT1BT ( = DSM 26781T = JCM 19279T).
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Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost
More LessA novel, psychrotolerant facultative anaerobe, strain WN1359T, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1–2 µm long and 0.4–0.5 µm wide. Growth occurred in the range of pH 5.8–9.0 with optimal growth at pH 7.8–8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0–37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359T was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359T and Carnobacterium inhibens . Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359T belonging to the species C. inhibens . On the basis of these results, the permafrost isolate WN1359T represents a novel subspecies of C. inhibens , for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359T ( = ATCC BAA-2557T = DSM 27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of C. inhibens is also provided.
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Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost
More LessA thermophilic, agar-degrading bacterium, strain FAB2T, was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2T belonged to the family Paenibacillaceae within the phylum Firmicutes . However, FAB2T was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus , 91.8 % for Paenibacillus barengoltzii , 89.4 % for Cohnella lupini , 90.1 % for Fontibacillus aquaticus , and 89.0 % for Saccharibacillus sacchari . Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50–65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0–8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2T ( = NBRC 109510T = KCTC 33130T) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae , for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.
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Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method
More LessA new, modified culture method that utilizes a transwell plate with a 0.4 µm pore-size microporous membrane was developed. This system allows only trace nutrients from the soil into the liquid culture through the microporous membrane. The method is a more powerful tool for the discovery of novel species from soils than are traditional methods. Such newly identified species could potentially produce useful metabolites. A bacterial strain, T515T, was isolated using this modified culture method. Growth of strain T515T occurred at pH 4–9 in a temperature range between 20 °C and 40 °C and in the presence of 0–2 % (w/v) NaCl on R2A agar. Colonies on the agar plates were tiny, white, and convex after 5 days incubation at 28 °C. Comparative analysis of the nearly full-length 16S rRNA gene sequence of strain T515T revealed close pairwise similarity with species of the genus Bacillus , and strain T515T was most closely related to Bacillus panaciterrae Gsoil 1517T (96.7 %) and Bacillus funiculus NAF001T (96.0 %). The major quinone of strain T515T was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0 (45.5 %), anteiso-C15 : 0 (23.2 %) and C16 : 0 (10.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain T515T was sensitive to streptomycin and tetracycline, but resistant to rifampicin (0.125 µg ml−1), ampicillin (0.5 µg ml−1) and chloramphenicol (1 µg ml−1). The strain showed antimicrobial activities against the six strains tested: Bacillus subtilis KEMB 51201-001, Staphylococcus aureus KEMB 4659, Pseudomonas aeruginosa KACC 10185, Staphylococcus epidermidis KACC 13234, Paenibacillus larvae KACC 14031 and Escherichia coli KEMB 212-234. Based on these results, strain T515T represents a novel species of the genus Bacillus with the proposed name, Bacillus polymachus sp. nov. The type strain is T515T ( = KEMB 9005-168T = KACC 18242T = NBRC 110614T).
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Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent
A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613T, was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613T were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44–72 °C (optimum 60–62 °C) and at hydrostatic pressures of 0.1–55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613T was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613T was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613T was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613T ( = JCM 19466T = DSM 28033T = MCCC 1A06456T).
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Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product
More LessA novel, moderately thermophilic, acidophilic, Gram-variable, rod-shaped, endospore-forming bacterium was isolated from a spoiled mixed vegetable and fruit juice product that had the off-flavour of guaiacol. The bacterium, strain 4FT, grew aerobically at 20–50 °C (optimum 40 °C) and pH 3.0–6.0 (optimum pH 4.0) and produced acid from glycerol, d-galactose and d-glucose. It contained menaquinone-7 (MK-7) as the major isoprenoid quinone and the DNA G+C content was 49.6 mol%. The predominant cellular fatty acids of strain 4FT were ω-alicyclic (ω-cyclohexane fatty acids), which are characteristic of the genus Alicyclobacillus . Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the Alicyclobacillus cluster, and is related most closely to the type strains of Alicyclobacillus acidoterrestris (97.4 % similarity) and Alicyclobacillus fastidiosus (97.3 %). Strain 4FT produced guaiacol from vanillic acid. It can be distinguished from related species by its acid production type and guaiacol production. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness values, it can be concluded that the strain represents a novel species of the genus Alicyclobacillus , for which the name Alicyclobacillus dauci sp. nov. is proposed; the type strain is 4FT ( = DSM 28700T = NBRC 108949T = NRIC 0938T).
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- Proteobacteria
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Perspicuibacter marinus gen. nov., sp. nov., a semi-transparent bacterium isolated from surface seawater, and description of Arenicellaceae fam. nov. and Arenicellales ord. nov.
More LessA Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2-9T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain was transparent on 1/5 strength marine broth plate but became easily visible when the plate was supplemented with pyruvate. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the strain fell within the class Gammaproteobacteria and was most closely related to the genus Arenicella (92.7–93.0 % 16S rRNA gene sequence similarities to type strains of species of this genus) of an unclassified order within this class. The DNA G+C content of strain 2-9T was 41.7 mol%. The major fatty acids were C18 : 1ω7c (37.6 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3; 19.1 %), C18 : 0 (10.8 %), C16 : 0 (10.2 %) and an unidentified fatty acid with an equivalent chain-length value of 11.799 (9.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. Ubiquinone-8 (Q-8) was detected as the sole isoprenoid quinone. From these taxonomic data, it is proposed that strain 2-9T represents a novel species of a new genus, Perspicuibacter marinus gen. nov., sp. nov. The type strain of the type species is 2-9T ( = NBRC 110144T = KCTC 42196T). A new family, Arenicellaceae fam. nov. (type genus Arenicella ), and order, Arenicellales ord. nov., of the class Gammaproteobacteria are proposed to accommodate the novel taxon.
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Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water
More LessA bacterial strain, JLT2016T, was isolated from a sample of South-eastern Pacific deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding and rod-shaped. Colonies were mucoid and cream. Growth occurred at 1.0–11.0 % (w/v) NaCl, 10–40 °C and pH 4.0–9.0. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (60.5 %), C19 : 0 cyclo ω8c (10.9 %) and C16 : 0 (9.0 %). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipids. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016T was Salipiger mucosus A3T (96.7 % 16S rRNA gene sequence similarity). The results of phylogenetic analyses with different treeing algorithms indicated that this strain belonged to the Roseobacter clade in the order Rhodobacterales . Based on polyphasic analysis, strain JLT2016T is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016T ( = LMG 27365T = CGMCC 1.12377T).
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Bisgaardia miroungae sp. nov., a new member of the family Pasteurellaceae isolated from the oral cavity of northern elephant seals (Mirounga angustirostris), and emended description of the genus Bisgaardia
More LessA total of 17 bacterial isolates from northern elephant seals, tentatively classified within the family Pasteurellaceae, were further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, closely related to the genus Bisgaardia within the family Pasteurellaceae . The rpoB gene sequence similarity was 97.2–100 % within the group and 16S rRNA gene sequence comparisons showed 99.2–99.8 % similarity within the group. According to 16S rRNA gene sequence analysis, the most closely related species with a validly published name was Bisgaardia hudsonensis with 96.9 % similarity and the most closely related species based on rpoB sequence comparison was Bisgaardia genomospecies 1 with an rpoB sequence similarity of 90.9 %. All the isolates investigated exhibited the phenotypic characteristics of the family Pasteurellaceae . However, these isolates could be separated from existing species of the genus Bisgaardia by the following characteristics: ability to grow at 42 °C, and acid production from lactose, melibiose, raffinose and l-rhamnose, but not from d-mannitol or trehalose. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the strains should be classified as representatives of a novel species within the genus Bisgaardia : Bisgaardia miroungae sp. nov. The type strain, WildatricT ( = CCUG 65148T = DSM 28141T), was isolated from the oral cavity of a wild northern elephant seal at The Marine Mammal Center, California, USA in 2011. To include the novel species, the description of the genus Bisgaardia has been emended.
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Sphingobium subterraneum sp. nov., isolated from ground water
More LessA Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, yellow, rod-shaped bacterium, designated S-II-13T, was isolated from ground water at Daejeon in Korea. Strain S-II-13T grew between 15 and 30 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0.3–1.5 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain S-II-13T was found to belong to the genus Sphingobium , showing closest phylogenetic similarity to Rhizorhapis suberifaciens CA1T (97.0 % 16S rRNA gene sequence similarity), Sphingobium sufflavum HL-25T (96.9 %) and Sphingobium vulgare HU1-GD12T (96.6 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone was Q-10. The major fatty acids were C18 : 1ω7c, C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain S-II-13T was 63.5 mol%. DNA–DNA relatedness between strain S-II-13T and Rhizorhapis suberifaciens LMG 17323T, Sphingobium sufflavum KCTC 23953T and Sphingobium vulgare KCTC 22289T was 24, 52 and 55 %, respectively. On the basis of evidence from this taxonomic study using a polyphasic approach, strain S-II-13T represents a novel species of the genus Sphingobium for which the name Sphingobium subterraneum sp. nov. is proposed. The type strain is S-II-13T ( = KACC 17606T = NBRC 109814T).
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Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens
Two novel Gram-stain-negative strains (CCBAU 03422T and CCBAU 03415) isolated from root nodules of Sophora flavescens were classified phylogenetically into the genus Phyllobacterium based on the comparative analysis of 16S rRNA and atpD genes. They showed 99.8 % rRNA gene sequence similarities to Phyllobacterium brassicacearum LMG 22836T, and strain CCBAU 03422T showed 91.2 and 88.6 % atpD gene sequence similarities to strains Phyllobacterium endophyticum LMG 26470T and Phyllobacterium brassicacearum LMG 22836T, respectively. Strain CCBAU 03422T contained Q-10 as its major quinone and showed a cellular fatty acid profile, carbon source utilization and other phenotypic characteristics differing from type strains of related species. DNA–DNA relatedness (lower than 48.8 %) further confirmed the differences between the novel strains and the type strains of related species. Strain CCBAU 03422T could nodulate and fix nitrogen effectively on its original host plant, Sophora flavescens. Based upon the results mentioned above, a novel species named Phyllobacterium sophorae is proposed and the type strain is CCBAU 03422T ( = A-6-3T = LMG 27899T = HAMBI 3508T).
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Rhizobium yantingense sp. nov., a mineral-weathering bacterium
More LessA Gram-stain-negative, rod-shaped bacterial strain, H66T, was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66T were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66T belongs to the genus Rhizobium . It is closely related to Rhizobium huautlense SO2T (98.1 %), Rhizobium alkalisoli CCBAU 01393T (98.0 %) and Rhizobium cellulosilyticum ALA10B2T (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66T and other recognized species of the genus Rhizobium . The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66T was 60.3 mol%. Strain H66T is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA–DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279 Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66T ( = CCTCC AB 2014007T = LMG 28229T).
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Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment
More LessA psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).
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Brenneria populi sp. nov., isolated from symptomatic bark of Populus×euramericana canker
Five Gran-stain-negative, facultatively anaerobic, motile, bacterial strains were isolated from symptomatic bark tissue of Populus×euramericana canker. Strains grew at 4–41 °C, pH 4–10 and 0–6 % (w/v) salinity. They were positive with respect to catalase activity and negative for oxidase activity, nitrate reduction and the Voges–Proskauer reaction. Analysis of 16S rRNA gene sequences indicated that these five poplar isolates belong to the genus Brenneria , having highest sequence similarity of 95.98 % with Brenneria goodwinii LMG 26270T. These five isolates formed a single cluster based on multilocus sequence analysis, indicating that they all belong to a single taxon within the genus Brenneria , which was confirmed by DNA–DNA hybridization. The DNA G+C content was 54.9–55.7 mol%, and the main fatty acids were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and C16 : 1ω7c/iso-C15 : 0 2-OH. Based on these results, we describe a novel species of the genus Brenneria with the proposed name Brenneria populi sp. nov. The type strain is D9-5T ( = CFCC 11963T = KCTC 42088T).
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Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from larvae of Anopheles arabiensis, as members of the family Thorselliaceae fam. nov.
Two Gram-negative, rod-shaped strains, T2.1T and W5.1.1T, isolated from larvae of the mosquito Anopheles arabiensis, were investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strains T2.1T and W5.1.1T were shown to belong to the genus Thorsellia , both showing 97.8 % similarity to the type strain of Thorsellia anophelis , with 98.1 % similarity to each other. Chemotaxonomic data supported the allocation of the strains to the genus Thorsellia : their major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0 and they harboured a ubiquinone Q-8 quinone system and a polyamine pattern with the major compound 1,3-diaminopropane. Qualitative and quantitative differences in their polar lipid profiles distinguished strains T2.1T and W5.1.1T from each other and from T. anophelis . Average nucleotide identity (ANI), DNA–DNA hybridization, multilocus sequence analysis (MLSA) as well as physiological and biochemical tests allowed T2.1T and W5.1.1T to be distinguished both genotypically and phenotypically from each other and from the type strain of T. anophelis . Thus, we propose that these isolates represent two novel species of the genus Thorsellia , named Thorsellia kenyensis sp. nov. (type strain T2.1T = CCM 8545T = LMG 28483T = CIP 110829T) and Thorsellia kandunguensis sp. nov. (type strain W5.1.1T = LMG 28213T = CIP 110794T). Furthermore, phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the genus Thorsellia forms a separate branch, distinct from the families Enterobacteriaceae , Pasteurellaceae and Orbaceae . As a consequence, a new family Thorselliaceae fam. nov. is proposed. An emended description of Thorsellia anophelis is also provided.
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Neisseria weaveri Andersen et al. 1993 is a later heterotypic synonym of Neisseria weaveri Holmes et al. 1993
Hana Yi and Jongsik ChunTwo species of the genus Neisseria , namely Neisseria weaveri Andersen et al. 1993 and Neisseria weaveri Holmes et al. 1993, were simultaneously proposed and described in the same volume of International Journal of Systematic Bacteriology, and have been maintained as heterotypic homonyms. However, the identical 16S rRNA gene sequence and high (99.1 %) average nucleotide identity (ANI) between the genome sequences of the two type strains implied that these two taxa should be united as a single genomic species. To clarify their taxonomic status, phenotypic properties including enzymic activities and substrate-utilization profiles were investigated. The results demonstrated that the two taxa have no pronounced differences and should constitute a single species. Therefore, the reclassification of N. weaveri Andersen et al. 1993 as a later heterotypic synonym of N. weaveri Holmes et al. 1993 is proposed.
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Rhizobium alvei sp. nov., isolated from a freshwater river
More LessA bacterial strain designated TNR-22T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-22T were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by a single polar flagellum and formed cream-coloured colonies. Growth occurred at 4–45 °C (optimum, 25–30 °C), with 0–1.0 % (w/v) NaCl (optimum, 0.5 %) and at pH 7.0–8.0 (optimum, pH 7.0). Strain TNR-22T did not form nodules on Macroptilium atropurpureum. The nifH gene encoding denitrogenase reductase was not detected by PCR. The major fatty acids (>10 %) of strain TNR-22T were C18 : 1ω7c and C16 : 0. The DNA G+C content was 60.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminoglycolipid and an uncharacterized phospholipid. Comparative analysis of 16S rRNA gene sequences showed that strain TNR-22T constituted a distinct branch within the genus Rhizobium , showing the highest level of sequence similarity with Rhizobium rosettiformans W3T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TNR-22T represents a novel species in the genus Rhizobium , for which the name Rhizobium alvei sp. nov. is proposed. The type strain is TNR-22T ( = BCRC 80408T = LMG 26895T = KCTC 23919T).
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Rhizobacter bergeniae sp. nov., isolated from the root of Bergenia scopulosa
A yellowish-pigmented bacterium, designated strain PLGR-1T, was isolated from the root of Bergenia scopulosa collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain PLGR-1T were Gram-stain-negative, strictly aerobic, rod-shaped, non-spore-forming and motile with a single polar flagellum. Growth occurred at 7–33 °C (optimum, 25–28 °C), at pH 5.0–10.0 (optimum, pH 6.0–7.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). The predominant respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polyamines were putrescine and 2-hydroxyputrescine and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PLGR-1T belonged to the class Betaproteobacteria and formed a tight phyletic lineage with members of the genus Rhizobacter . Strain PLGR-1T was most closely related to Rhizobacter dauci DSM 11587T and Rhizobacter fulvus DSM 19916T, with 16S rRNA gene sequence similarities of 98.5 and 98.0 %, respectively. The DNA–DNA relatedness values between strain PLGR-1T and the type strains of Rhizobacter dauci and Rhizobacter fulvus were 46.3 and 14.7 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain PLGR-1T is considered to represent a novel species of the genus Rhizobacter , for which the name Rhizobacter bergeniae sp. nov. is proposed. The type strain is PLGR-1T ( = CCTCC AB 2013018T = KCTC 32299T = LMG 27607T).
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Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens
Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus Rhizobium based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to Rhizobium leguminosarum USDA 2370T (95.6 % similarity for group I) and Rhizobium phaseoli ATCC 14482T (93.4 % similarity for group II) in multilocus sequence analysis. In DNA–DNA hybridization experiments, the reference strains CCBAU 03386T (group I) and CCBAU 03470T (group II) showed levels of relatedness of 17.9–57.8 and 11.0–42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386T and CCBAU 03470T contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus Rhizobium were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386T = E5T = LMG 27901T = HAMBI 3615T) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470T = C-5-1T = LMG 27898T = HAMBI 3510T), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli.
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Burkholderia monticola sp. nov., isolated from mountain soil
More LessAn ivory/yellow, Gram-stain-negative, short-rod-shaped, aerobic bacterial strain, designated JC2948T, was isolated from a soil sample taken from Gwanak Mountain, Republic of Korea. 16S rRNA gene sequence analysis indicated that strain JC2948T belongs to the genus Burkholderia . The test strain showed highest sequence similarities to Burkholderia tropica LMG 22274T (97.6 %), Burkholderia acidipaludis NBRC 101816T (97.5 %), Burkholderia tuberum LMG 21444T (97.5 %), Burkholderia sprentiae LMG 27175T (97.4 %), Burkholderia terricola LMG 20594T (97.3 %) and Burkholderia diazotrophica LMG 26031T (97.1 %). Based on average nucleotide identity (ANI) values, the new isolate represents a novel genomic species as it shows less than 90 % ANI values with other closely related species. Also, other phylosiological and biochemical comparisons allowed the phenotypic differentiation of strain JC2948T from other members of the genus Burkholderia . Therefore, we suggest that this strain should be classified as the type strain of a novel species of the genus Burkholderia . The name Burkholderia monticola sp. nov. (type strain, JC2948T = JCM 19904T = KACC 17924T) is proposed.
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Description of Pseudobacteriovorax antillogorgiicola gen. nov., sp. nov., a bacterium isolated from the gorgonian octocoral Antillogorgia elisabethae, belonging to the family Pseudobacteriovoracaceae fam. nov., within the order Bdellovibrionales
More LessA bacterial strain designated RKEM611T was isolated from the octocoral Antillogorgia elisabethae, collected off the coast of San Salvador, The Bahamas. The strain is Gram-stain-negative, an obligate aerobe, and pleomorphic. It requires NaCl for growth and exhibits optimal growth at 1–2 % (w/v) NaCl, 30–37 °C and pH 6.0–8.0. The predominant cellular fatty acids are C16 : 1ω5c and C16 : 0; the major respiratory quinone is menaquinone MK-6, and the DNA G+C content is 46.3 mol%. Based on phylogenetic analysis of the 16S rRNA gene, in addition to phenotypic characteristics, RKEM611T represents a novel species and genus of a novel family within the order Bdellovibrionales . The names Pseudobacteriovoracaceae fam. nov. and Pseudobacteriovorax antillogorgiicola gen., nov., sp., nov. are proposed. Isolate RKEM611T ( = NCCB 100521T = LMG 28452T) is the type strain.
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Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus
More LessA taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.
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Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil
A Gram-stain negative, facultatively anaerobic, non-motile, rod-shaped bacterium, designated strain THG-A13T, was isolated from Aglaia odorata rhizosphere soil in Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-A13T had close similarity with Lysobacter niabensis GH34-4T (98.5 %), Lysobacter oryzae YC6269T (97.9 %) and Lysobacter yangpyeongensis GH19-3T (97.3 %). Chemotaxonomic data revealed that strain THG-A13T possesses ubiquinone-8 (Q8) as the predominant isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol) and diphosphatidylglycerol. The G+C content was 66.3 mol%. The DNA–DNA relatedness values between strain THG-A13T and its closest phylogenetic neighbours were below 18.0 %. These data corroborated the affiliation of strain THG-A13T to the genus Lysobacter . These data suggest that the isolate represents a novel species for which the name Lysobacter terrae sp. nov. is proposed, with THG-A13T as the type strain ( = KACC 17646T = JCM 19613T).
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Reclassification of Bacteriovorax marinus as Halobacteriovorax marinus gen. nov., comb. nov. and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov.; description of Halobacteriovoraceae fam. nov. in the class Deltaproteobacteria
More LessThe taxonomic status of saltwater Bdellovibrio -like prokaryotic predators has been revised to assign species to Halobacteriovorax gen. nov. A reclassification of Bacteriovorax marinus as Halobacteriovorax marinus comb. nov. (type strain ATCC BAA-682T = DSM 15412T) and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov. (type strain ATCC BAA-684T = DSM 15409T) is proposed. This revision is necessary because a previous proposal to retain saltwater isolates as species of Bacteriovorax and reclassify Bacteriovorax stolpii as Bacteriolyticum stolpii was not approved. The type species of a genus cannot be reassigned to another genus. Bacteriovorax stolpii is thus retained as the type species of Bacteriovorax and Halobacteriovorax marinus is the type species of Halobacteriovorax and of Halobacteriovoraceae fam. nov.
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Legionella norrlandica sp. nov., isolated from the biopurification systems of wood processing plants
Fourteen isolates of an unknown species identified as belonging to the genus Legionella by selective growth on BCYE agar were isolated from the biopurification systems of three different wood processing plants. The mip gene sequence of all 14 isolates was identical and a close match alignment revealed 86 % sequence similarity with Legionella pneumophila serogroup 8. The whole genome of isolate LEGNT was sequenced, and a phylogenetic tree based on the alignment of 16S rRNA, mip, rpoB, rnpB and the 23S–5S intergenic region clustered LEGNT with L. pneumophila ATCC 33152T. Analysis of virulence factors showed that strain LEGNT carries the majority of known L. pneumophila virulence factors. An amoeba infection assay performed to assess the pathogenicity of strain LEGNT towards Acanthamoeba castellanii showed that it can establish a replication vacuole in A. castellanii but does not significantly affect replication of amoebae. Taken together, the results confirm that strain LEGNT represents a novel species of the genus Legionella , for which the name Legionella norrlandica sp. nov. is proposed. The type strain is LEGNT ( = ATCC BAA-2678T = CCUG 65936T).
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Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain
More LessDuring the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770T was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770T belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis , P. koreensis , P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770T in the genus Pseudomonas . DNA–DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas , for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770T ( = DSM 28040T = LMG 27940T).
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Tahibacter caeni sp. nov., isolated from activated sludge
More LessA Gram-reaction-negative, aerobic, rod-shaped, non-spore-forming, non-motile bacterial strain, designated BUT-6T, was isolated from activated sludge of a wastewater-treatment facility. The strain grew at 15–35 °C (optimum 30 °C), pH 4.0–10.0 (optimum pH 7.0) and 0–3.0 % (w/v) NaCl (optimum 1.0 %). Phylogenetic analysis based on 16S rRNA sequences showed that strain BUT-6T was most closely related to Tahibacter aquaticus PYM5-11T (98.6 % similarity). However, the DNA–DNA relatedness between strain BUT-6T and T. aquaticus PYM5-11T was 47.1 %. The major fatty acids (>10 % of total fatty acids) of strain BUT-6T were iso-C15 : 0, iso-C17 : 1ω9c and iso-C17 : 0. The major respiratory quinone was ubiquinone Q-8. The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and unidentified phospholipids. The DNA G+C content of strain BUT-6T was 71.7 mol%. On the basis of the data from the polyphasic taxonomic study presented, strain BUT-6T is considered to represent a novel species of the genus Tahibacter , for which the name Tahibacter caeni sp. nov. is proposed. The type strain is BUT-6T ( = CCTCC AB 2013266T = KACC 17139T).
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Falsirhodobacter deserti sp. nov., isolated from sandy soil
More LessA Gram-stain-negative, non-motile, heterotrophic, rod-shaped bacterium, designated strain W402T, was isolated from an enrichment culture of a Tamarix ramosissima rhizosphere soil sample from the Xinjiang desert in the PR China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to a species of the genus Falsirhodobacter , having a close relationship to Falsirhodobacter halotolerans JA744T (97 % similarity). However, DNA–DNA relatedness between W402T and F. halotolerans JA744T was 43.2±1.2 %. Strain W402T grew in 0–10 % (w/v) NaCl. The temperature and pH ranges for growth were 10–40 °C and pH 5.5–10.0, respectively. Optimal growth occurred at 1–3 % (w/v) NaCl, 30 °C and pH 7.0. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.4 %), C18 : 0 (9.8 %) and 11-methyl C18 : 1ω7c (8.2 %). The major quinone of strain W402T was Q-10. Phosphatidylethanolamine was predominant in the polar lipid profile. The DNA G+C content of strain W402T was 67.3 mol%. Taken together, these results confirm that W402T represents a novel species of the genus Falsirhodobacter , for which the name Falsirhodobacter deserti sp. nov. is proposed. The type strain is W402T ( = ACCC 05851T = KCTC 32408T).
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Novosphingobium marinum sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, short rod-shaped bacterium, strain LA53T, was isolated from a deep-sea water sample collected from the eastern Pacific Ocean. Strain LA53T grew in the presence of 0–7.0 % (w/v) NaCl and at 15-37 °C; optimum growth was observed with 1.0–2.0 % (w/v) NaCl and at 35 °C. Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone, C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as major polar lipids. The genomic DNA G+C content was 57.7 mol%. Phylogenetic analyses revealed that strain LA53T belongs to the genus Novosphingobium . 16S rRNA gene sequence similarities between strain LA53T and the type strains of species of the genus Novosphingobium with validly published names ranged from 93.1 to 96.3 %. In addition, strain LA53T could be differentiated from Novosphingobium pentaromativorans DSM 17173T and Novosphingobium indicum DSM 23608T as well as the type strain of the type species of the genus, Novosphingobium capsulatum DSM 30196T, by some phenotypic characteristics, including hydrolysis of substrates, utilization of carbon sources and susceptibility to antibiotics. On the basis of phenotypic and genotypic data, strain LA53T represents a novel species within the genus Novosphingobium , for which the name Novosphingobium marinum sp. nov. is proposed. The type strain is LA53T ( = CGMCC 1.12918T = JCM 30307T).
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Loktanella sediminum sp. nov., isolated from marine surface sediment
More LessA Gram-staining-negative, strictly aerobic and short rod-shaped bacterium, designated strain S3B03T, was isolated from the sediment of the northern Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S3B03T belonged to the genus Loktanella (family Rhodobacteraceae ) and showed the highest sequence similarity with Loktanella litorea KCTC 23883T (96.16 %) and 92.99–95.90 % 16S rRNA gene sequence similarity to other members of the genus Loktanella . Optimal growth occurred in the presence of 2–5 % (w/v) NaCl at pH 7.0–8.0 and 28–32 °C. Ubiquinone-10 (Q-10) was the predominant respiratory quinone. The major fatty acids (>10 % of the total fatty acids) were C18 : 1ω7c and/or C18 : 1ω6c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and two unidentified polar lipids. The DNA G+C content of strain S3B03T was 57.6 mol%. On the basis of polyphasic analysis, strain S3B03T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella sediminum sp. nov. is proposed. The type strain is S3B03T ( = JCM 30120T = DSM 28715T = MCCC 1K00257T).
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- Bacteroidetes
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Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory
More LessA novel aerobic, Gram-stain-negative, motile bacterium, designated strain BUT-10T, was isolated from the sludge of a pesticide manufacturing factory in Kunshan, China. Cells were rod-shaped (0.4–0.45×0.9–1.4 µm) and colonies were white, circular with entire edges and had a smooth surface. The strain grew at 25–37 °C, at pH 6.0–8.0 and with 0–0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BUT-10T was a member of the genus Phenylobacterium , and showed highest sequence similarities to Phenylobacterium muchangponense A8T (97.49 %), Phenylobacterium immobile DSM 1986T (97.14 %) and Phenylobacterium lituiforme FaiI3T (96.34 %). Major fatty acids (>5 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 71.85 mol%. Strain BUT-10T showed low DNA–DNA relatedness with P. muchangponense A8T (15.7±2.9 %) and P. immobile DSM 1986T (12.8±1.1 %). On the basis of the phenotypic, phylogenetic and genotypic data, strain BUT-10T is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium kunshanense sp. nov. is proposed. The type strain is BUT-10T ( = CCTCC AB 2013085T = KCTC 42014T).
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Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, Antarcticimonas flava Yang et al. 2009 and Hoppeia youngheungensis Kwon et al. 2014
A Gram-staining-negative, strictly aerobic, yellowish-orange, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50T, was isolated from estuarine water off Pingtung, Taiwan. The strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to Bizionia hallyeonensis T-y7T (93.9 %) followed by Corallibacter vietnamensis KMM 6217T (93.8 %), Geojedonia litorea YCS-16T (93.7 %) and other members of the family Flavobacteriaceae (<93.7 %). Strain CC-PY-50T established a distinct phyletic lineage associated with Mangrovimonas yunxiaonensis LYYY01T (93.1 % sequence similarity) with poor bootstrap support during neighbour-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50T was determined to accommodate large numbers of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, C16 : 0 and C16 : 1ω6c and/or C16 : 1ω7c. The DNA G+C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50T is proposed to represent a novel genus and species of the family Flavobacteriaceae , for which the name Hanstruepera neustonica gen. nov., sp. nov. is proposed. The type strain of the type species Hanstruepera neustonica gen. nov., sp. nov. is CC-PY-50T ( = JCM 19743T = BCRC 80747T). Emended descriptions of the species Sediminibacter furfurosus , Mangrovimonas yunxiaonensis , Antarcticimonas flava and Hoppeia youngheungensis are also proposed.
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Flavobacterium suzhouense sp. nov., isolated from farmland river sludge
More LessA Gram-stain-negative bacterium, designated XIN-1T, was isolated from a farmland river sludge sample in Suzhou, China. Cells of strain XIN-1T were strictly aerobic, non-motile and rod-shaped. Strain XIN-1T grew optimally at pH 7.0 and 28 °C. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain XIN-1T was most closely related to Flavobacterium hauense BX12T (98.2 % sequence similarity), followed by Flavobacterium beibuense F44-8T (96.3 %). The major respiratory quinone was menaquinone-6 and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>5 %) were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0, C16 : 0 and iso-C17 : 0 3-OH. The genomic DNA G+C content of strain XIN-1T was 39.8 mol%. Strain XIN-1T showed low DNA–DNA relatedness with F. hauense BX12T (38.7±0.5 %). On the basis of genotypic and phenotypic data, strain XIN-1T is considered to represent a novel species of the genus Flavobacterium , for which the name Flavobacterium suzhouense sp. nov. is proposed. The type strain is XIN-1T ( = CCTCC AB 2014200T = KCTC 42107T).
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Litoribaculum gwangyangense gen. nov., sp. nov., isolated from a sea-tidal flat sediment
More LessA Gram-stain-negative, strictly aerobic bacterium, designated strain GY12T, was isolated from a tidal flat of South Korea. Cells were moderately halotolerant, catalase- and oxidase-positive rods with gliding motility, and were devoid of flagella. Growth of strain GY12T was observed at 15–40 °C (optimum 25–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5) and with 1–5 % (w/v) NaCl (optimum 1–2 %). The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C15 : 0 3-OH. The polar lipids consisted almost entirely of phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The G+C content of the genomic DNA was 34.8 mol% and the only respiratory quinone detected was menaquinone-6 (MK-6). Strain GY12T was most closely related to the genera Gaetbulibacter , Flaviramulus , Mariniflexile and Tamlana with 16S rRNA gene sequence similarities of 94–97 %, but phylogenetic inferences based on 16S rRNA gene sequences showed that the strain formed phyletic lineages distinct from these genera within the family Flavobacteriaceae . On the basis of phenotypic and molecular features, strain GY12T represents a novel species of a new genus in the family Flavobacteriaceae , for which the name Litoribaculum gwangyangense gen. nov., sp. nov. is proposed. The type strain of the type species is GY12T ( = KACC 16441T = JCM 18325T).
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Muriicola marianensis sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, orange-pigmented, rod-shaped and non-motile bacterium, designated strain A6B8T, was isolated from seawater of the Mariana Trench. The isolate grew at 4–50 °C (optimum 30–35 °C), at pH 6.5–8.0 (optimum pH 7.5) and with 0.5–4.0 % (w/v) NaCl (optimum 1.0–2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A6B8T was related most closely to the genus Muriicola and shared highest sequence similarity of 97.7 % with Muriicola jejuensis EM44T. Chemotaxonomic analysis showed menaquinone 6 (MK-6) was the predominant isoprenoid and iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH were the major cellular fatty acids. The polar lipid profile of strain A6B8T included phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. The genomic DNA G+C content was 47.1 mol%. The DNA–DNA relatedness value (23.3 %) clearly demonstrated that strains A6B8T and M. jejuensis EM44T were representatives of two different species. Based on the phenotypic, phylogenetic and chemotaxonomic characterizations, A6B8T ( = CGMCC 1.12606T = KCTC 32436T) is considered to be the type strain of a novel species of the genus Muriicola , for which the name Muriicola marianensis sp. nov. is proposed.
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Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock
More LessA Gram-stain-negative, aerobic, yellow-pigmented, non-motile, non-spore-forming, rod-shaped bacterial strain, Z29T, was isolated from the surface of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain Z29T belongs to the genus Chitinophaga in the family Chitinophagaceae . Levels of 16S rRNA gene sequence similarity between strain Z29T and the type strains of recognized species of the genus Chitinophaga ranged from 92.7 to 98.2 %. The main fatty acids of strain Z29T were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. It also contained menaquinone 7 (MK-7) as the respiratory quinone and homospermidine as the main polyamine. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids, unknown phospholipids and unknown lipids. The total DNA G+C content of strain Z29T was 51.3 mol%. Phenotypic properties and chemotaxonomic data supported the affiliation of strain Z29T with the genus Chitinophaga . The low level of DNA–DNA relatedness (ranging from 14.6 to 29.8 %) to the type strains of other species of the genus Chitinophaga and differential phenotypic properties demonstrated that strain Z29T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga longshanensis sp. nov. is proposed. The type strain is Z29T ( = CCTCC AB 2014066T = LMG 28237T).
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Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea
More LessA novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000T, was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000T was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000T formed a branch within the genus Marivirga , but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea . The 16S rRNA gene sequence similarity of strain JLT2000T with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000T had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. In addition, strain JLT2000T could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. Based on this polyphasic analysis, strain JLT2000T represents a novel species of the genus Marivirga , for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000T ( = JCM 18012T = CGMCC 1.10832T).
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Belliella kenyensis sp. nov., isolated from an alkaline lake
A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164T, was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella , with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698T. Optimal growth temperature was 30–35 °C, at pH 7.0–12.0 in the presence of 0–4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164T were consistent with those of other members of the genus Belliella . The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella . The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella . The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164T ( = DSM 46651T = CECT 8551T).
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Lutibacter oricola sp. nov., a marine bacterium isolated from seawater
More LessA bacterial strain, UDC377T, was isolated from seawater samples collected at Seo-do on the coast of Dokdo island in the East Sea, and was subjected to taxonomic study using a polyphasic approach. Strain UDC377T was pale-yellow, Gram-staining-negative, non-motile, rod-shaped and aerobic. The strain grew optimally at 25–28 °C, in the presence of 2 % (w/v) NaCl and at pH 7.0–7.5. Strain UDC377T produced carotenoid pigments; however, it did not produce flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UDC377T clustered with members of the genus Lutibacter and appeared most closely related to Lutibacter agarilyticus KYW566T (96.0 % 16S rRNA gene sequence similarity) followed by L. aestuarii MA-My1T (95.0 %), L. litoralis CL-TF09T (94.9 %), L. maritimus S7-2T (94.1 %) and L. flavus IMCC1507T (94.0 %). The DNA G+C content of strain UDC377T was 30.8 mol%. Strain UDC377T contained MK-6 as the predominant menaquinone, iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 0 3-OH as the major fatty acids, and phosphatidylethanolamine, two unknown aminolipids and six unknown lipids as the major polar lipids. Based on phenotypic properties and phylogenetic data presented, strain UDC377T is considered to represent a novel species of the genus Lutibacter , for which the name Lutibacter oricola sp. nov. is proposed. The type strain is UDC377T ( = DSM 24956T = KCTC 23668T).
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Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil
Three novel bacterial strains, designated Vu-144T, Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144T was affiliated with an uncultivated lineage of the phylum Bacteroidetes . Its closest phylogenetic neighbour was the recently described species Niastella populi , a member of the family Chitinophagaceae , with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1–APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1–UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45–60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144T represents a novel genus and species in the family Chitinophagaceae , for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144T ( = KCTC 22378T = NCIMB 14473T).
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Arcticibacter eurypsychrophilus sp. nov., isolated from ice core
A Gram-stain-negative, rod-shaped, non-flagellated bacterium, strain MJ9-5T, was isolated from ice core of Muji Glacier. Colonies of strain MJ9-5T were pink, convex and round on R2A agar. Strain MJ9-5T grew between −1 to 25 °C with an optimum growth temperature of 10–15 °C. The strain tolerated 0–1.2 % (w/v) NaCl with an optimum of 1 %. The major cellular fatty acids of strain MJ9-5T were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C1 6 : 1ω7c). The G+C content of the genomic DNA was 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ9-5T was related to members of the genus Arcticibacter . On the basis of the phenotypic characteristics and phylogenetic analysis, a novel species of this genus, Arcticibacter eurypsychrophilus sp. nov., is proposed. The type strain is MJ9-5T ( = KCTC 42008T = JCM 19862T).
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Flaviramulus aquimarinus sp. nov., isolated from seawater
More LessA yellow-coloured, rod-shaped, non-motile, Gram-stain-negative and facultative anaerobic bacterium, designated KYW499T, was isolated from seawater collected at Suncheon Bay, Republic of Korea. The isolate required sea salts for growth. Flexirubin-type pigments were absent. Major cellular fatty acids (>10 % of total) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH. The main polar lipids were phosphatidylethanolamine and two unidentified polar lipids. The predominant isoprenoid quinone was MK-6. The genomic DNA G+C content was 31.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW499T belonged to the family Flavobacteriaceae , and was related to the genus Flaviramulus . Data from a polyphasic taxonomy study suggested that the isolate represents a novel species of the genus Flaviramulus , for which the name Flaviramulus aquimarinus sp. nov. is proposed. The type strain is KYW499T ( = KCTC 23924T = JCM 18274T).
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Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus
More LessA facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, strain N-10T, was isolated from the gut of the termite Reticulitermes speratus. Strain N-10T was closely related to Dysgonomonas gadei JCM 16698T according to 16S rRNA gene sequence similarity analysis (98 %) and DNA–DNA relatedness value (≤61.3 %). The optimum growth temperature of strain N-10T was 30 °C, which was distinct from that (37 °C) of known species of the genus Dysgonomonas . Growth of strain N-10T was inhibited on medium containing 5 or 20 % bile, unlike other species of the genus Dysgonomonas . In addition, acid production in the API 20A system and enzymic reactions in the Rapid ID 32A system of strain N-10T differed from those of other species of the genus Dysgonomonas . Based on these characteristics, strain N-10T represents a novel species of the genus Dysgonomonas , for which the name Dysgonomonas termitidis sp. nov. is proposed. The type strain is N-10T ( = JCM 30204T = CCUG 66188T).
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Vitellibacter nionensis sp. nov., isolated from a shallow water hydrothermal vent
A novel, Gram-stain-negative, non-motile, rod-shaped yellow bacterium, designated VBW088T was isolated from a shallow water hydrothermal vent in Espalamaca in the Azores. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain VBW088T clustered with three type strains of species of the genus Vitellibacter and exhibited a sequence similarity of 97.3 % with Vitellibacter soesokkakensis RSSK-12T. However, strain VBW088T and V. soesokkakensis RSSK-12T exhibited low DNA–DNA relatedness (12.7±3.5 %). Strain VBW088T was positive for catalase and oxidase. Growth occurred at 10–37 °C, with the optimum at 30 °C, and at pH 6.0–8.0 (optimum pH 6.0) and in up to 5 % (w/v) NaCl with optimum growth at 1–2 % (w/v) NaCl. The major fatty acids (>10 %) were iso-C15 : 0 (33.5 %) and iso-C17 : 0 3-OH (32.0 %). The polar lipids detected in strain VBW088T consisted of phosphatidylethanolamine, one unidentified aminolipid and three unidentified phospholipids. The DNA G+C content of strain VBW088T was 36.7 mol%. On the basis of phylogenetic inference, DNA–DNA relatedness, chemotaxonomic analysis and physiological data, the isolate represents a novel species of the genus Vitellibacter , for which the name Vitellibacter nionensis sp. nov. is proposed, with the type strain as VBW088T ( = KCTC 32420T = MCC 2354T).
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Mucilaginibacter aquaedulcis sp. nov., isolated from fresh water
More LessAn aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain PGW1-R01T, was isolated from fresh water from the Yeongju in the Republic of Korea. The strain grew optimally at 30 °C and at pH 6-8 on R2A agar. The major cellular fatty acids were summed feature 3 [comprising C16 : 1ω7c and/or C16 : 1ω6c (50.2 %) and iso-C15 : 0 (24.8 %)]. The major respiratory quinone was MK-7. The G+C contents were 39.4 mol% and the predominant respiratory quinone was MK-7. Based on 16S rRNA gene phylogeny, the strain belongs to the genus Mucilaginibacter . The strain PGW1-R01T was closely related to ‘ Mucilaginibacter ginsenosidivorax’ (96.6 % sequence similarity), Mucilaginibacter lappiensis (96.4 %) and Mucilaginibacter flavus (96.4 %). On the basis of the evidence presented in this study, strain PGW1-R01T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter http://dx.doi.org/10.1601/nm.11437 aquaedulcis sp. nov., is proposed. The type strain is PGW1-R01T( = KCTC 23942T = CECT 8102T).
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- Other Bacteria
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Deinococcus antarcticus sp. nov., isolated from soil
More LessA pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20T, was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m−2) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans . Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus . Highest sequence similarities were with Deinococcus ficus CC-FR2-10T (93.5 %), Deinococcus xinjiangensis X-82T (92.8 %), Deinococcus indicus Wt/1aT (92.5 %), Deinococcus daejeonensis MJ27T (92.3 %), Deinococcus wulumuqiensis R-12T (92.3 %), Deinococcus aquaticus PB314T (92.2 %) and Deinococcus radiodurans DSM 20539T (92.2 %). Major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20T was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20T represents a novel species of the genus Deinococcus , for which the name Deinococcus antarcticus sp. nov. is proposed. The type strain is G3-6-20T ( = DSM 27864T = CCTCC AB 2013263T).
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Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.
Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 °C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47–50 °C and pH 7.0–7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7–100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes . The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2T and Phycisphaera mikurensis FYK2301M01T with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842T, 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842T ( = VKM B-2832T = JCM 19875T). We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.
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Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes
A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102T, was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6–2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102T grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102T required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102T oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102T was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102T was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes . On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102T is proposed to represent a novel species of the genus Aminobacterium , Aminobacterium thunnarium sp. nov. The type strain is OTA 102T ( = DSM 27500T = JCM 19320T).
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Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments
Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the ‘true Nostoc’ group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc , these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the ‘true Nostoc’ clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1–10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc , Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants.
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- Evolution, Phylogeny and Biodiversity
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Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa
More LessGreening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.
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- Letter to Editor
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- Taxonomic Note
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Proposal for ‘Candidatus Mycoplasma haemomuris subsp. musculi’ in mice, and ‘Candidatus Mycoplasma haemomuris subsp. ratti’ in rats
More LessMycoplasma haemomuris is causative of infectious anaemia or splenomegaly in rodents. We examined the nucleotide sequences of the non-ribosomal genes, rnpB and dnaK, in strains of the species M. haemomuris detected in small field mice and black rats. rnpB nucleotide sequences in strains of the species M. haemomuris isolated from small field mice and black rats had only 89 % sequence similarity, suggesting their separation into two distinct subgroups. dnaK had a nucleotide sequence similarity of 84 % between the subgroups. These results support the classification of M. haemomuris into two genetically distinct subgroups. Here we propose the establishment of these subgroups as ‘Candidatus Mycoplasma haemomuris subsp. musculi’, detected in small field mice (Apodemus argenteus), and ‘Candidatus Mycoplasma haemomuris subsp. ratti’, detected in black rats (Rattus rattus).
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Volumes and issues
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