- Volume 64, Issue Pt_6, 2014
Volume 64, Issue Pt_6, 2014
- Notification List
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Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 64, part 3, 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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- Review
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Classification and phylogeny of the cyanobiont Anabaena azollae Strasburger: an answered question?
More LessThe symbiosis Azolla–Anabaena azollae, with a worldwide distribution in pantropical and temperate regions, is one of the most studied, because of its potential application as a biofertilizer, especially in rice fields, but also as an animal food and in phytoremediation. The cyanobiont is a filamentous, heterocystic cyanobacterium that inhabits the foliar cavities of the pteridophyte and the indusium on the megasporocarp (female reproductive structure). The classification and phylogeny of the cyanobiont is very controversial: from its morphology, it has been named Nostoc azollae, Anabaena azollae, Anabaena variabilis status azollae and recently Trichormus azollae, but, from its 16S rRNA gene sequence, it has been assigned to Nostoc and/or Anabaena , and from its phycocyanin gene sequence, it has been assigned as non-Nostoc and non-Anabaena. The literature also points to a possible co-evolution between the cyanobiont and the Azolla host, since dendrograms and phylogenetic trees of fatty acids, short tandemly repeated repetitive (STRR) analysis and restriction fragment length polymorphism (RFLP) analysis of nif genes and the 16S rRNA gene give a two-cluster association that matches the two-section ranking of the host (Azolla). Another controversy surrounds the possible existence of more than one genus or more than one species strain. The use of freshly isolated or cultured cyanobionts is an additional problem, since their morphology and protein profiles are different. This review gives an overview of how morphological, chemical and genetic analyses influence the classification and phylogeny of the cyanobiont and future research.
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- New Taxa
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- Archaea
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Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides
More LessA novel, strictly anaerobic, methylotrophic marine methanogen, strain SLH33T, was isolated from deep sediment samples covered by an orange microbial mat collected from the Napoli Mud Volcano. Cells of strain SLH33T were Gram-stain-negative, motile, irregular cocci that occurred singly. Cells utilized trimethylamine, dimethylamine, monomethylamine, methanol, betaine, N,N-dimethylethanolamine and choline (N,N,N-trimethylethanolamine) as substrates for growth and methanogenesis. The optimal growth temperature was 30 °C; maximum growth rate was obtained at pH 7.0 in the presence of 0.5 M Na+. The DNA G+C content of strain SLH33T was 43.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLH33T within the genus Methanococcoides . The novel isolate was related most closely to Methanococcoides methylutens TMA-10T (98.8 % 16S rRNA gene sequence similarity) but distantly related to Methanococcoides burtonii DSM 6242T (97.6 %) and Methanococcoides alaskense AK-5T (97.6 %). DNA–DNA hybridization studies indicated that strain SLH33T represents a novel species, given that it shared less than 16 % DNA–DNA relatedness with Methanococcoides methylutens TMA-10T. The name Methanococcoides vulcani sp. nov. is proposed for this novel species, with strain SLH33T ( = DSM 26966T = JCM 19278T) as the type strain. An emended description of the genus Methanococcoides is also proposed.
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Salinigranum rubrum gen. nov., sp. nov., a member of the family Halobacteriaceae isolated from a marine solar saltern
More LessHalophilic archaeal strain GX10T was isolated from the Gangxi marine solar saltern in China. Strain GX10T was observed to have pleomorphic cells that lysed in distilled water, stained Gram-negative and produced red-pigmented colonies. Strain GX10T was able to grow at 20–50 °C (optimum 37 °C), with 1.4–4.8 M NaCl (optimum 3.1 M NaCl), with 0–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.0–9.0 (optimum pH 7.0). The major polar lipids of strain GX10T were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, and five unidentified glycolipids. Phylogenetic tree reconstructions based on 16S rRNA gene and rpoB′ sequences revealed that strain GX10T was distinct from the related genera, Halogranum , Haloferax , Halopelagius , Halogeometricum , Halobellus , Haloplanus and Halorubrum . The DNA G+C content of strain GX10T was 62.9 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain GX10T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Salinigranum rubrum gen. nov., sp. nov. is proposed. The type strain of the type species is GX10T ( = CGMCC 1.10385T = JCM 17116T).
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Methanohalophilus levihalophilus sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and emended description of the genus Methanohalophilus
A mesophilic, slightly halophilic, obligately methylotrophic, methanogenic archaeon, designated strain GTA13T, was isolated from natural gas-bearing confined aquifers in the Minami-Kanto gas field, Japan. The cells were non-motile, slightly irregular cocci, 0.7–1.0 µm in diameter and occurred singly, in pairs or as small aggregates. The cells grew with tri- or dimethylamine but not with H2/CO2, formate, acetate, methanol or dimethyl sulphide. Vitamins, sodium and magnesium were required for growth. Optimal growth occurred at pH 7.0–7.5, 35 °C, 0.35–0.40 M NaCl and 15–50 mM MgCl2. The NaCl range for growth was 0.2–1.3 M. The DNA G+C content was 43.7 mol%. Strain GTA13T showed highest levels of 16S rRNA gene sequence similarity with Methanohalophilus portucalensis FDF-1T (96.4 % sequence similarity) and Methanohalophilus halophilus DSM 3094T (96.0 %). On the basis of physiological and phylogenetic features, strain GTA13T is considered to represent a novel species of the genus Methanohalophilus , for which the name Methanohalophilus levihalophilus sp. nov. is proposed. The type strain is GTA13T ( = NBRC 110099T = DSM 28452T). An emended description of the genus Methanohalophilus is also proposed.
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- Actinobacteria
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Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora
A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.
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Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim
More LessThe taxonomic status of a carbendazim-degrading strain, mbc-2T, isolated from soil under the long-term application of carbendazim in China was determined by means of a polyphasic study. The cells were Gram-stain-positive, motile and rod-shaped. Strain mbc-2T grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain mbc-2T fell within the genus Nocardioides , forming a coherent cluster with the type strain of Nocardioides hankookensis , with which it exhibited 16S rRNA gene sequence similarity values of 97.9 %. The chemotaxonomic properties of strain mbc-2T were consistent with those of the genus Nocardioides : the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8 (H4) and the major fatty acid was iso-C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unknown phospholipids and an unknown aminolipid. The DNA G+C content was 72 mol%. Strain mbc-2T exhibited DNA–DNA relatedness values of 12.5±1.5 %, 23.7±2.7 % and 26.3±3.2 % with respect to Nocardioides hankookensis DS-30T, Nocardioides aquiterrae GW-9T and Nocardioides pyridinolyticus OS4T. On the basis of the data obtained, strain mbc-2T represents a novel species of the genus Nocardioides , for which the name Nocardioides soli sp. nov. is proposed. The type strain is mbc-2T ( = KACC 17152T = CCTCC AB 2012934T).
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Nocardioides opuntiae sp. nov., isolated from soil of a cactus
More LessA novel high G+C actinobacterium, designated strain OS1-21T, was isolated from the rhizosphere soil of a cactus (Opuntia fiscus-indica var. sanboten) and the taxonomic status was investigated using a polyphasic approach. Cells of strain OS1-21T were aerobic, Gram-stain-positive, non-endospore-forming, non-motile rods; colonies of the cells were circular, translucent, smooth and moderate yellow in colour. ll-Diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, 10-methyl C17 : 0, 10-methyl C18 : 0 and C17 : 1 cis9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. The DNA G+C content was 73.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours were Nocardioides panacihumi Gsoil 616T (98.7 % sequence similarity) and Nocardioides terrae VA15T (97.8 %), followed by Nocardioides marinus CL-DD14T (97.1 %). DNA–DNA relatedness values of strain OS1-21T with the type strains of the closest phylogenetic neighbours were low (<16.0 %). Combined data of polyphasic taxonomic analyses revealed that the organism could be assigned to a novel species of the genus Nocardioides , for which the name Nocardioides opuntiae sp. nov. is proposed. The type strain is OS1-21T ( = KCTC 19804T = NBRC 107915T).
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Streptomyces catbensis sp. nov., isolated from soil
More LessStrain VN07A0015T was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015T was near Streptomyces aomiensis M24DS4T (98.5 % 16S rRNA gene sequence similarity) and Streptomyces scabrisporus NBRC 100760T (95.6 %), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus Streptomyces . The aerial mycelia of strain VN07A0015T were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015T were different from those of the type strains of S. aomiensis and S. scabrisporus . The chemotaxonomic characteristics of strain VN07A0015T were typical for all members of the genus Streptomyces , which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C16 : 0 and iso-C15 : 0. DNA–DNA relatedness between strain VN07A0015T and S. aomiensis NBRC 106164T was less than 30 %. In addition, some physiological and biochemical traits differed from those of S. aomiensis . Therefore, we propose that strain VN07A0015T be classified in the genus Streptomyces as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015T = VTCC-A-1889T = NBRC 107860T).
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- Firmicutes and Related Organisms
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Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments
Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average blast nucleotide identity (ANIb) of less than 85 % to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria ; (i) a clade representing Listeria monocytogenes , L. marthii , L. innocua , L. welshimeri , L. seeligeri and L. ivanovii , which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188T = DSM 26686T = LMG 28120T = BEI NR-42633T) and Listeria floridensis sp. nov. (type strain FSL S10-1187T = DSM 26687T = LMG 28121T = BEI NR-42632T), (iii) a clade consisting of Listeria rocourtiae , L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210T = FSL F6-0969T = DSM 26689T = LMG 28123T = BEI NR-42630T), Listeria grandensis sp. nov. (type strain TTU A1-0212T = FSL F6-0971T = DSM 26688T = LMG 28122T = BEI NR-42631T) and Listeria riparia sp. nov. (type strain FSL S10-1204T = DSM 26685T = LMG 28119T = BEI NR- 42634T) and (iv) a clade containing Listeria grayi . Genomic and phenotypic data suggest that the novel species are non-pathogenic.
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‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique
In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus Phytoplasma ’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus Phytoplasma ’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.
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Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake
A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76T, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76T grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5 % (w/v) NaCl (optimal growth at 7.5 %, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76T was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1 %, to the type species of the genera Jeotgalicoccus , Salinicoccus and Nosocomiicoccus , respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76T were anteiso-C15 : 0 and iso-C15 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94 %), MK-5 (3 %) and MK-7 (3 %). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76T and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae , for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76T ( = CECT 8508T = DSM 28306T = IBRC-M 10081T).
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Bacillus tianshenii sp. nov., isolated from a marine sediment sample
A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus Bacillus . The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2–4 % (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235T exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and summed feature 4 (anteiso-C17 : 1 and/or iso-C17 : 1). The genomic DNA G+C content was 42.1 mol%. The DNA–DNA relatedness values between strain YIM M13235T and its close relatives (16S rRNA gene sequence similarities >97 %) including Bacillus halmapalus DSM 8723T, Bacillus horikoshii DSM 8719T and Bacillus zhanjiangensis JSM 099021T were 41 %, 44 % and 44 %, respectively. On the basis of genotypic, phenotypic and DNA–DNA relatedness data, it is apparent that strain YIM M13235T represents a novel species of the genus Bacillus , for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235T ( = DSM 25879T = KCTC 33044T).
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Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens
Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.
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Alkalibacillus almallahensis sp. nov., a halophilic bacterium isolated from an inland solar saltern
More LessA halophilic, Gram-staining-positive, non-motile, endospore forming rod-shaped bacterial strain, S1LM8T, was isolated from a sediment sample collected from an inland solar saltern located in La Malahá, Granada (Spain). Growth was observed in media containing 7.5–30 % total salts (optimum 15 % total salts), at pH 7–10 (optimum pH 8) and at 15–50 °C (optimum 35–38 °C). The predominant isoprenoid quinone was MK-7. It contained A1γ-type peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of its genomic DNA was 38.2 mol%. The affiliation of strain S1LM8T with the species of the genus Alkalibacillus was determined by 16S rRNA gene sequence comparison. The most closely related species were Alkalibacillus halophilus YIM 012T with 99.8 % similarity, Alkalibacillus salilacus BH163T with 99.8 % similarity and Alkalibacillus flavidus ISL-17T with 98.1 % similarity between their 16S rRNA gene sequences. However, DNA–DNA relatedness between the novel isolate and the related species of the genus Alkalibacillus was less than 34 %. Based on the phylogenetic, phenotypic and chemotaxonomic features, a novel species, Alkalibacillus almallahensis sp. nov. is proposed. The type strain is S1LM8T ( = CECT 8373T = DSM 27545T).
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- Proteobacteria
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Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat
More LessA Gram-stain-negative, non-motile, aerobic, curved-to-spiral-rod-shaped bacterium, designated AH-MY2T, was isolated from a tidal flat on Aphae island in the sea to the south-west of South Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain AH-MY2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain AH-MY2T clustered with the type strain of Terasakiella pusilla and that this cluster joined the clade comprising the type strains of species of the genus Thalassospira . Strain AH-MY2T exhibited 16S rRNA gene sequence similarity values of 90.6 % to the type strain of Terasakiella pusilla and of less than 91.0 % to the type strains of other species with validly published names. Strain AH-MY2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain AH-MY2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids and one unidentified glycolipid. The DNA G+C content of strain AH-MY2T was 56.0 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY2T represented a novel genus and species within the family Rhodospirillaceae of the class Alphaproteobacteria , for which the name Aestuariispira insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariispira insulae is AH-MY2T ( = KCTC 32577T = CECT 8488T).
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Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules
More LessThree slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium . To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium , indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium . Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium , for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (T m).
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Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb
More LessDuring a study to investigate the diversity of rhizobia associated with native legumes in South Africa’s Cape Floristic Region, a Gram-negative bacterium designated VG1CT was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1CT belongs to the genus Burkholderia , with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5 % and 98 %, respectively). The DNA G+C content of strain VG1CT was 60.1 mol%, and DNA–DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70 %. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1CT represents a novel rhizosphere-associated species in the genus Burkholderia , for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1CT ( = DSM 27239T = LMG 27731T).
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Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples
More LessTwo Gram-stain-negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter . This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0 %; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T ( = CECT 8410T = LMG 27920T).
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Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent
More LessA novel bacterium, PB3-7BT, was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7BT belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07T (97.5 %), Candidimonas bauzanensis BZ59T (97.3 %) and Pusillimonas noertemannii BN9T (97.2 %). Strain PB3-7BT was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and C14 : 0 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7BT was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7BT is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7BT ( = DSM 25520T = NCAIM B 02512T).
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Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil
More LessA Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8T, was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Xenophilus azovorans , Xenophilus aerolatus , Simplicispira metamorpha , Variovorax soli , and Xylophilus ampelinus . However, the phylogenetic tree indicated that strain YW8T formed a separate clade from Xenophilus azovorans . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain YW8T and its closest phylogenetic neighbours were below 24.2–35.5 %, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8T were C16 : 0, C 17 : 0 cyclo, C18 : 1ω7c, and summed feature 3(C16 : 1ω6c and/or C16 : 1ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA–DNA hybridization and chemotaxonomic data, strain YW8T is considered to represent a novel species of the genus Xenophilus , for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8T ( = CCTCC AB2012103T = KACC 16853T).
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Melaminivora alkalimesophila gen. nov., sp. nov., a melamine-degrading betaproteobacterium isolated from a melamine-producing factory
More LessA taxonomic study was carried out on strain CY1T, which is a novel bacterium isolated from wastewater sludge of a melamine-producing factory in Sanming city, Fujian, China. Strain CY1T was shown to rapidly and completely degrade melamine to NH3 and CO2 under aerobic conditions. The isolate was Gram-stain-negative, short-rod-shaped and motile by one unipolar flagellum. Growth was observed at salinities from 0 to 7 % NaCl (optimum, 0.1 %), at temperatures from 15 to 50 °C (optimum, 40–45 °C) and at pH 7–9.5 (optimum pH 9.5). Quinone-8 was detected as the major respiratory quinone. 16S rRNA gene sequence comparisons showed that strain CY1T was affiliated to the family Comamonadaceae in the class Betaproteobacteria . It was most closely related to members of the genera Alicycliphilus (95.5 %), Diaphorobacter (94.6–95.1 %), Acidovorax (92.9–95.4 %), Delftia (93.0–93.6 %) and Comamonas (92.6–93.9 %). The average nucleotide identity (ANI) values between strain CY1T and those representing related genera ranged from 84.0 to 86.1 % using Mummer, and from 74.9 to 81.1 % using blast. The dominant fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0, C10 : 0 3-OH and C18 : 1ω7c and/or C18 : 1ω6c, and the major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 69.5 mol%. On the basis of the phenotypic and phylogenetic data, strain CY1T represents a novel species of a new genus, for which the name Melaminivora alkalimesophila gen. nov., sp. nov. is proposed. The type strain of Melaminivora alkalimesophila is CY1T ( = CCTCC AB 2012024T = DSM 26006T).
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Psychrosphaera aestuarii sp. nov. and Psychrosphaera haliotis sp. nov., isolated from the marine environment, and emended description of the genus Psychrosphaera
More LessTwo motile, rod-shaped and agarolytic bacterial strains, designated PSC101T and KDW4T, were isolated from seawater and gut microflora of abalone, respectively, collected from the South Sea (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive. Strains PSC101T and KDW4T showed high 16S rRNA gene sequence similarity to each other (98.6 %). Psychrosphaera saromensis SA4-48T was the nearest neighbour of strains PSC101T and KDW4T with 96.6 % and 97.0 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness among strains PSC101T, KDW4T and Psychrosphaera saromensis KCTC 23240T was less than 70 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belonged to the genus Psychrosphaera and formed a distinct phyletic line from Psychrosphaera saromensis SA4-48T. The common major cellular fatty acids of the two novel isolates were C16 : 0, C17 : 1ω8c and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). Flexirubin-type pigments were absent. The main ubiquinone was UQ-8 and the DNA G+C content of strains PSC101T and KDW4T was 49.5 and 42.5 mol%, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. On the basis of the polyphasic characterization of the two strains, it is suggested that the two isolates represent two novel species of the genus Psychrosphaera , for which the names Psychrosphaera aestuarii sp. nov. (type strain, PSC101T = KCTC 32274T = JCM 19496T) and Psychrosphaera haliotis sp. nov. (type strain, KDW4T = KCTC 22500T = JCM 16340T) are proposed. An emended description of the genus Psychrosphaera is also proposed.
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Wenxinia saemankumensis sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-motile, ovoid- or rod-shaped bacterial strain, designated S-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain S-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain S-22T joined Wenxinia marina HY34T, with which it exhibited highest 16S rRNA gene sequence similarity (98.0 %). The DNA G+C content was 72.3 mol% and the mean DNA–DNA relatedness value between strain S-22T and the type strain of W. marina was 3.7 %. Strain S-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-22T is distinguishable from W. marina . On the basis of the data presented, strain S-22T is considered to represent a novel species of the genus Wenxinia , for which the name Wenxinia saemankumensis sp. nov. is proposed. The type strain of is S-22T ( = KCTC 32548T = CECT 8456T).
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Burkholderia cordobensis sp. nov., from agricultural soils
Two Gram-negative, rod-shaped bacteria were isolated from agricultural soils in Córdoba province in central Argentina. Their 16S rRNA gene sequences demonstrated that they belong to the genus Burkholderia , with Burkholderia zhejiangensis as most closely related formally named species; this relationship was confirmed through comparative gyrB sequence analysis. Whole-cell fatty acid analysis supported their assignment to the genus Burkholderia . Burkholderia sp. strain YI23, for which a whole-genome sequence is available, represents the same taxon, as demonstrated by its highly similar 16S rRNA (100 % similarity) and gyrB (99.1–99.7 %) gene sequences. The results of DNA–DNA hybridization experiments and physiological and biochemical characterization further substantiated the genotypic and phenotypic distinctiveness of the Argentinian soil isolates, for which the name Burkholderia cordobensis sp. nov. is proposed, with strain MMP81T ( = LMG 27620T = CCUG 64368T) as the type strain.
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Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river
More LessA bacterial strain, designated Npb-03T, was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10–37 °C (optimum, 30–35 °C), at pH 6.0–8.0 (optimum, pH 6.0–7.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03T forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria , most closely related to the genera Aquaspirillum , Laribacter , Leeia and Microvirgula , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the genotypic and phenotypic data, strain Npb-03T represents a novel genus and species of the family Neisseriaceae , for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03T ( = BCRC 80376T = LMG 26668T = KCTC 23712T).
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Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos
More LessA Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14T, was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14T did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14T belonged to the genus Rhizobium . Strain YW14T showed 16S rRNA gene sequence similarity of 93.4–97.3 % to the type strains of recognized species of the genus Rhizobium . DNA–DNA relatedness between strain YW14T and the type strains of Rhizobium sullae IS123T and Rhizobium yanglingense CCBAU 71623T was 19.6–25.7 %, indicating that strain YW14T was distinct from them genetically. Strain YW14T could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14T ( = KACC 17222T = CCTCC AB2013042T).
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Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock
A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7T) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7T grew at temperatures between −4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0 %, with an optimum of 0.5 %. Strain 262-7T showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C17 : 1ω6c (28.2 %), C16 : 1ω7c (22.6 %), C18 : 1ω7c (12.9 %) and C15 : 0 2-OH (12.3 %). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7T belongs to the family Sphingomonadaceae , and that 262-7T should be distinguished from known genera in the family Sphingomonadaceae . According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7T should be classified as a representative of a novel genus of the family Sphingomonadaceae . Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7T = JCM 18140T = ATCC BAA-2413T). The novel species was named after its morphological diversity and formation of unique projections.
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Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru
A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of Bradyrhizobium lablabi CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus Bradyrhizobium . Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus Bradyrhizobium (≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus Bradyrhizobium were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.
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Thalassomonas eurytherma sp. nov., a marine proteobacterium
Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12T and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12T and Za6a-17 were approximately 1.5–2.0 µm×0.5–0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5–3.0 % (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12T and Za6a-17 was ubiquinone-8 (>97 %), and the major fatty acids were C14 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C17 : 1ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722T (95.9 %). Strains Za6a-12T and Za6a-17 could be differentiated from T. loyana CBMAI 722T according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12T and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12T ( = CGMCC 1.12115T = JCM 18482T) is the type strain of this novel species.
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Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment
More LessA Gram-stain-negative, strictly aerobic, chemoheterotrophic marine bacterium, designated 20V17T, was isolated from a deep-sea hydrothermal vent chimney collected from the South-west Indian Ridge. Cells of strain 20V17T were motile, short rods, 1.2–1.8 µm in length and 0.5–0.7 µm in width. Growth was observed at between 20 and 37 °C (optimum 25 °C–28 °C), pH 5.0 and 8.0 (optimum pH 7.0) and 0.5 and 8 % (w/v) NaCl (optimum 1.5–2.0 % NaCl). The major fatty acids were C18 : 1ω7c (74.4 %), C19 : 0 cyclo ω8c (11 %), C18 : 0 (5.1 %) and C18 : 0 3-OH (2.8 %), and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and four unidentified phospholipids. Ubiquinone 10 was the major quinone. The G+C content of genomic DNA was 66.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 20V17T belonged to the genus Defluviimonas and shared 96.5 and 96.1 % sequence similarity with Defluviimonas denitrificans D9-3T and Defluviimonas aestuarii BS14T, respectively. On the basis of the taxonomic data obtained in this study, strain 20V17T represents a novel species of the genus Defluviimonas , for which the name Defluviimonas indica sp. nov. is proposed. The type strain is 20V17T (CGMCC 1.10859T = JCM 17871T = MCCC 1A01802T).
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Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water
Two novel methanotrophic strains, R-49797T and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797T and OS501 shared 99.7 % 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25–33 °C (range 20–37 °C) and at pH 6.3–6.8 (range 5.8–9.0). The strains did not support growth in media supplemented with 1 % (w/v) NaCl. For both strains, the two major fatty acids were C16 : 1ω7c and C16 : 0 and the DNA G+C content was 65.6 mol%. The isolates belong to the family Methylococcaceae of the class Gammaproteobacteria and cluster most closely among the genera Methylocaldum , Methylococcus and Methylogaea , with a 16S rRNA gene sequence similarity of 94.2 % between strain R-49797T and its closest related type strain ( Methylocaldum gracile VKM 14LT). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera Methylocaldum , Methylococcus and Methylogaea , we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family Methylococcaceae . The type strain of Methyloparacoccus murrellii is R-49797T ( = LMG 27482T = JCM 19379T).
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- Bacteroidetes
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Pseudopedobacter beijingensis gen. nov., sp. nov., isolated from coking wastewater activated sludge, and reclassification of Pedobacter saltans as Pseudopedobacter saltans comb. nov.
More LessA taxonomic study was carried out on strain GCS-AE-31T, which was isolated from a phenol-degrading consortium, enriched from coking wastewater activated sludge of the Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AE-31T were Gram-stain-negative, short rods, motile by gliding, oxidase- and catalase-positive. Growth was observed at salinities of 0–3 % and at temperatures of 10–37 °C. On the basis of 16S rRNA gene sequence similarity, strain GCS-AE-31T was most closely related to Pedobacter saltans LMG 10337T (96.17 %), but it showed low similarity to all other species of the genus Pedobacter (89.28–92.45 %). It also showed low 16S rRNA gene similarity to all other species of the family Sphingobacteriaceae (87.25–92.45 %) examined. The dominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), anteiso-C15 : 0 and iso-C17 : 0 3-OH. The menaquinones were MK-7 (95.5 %) and MK-6 (4.5 %). The polar lipids were phosphatidylethanolamine, three aminolipids and three unknown phospholipids. Sphingolipid was present. The G+C content of the chromosomal DNA was 36.2 mol%. According to its phylogenetic position and phenotypic traits, the novel strain could not be assigned to the genus Pedobacter ; it should be classified as representing a novel species of a novel genus in the family Sphingobacteriaceae , for which the name Pseudopedobacter beijingensis gen. nov., sp. nov. is proposed (type strain GCS-AE-31T = MCCC 1A01299T = CGMCC 1.12329T = LMG 27180T). The misclassified species Pedobacter saltans is transferred to the novel genus as Pseudopedobacter saltans comb. nov. (type strain LMG 10337T = MCCC 1A06472T = DSM 12145T = CCUG 39354T = CIP 105500T = JCM 21818T = NBRC 100064T).
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Seonamhaeicola aphaedonensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-motile, rod-shaped bacterial strain, AH-M5T, which was isolated from a tidal flat sediment at Aphae Island in South Korea, was characterized taxonomically. Strain AH-M5T grew optimally at 25 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain AH-M5T clustered coherently with the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus , showing 93.4–94.3 % sequence similarity. The novel strain exhibited 16S rRNA gene sequence similarity values of less than 93.4 % to the type strains of other recognized species. Strain AH-M5T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipid profile of strain AH-M5T containing phosphatidylethanolamine and one unidentified lipid as major components was differentiated from those of the type strains of Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . The DNA G+C content of strain AH-M5T was 34.8 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain AH-M5T is distinguished from Mangrovimonas yunxiaonensis and Meridianimaribacter flavus . On the basis of the data presented, strain AH-M5T is considered to represent a novel genus and species within the family Flavobacteriaceae , for which the name Seonamhaeicola aphaedonensis gen. nov., sp. nov. is proposed. The type strain of the type species is AH-M5T ( = KCTC 32578T = CECT 8487T).
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Mesoflavibacter aestuarii sp. nov., a zeaxanthin-producing marine bacterium isolated from seawater
More LessAn orange, rod-shaped, Gram-reaction-negative, aerobic and gliding bacterial strain devoid of flagella, designated strain KYW614T, was isolated from seawater collected from Gwangyang Bay, Republic of Korea. Zeaxanthin was the major carotenoid pigment produced and flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW614T belonged to the family Flavobacteriaceae and it was most closely related to Mesoflavibacter zeaxanthinifaciens TD-ZX30T (96.5 %, sequence similarity). The predominant cellular fatty acids of strain KYW614T were iso-C15 : 1 G (10.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 10.0 %), iso-C15 : 0 (9.5 %), C15 : 0 (7.5 %) and iso-C17 : 0 3-OH (7.4 %). MK-6 was the only isoprenoid quinone and the DNA G+C content was 32.6 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in the genus Mesoflavibacter , for which the name Mesoflavibacter aestuarii sp. nov. is proposed. The type strain is KYW614T ( = KCTC 32269T = JCM 19524T).
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Description of Lutimonas halocynthiae sp. nov., isolated from a golden sea squirt (Halocynthia aurantium), reclassification of Aestuariicola saemankumensis as Lutimonas saemankumensis comb. nov. and emended description of the genus Lutimonas
A Gram-stain-negative, non-motile, coccoid, ovoid or rod-shaped bacterial strain, designated RSS3-C1T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS3-C1T was found to grow optimally at 20–25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS3-C1T clustered with the type strains of Lutimonas vermicola and Aestuariicola saemankumensis . Strain RSS3-C1T exhibited 98.8 % 16S rRNA gene sequence similarity to each type strain. Strain RSS3-C1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain RSS3-C1T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain RSS3-C1T was 39.2 mol%, and DNA–DNA relatedness to the type strains of and was 21±5.3 and 26±7.5 %, respectively. The differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RSS3-C1T is separated from and . On the basis of the data presented, strain RSS3-C1T is considered to represent a novel species of the genus Lutimonas , for which the name Lutimonas halocynthiae sp. nov. is proposed. The type strain is RSS3-C1T ( = KCTC 32537T = CECT 8444T). In this study, it is also proposed that Aestuariicola saemankumensis should be reclassified as a member of the genus Lutimonas , as Lutimonas saemankumensis comb. nov. (type strain SMK-142T = KCTC 22171T = CCUG 55329T), and the description of the genus Lutimonas is emended.
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Aquimarina pacifica sp. nov., isolated from seawater
More LessA Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic bacterium with gliding motility, designated strain SW150T, was isolated from surface seawater of the South Pacific Gyre (39° 19′ S 139° 48′ W) during the Integrated Ocean Drilling Program Expedition 329. Optimal growth occurred in the presence of 2–4 % (w/v) NaCl, at pH 7–8 and at 28–30 °C. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 1ω6c and/or C16 : 1ω7c and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c. The polar lipids of strain SW150T comprised phosphatidylethanolamine, three unknown polar lipids and one unknown aminolipid. The major respiratory quinone was MK-6. The DNA G+C content of strain SW150T was 33.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27T and Aquimarina muelleri KMM 6020T with 97.8 and 96.8 % sequence similarities, respectively. The estimated DNA–DNA hybridization values were 21.00±2.33 % between strain SW150T and A. macrocephali JAMB N27T and 20.60±2.32 % between strain SW150T and Aquimarina megaterium XH134T. On the basis of polyphasic analyses, strain SW150T represents a novel species of the genus Aquimarina , for which the name Aquimarina pacifica sp. nov. is proposed. The type strain is SW150T ( = JCM 18214T = CGMCC 1.12180T).
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Rhodanobacter glycinis sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean
More LessA novel, yellow-pigmented bacterium, designated strain MO64T, was isolated from the rhizoplane of field-grown soybean, collected from an experimental plot at Coimbatore, India. Cells were Gram-reaction-negative, motile, non-spore-forming rods that produced yellow-pigmented colonies on R2A agar. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MO64T belonged to the genus Rhodanobacter . Strain MO64T was related most closely to Rhodanobacter ginsengisoli GR17-7T (98.0 % 16S rRNA gene sequence similarity), Rhodanobacter spathiphylli B39T (97.9 %), Rhodanobacter panaciterrae LnR5-47T (97.7 %), Rhodanobacter terrae GP18-1T (97.6 %), Rhodanobacter soli DCY45T (97.3 %) and Rhodanobacter caeni MJ01T (97.2 %); levels of similarity to the type strains of all other recognized species of the genus Rhodanobacter were less than 97.0 %. Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C16 : 0, iso-C15 : 0, C17 : 0 cyclo, iso-C17 : 1ω9c, iso-C17 : 0 and iso-C11 : 0 as the major fatty acids) also supported the affiliation of strain MO64T with the genus Rhodanobacter . The G+C content of the genomic DNA was 64 mol%. The results of DNA–DNA hybridization and phenotypic analysis showed that strain MO64T can be distinguished from all known species of the genus Rhodanobacter and therefore represents a novel species of the genus, for which the name Rhodanobacter glycinis sp. nov. is proposed. The type strain is MO64T ( = ICMP 17626T = NBRC 105007T).
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Ulvibacter marinus sp. nov., isolated from coastal seawater
More LessA Gram-stain-negative, aerobic, chemoheterotrophic, yellow, non-motile and flexirubin-positive bacterium, designated strain IMCC12008T, was isolated from coastal seawater of the Yellow Sea and subjected to polyphasic taxonomy. Optimal growth was observed at 25 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis and subsequent phylogenetic analyses, strain IMCC12008T belonged to the genus Ulvibacter of the family Flavobacteriaceae , with Ulvibacter antarcticus IMCC3101T (96.0 %) and Ulvibacter litoralis KMM 3912T (95.8 %) having the highest sequence similaries. The major fatty acids were iso-C15 : 0 (26.2 %) and iso-C15 : 1 G (10.5 %). The DNA G+C content was 38.1 mol%. Strain IMCC12008T contained menaquinone-6 (MK-6) as the respiratory quinone, and polar lipids comprising phosphatidylethanolamine, two unidentified aminolipids and an unknown aminophospholipid. On the basis of data collected from this study, strain IMCC12008T ( = NBRC 109484T = KCTC 32322T) represents a novel species of the genus Ulvibacter , for which the name Ulvibacter marinus sp. nov. is proposed.
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Hoppeia youngheungensis gen. nov., sp. nov., a member of the Flavobacteriaceae isolated from tidal flat sediment, and emended descriptions of the genus Sediminibacter and Sediminibacter furfurosus
More LessA Gram-reaction-negative, proteorhodopsin-containing, yellow-pigmented, rod-shaped, non-gliding and strictly aerobic bacterium, designated strain YIK12T, was isolated from tidal flat sediment of Yeongheung Island at the coast of the West Sea of Korea. Cells produced non-diffusible carotenoid pigments, but not flexirubin-type pigment. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate was affiliated to the family Flavobacteriaceae and showed highest similarity to Sediminibacter furfurosus MAOS-86T (93.3 %). Growth was observed at 24–44 °C (optimum 30 °C), at pH 6.5–8.0 (optimum 7.0) and in the presence of 1.5–7.0 % sea salts (optimum 2 %). The DNA G+C content was 40.4 mol% and the predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, anteiso-C15 : 0 and iso-C15 : 0 3-OH. The major respiratory quinone was MK-6. On the basis of data from the present polyphasic taxonomic study, strain YIK12T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Hoppeia youngheungensis gen. nov., sp. nov. is proposed. The type strain of H. youngheungensis is YIK12T ( = KCCM 43023T = JCM 19488T). Emended descriptions of the genus Sediminibacter and Sediminibacter furfurosus are given.
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Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium
More LessA Gram-reaction-negative, rod-shaped, non-motile, red-pigmented, radiation-resistant, aerobic bacterium designated T-3T was isolated from a soil sample from the Qinghai–Tibet Plateau in Tibet, China, after exposure to 10 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA sequences indicated that this isolate represented a novel member of the genus Hymenobacter . Sequence identities of the 16S rRNA gene of strain T-3T with the type strains of species of the genus Hymenobacter with validly published names range from 89 % to 97 %, and the most closely related species is Hymenobacter psychrotolerans Tibet-IIU11T (97 %). The DNA–DNA relatedness between strain T-3T and H. psychrotolerans is 59.10 %. The major fatty acids of strain T-3T were iso-C15 : 0 (27.66 %), summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B, 15.84 %), anteiso-C15 : 0 (14.08 %) and summed feature 3 (C16 : 1ω7c and/orC16 : 1ω6c, 12.38 %). The major menaquinone of strain T-3T was MK-7. Phosphatidylethanolamine (PE) was predominant in the polar lipid profile. The G+C content of the DNA of strain T-3T was 69.17 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain T-3T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter kanuolensis is proposed. The type strain is T-3T ( = ACCC 05760T = KCTC 32407T).
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Hymenobacter arcticus sp. nov., isolated from glacial till
A novel, red–pink-pigmented strain, designated R2-4T, was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4–30 °C (optimum, 20–22 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4T belonged to the genus Hymenobacter . 16S rRNA gene sequence similarity between strain R2-4T and the type strains of related species of the genus ranged from 94.51 to 96.05 %. Strain R2-4T contained iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 4 (C17 : 1 anteiso B and/or iso I) and C16 : 1ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4T was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4T is considered to represent a novel species of the genus Hymenobacter , for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4T ( = CCTCC AB 2012104T = KACC 16881T).
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- Other Bacteria
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Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi
A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).
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Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil
More LessAcidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4HT and Ac_23_E3T were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4HT and Ac_23_E3T were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4HT and Ac_23_E3T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and anteiso-C17 : 0. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4HT and Ac_23_E3T were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16T, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4HT and Ac_23_E3T displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4HT = DSM 26555T = LMG 27985T) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3T = DSM 26558T = LMG 27597T).
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Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.
A thermophilic, filamentous, heterotrophic bacterium, designated strain JAD2T, a member of an as-yet uncultivated lineage that is present and sometimes abundant in some hot springs worldwide, was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had a mean diameter of 0.3 µm and length of 4.0 µm, and formed filaments that typically ranged in length from 20 to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed and motility was not observed. The optimum temperature for growth was 72.5–75 °C, with a range of 67.5–75 °C, and the optimum pH for growth was 6.75, with a range of pH 6.5–7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with vitamins, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was microaerophilic and facultatively anaerobic, with optimal growth at 1 % (v/v) O2 and an upper limit of 8 % O2. The major cellular fatty acids (>5 %) were C16 : 0, C19 : 0, C18 : 0, C20 : 0 and C19 : 1. The genomic DNA G+C content was 69.3 mol%. Phylogenetic and phylogenomic analyses using sequences of the 16S rRNA gene and other conserved genes placed JAD2T within the phylum Chloroflexi , but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a novel lineage within the phylum Chloroflexi , for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., within Thermoflexia classis nov., Thermoflexales ord. nov. and Thermoflexaceae fam. nov. The type strain of Thermoflexus hugenholtzii is JAD2T ( = JCM 19131T = CCTCC AB-2014030T).
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Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs
Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).
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Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes
More LessA mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7T, was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7T were motile, curved rods (0.7–1.0×5.0–8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25–40 °C) and pH 7.0 (pH 6.0–7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864T, strain 7WAY-8-7T could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, l-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called ‘PD-UASB-13’ in the Greengenes database) in the bacterial phylum Synergistetes , showing less than 90 % sequence similarity with closely related described species such as Aminivibrio pyruvatiphilus and Aminobacterium colombiense (89.7 % and 88.7 %, respectively). The major cellular fatty acids were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 1, C19 : 1, C20 : 1 and C21 : 1. A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7T ( = JCM 17151T = DSM 24196T = CGMCC 1.5159T).
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- Eukaryotic Micro-organisms
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Metschnikowia laotica f.a., sp. nov., a dimorphic, pigment-producing yeast species isolated from fruit
More LessEight strains with identical sequences of the D1/D2 domains of the large subunit rRNA genes were isolated from fallen fruits in two distant localities in Laos. These strains represent a novel dimorphic budding yeast species producing invasive pseudohyphae and a brown pigment when growing on media containing quinic acid as the sole carbon source or tryptophan as the sole nitrogen source. Phylogenetic analysis of the sequences of the D1/D2 domains, the internal transcribed spacer (ITS) regions and the 18S rRNA genes placed the novel species in the Metschnikowia clade close to Candida torresii, Metschnikowia drosophilae and C andida danieliae. The taxonomic name Metschnikowia laotica f.a., sp. nov., reflecting the geographical origin of the isolates, is proposed for the novel species. The type strain is 11-524T ( = CBS 12961T = NCAIM Y.02124T = CCY 64-4-1T). The Mycobank number is MB 807383.
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Hannaella pagnoccae sp. nov., a tremellaceous yeast species isolated from plants and soil
Melissa Fontes Landell, Luciana R. Brandão, Anne C. Barbosa, Jesus P. Ramos, Silvana V. B. Safar, Fatima C. O. Gomes, Francisca M. P. Sousa, Paula B. Morais, Leonardo Broetto, Orílio Leoncini, José Roberto Ribeiro, Bundit Fungsin, Masako Takashima, Takashi Nakase, Ching-Fu Lee, Marilene H. Vainstein, Jack W. Fell, Gloria Scorzetti, Helen S. Vishniac, Carlos A. Rosa and Patricia ValenteSeveral independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118T ( = CBS 11142T = ATCC MYA-4530T).
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Wickerhamiella kiyanii f.a., sp. nov. and Wickerhamiella fructicola f.a., sp. nov., two yeasts isolated from native plants of Atlantic rainforest in Brazil
More LessTwo novel species, Wickerhamiella kiyanii f.a., sp. nov. (type strain FB1-1DASPT = CBS 12905T = CBMAI 1613T) and Wickerhamiella fructicola f.a., sp. nov. (type strain H10YT = CBS 12902T = CBMAI 1614T) are proposed in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales) to accommodate three strains isolated from flowers and fruits typical of the Brazilian Atlantic rainforest. The novel status of these yeast species was established by sequence divergence observed in the D1/D2 domains of the LSU rRNA gene from the most closely related, described species as well as by phylogenetic analysis. Wickerhamiella kiyanii sp. nov. differs from its nearest phylogenetic neighbours W. pagnoccae CBS 12178T, Candida jalapaonensis CBS 10935T and Candida drosophilae CBS 8459T by 2.2–4.2 % in the D1/D2 sequences. By contrast, a sequence divergence of 13.2–13.8 % was observed between W. fructicola sp. nov. and its closest, described phylogenetic relative Candida kazoui JCM 12558T and Candida hasegawae JCM 12559T. Taxonomic descriptions of the two novel species are given.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 62 (2012)
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Volume 58 (2008)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)