- Volume 65, Issue Pt_11, 2015
Volume 65, Issue Pt_11, 2015
- Editorial
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- Validation List
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List of new names and new combinations previously effectively, but not validly, published
More LessThe purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 8, 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). ijsem000615-t01
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- NEW TAXA
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- Archaea
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Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample
Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange–red-pigmented. Strain MH1-243-3T was able to grow at 15–27 % (w/v) NaCl (optimum 24 °C), at pH 4.5–6.5 (pH 5.5) and at 35–50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew within slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest phylogenetic relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarity. The rpoB′ gene sequences of the three strains were also identical, and the closest phylogenetic relative was Halarchaeum acidiphilum JCM 16109T with 92.0 % similarity. The DNA G+C content of MH1-243-3T, MH1-243-5 and MH1-243-6 was 65.2 mol%. The levels of DNA–DNA relatedness amongst the three strains were 84.1–99.8 %, while that between MH1-243-3T and H. salinum MH1-34-1T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3–29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T ( = JCM 19585T = KCTC 4142T), isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 ( = JCM 19586) and MH1-243-6 ( = JCM 18422) are additional strains of the species.
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Halobellus ramosii sp. nov., an extremely halophilic archaeon isolated from a saline-wetland wildfowl reserve
An extremely halophilic archaeon, strain S2FP14T, was isolated from a brine sample from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Colonies were red-pigmented and the cells were Gram-staining-negative, motile and pleomorphic. S2FP14T was able to grow in media containing 12.5–30 % (w/v) total salts (optimum 20 %) at pH 7–8.5 (optimum 7.5) and at 25–50 °C (optimum 37 °C). The 16S rRNA gene sequence analysis indicated that this strain represented a member of the genus Halobellus. S2FP14T showed a similarity of 99.5 % to Halobellus inordinatus YC20T, 96.1 % to Halobellus litoreus GX31T, 95.9 % to Halobellus limi TBN53T, 95.5 % to Halobellus rarus YC21T, 95.2 % to Halobellus rufus CBA1103T, 94.6 % to Halobellus salinus CSW2.24.4T and 94.6 % to Halobellus clavatus TNN18T. The rpoB′ gene sequence similarity of strain S2FP14T was 97.4 % to 87.6 % with members of genus Halobellus. The major phospholipids of strain S2FP14T were phosphatidylglycerol phosphate methyl ester and phosphatidylglycerosulfate, plus a very small amount of phosphatidylglycerol and an archaeal analogue of bisphosphatidylglycerol. With regard to glycolipid composition, the most abundant glycolipids were the sulfated diglycosyl diphytanilglyceroldiether and a glycosyl-cardiolipin. The G+C content of strain S2FP14T genomic DNA was 61.4 mol%. The DNA–DNA hybridization between strain S2FP14T and Halobellus inordinatus JCM 18361T was 51 %. Based on the phylogenetic, phenotypic and chemotaxonomic features, a novel species, Halobellus ramosii sp. nov. is proposed. The type strain is S2FP14T ( = CECT 8167T = DSM 26177T).
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- Actinobacteria
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Proposal for creation of a new genus Neomicrococcus gen. nov. to accommodate Zhihengliuella aestuarii Baik et al. 2011 and Micrococcus lactis Chittpurna et al. 2011 as Neomicrococcus aestuarii comb. nov. and Neomicrococcus lactis comb. nov.
More LessMicrococcus lactis and Zhihengliuella aestuarii were described independently in 2011. Their type strains showed high levels of 16S rRNA gene sequence similarity (99.3 %). Phylogenetic analysis revealed that M. lactis MCC 2278T and Z. aestuarii JCM 16166T formed a monophyletic group and showed distant relationships to other members of closely related genera such as Micrococcus, Zhihengliuella, Arthrobacter and Citricoccus. The presence of large proportions of iso-C14 : 0 and iso-C16 : 0 with small amounts of iso-C15 : 0 distinguished M. lactis MCC 2278T and Z. aestuarii JCM 16166T from other members of the genera Micrococcus and Zhihengliuella. Unlike other members of the genera Zhihengliuella and Micrococcus, M. lactis MCC 2278T and Z. aestuarii JCM 16166T showed growth at low concentrations of NaCl. Thus, based on distinctive phylogenetic, chemotaxonomic and physiological features of these two organisms in comparison with other members of the genera Micrococcus and Zhihengliuella, it is clear that they do not fit within the existing classification and deserve separate status. DNA–DNA hybridization between the two type strains was 63 %, indicating that they represent separate species. In this study, we propose the creation of a novel genus, Neomicrococcus gen. nov., to accommodate the two species with Neomicrococcus aestuarii gen. nov., comb. nov. (type strain JCM 16166T = KCTC 19557T) as the type species. Neomicrococcus lactis comb. nov. (type strain MCC 2278T = DSM 23694T) is also proposed.
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Micromonospora oryzae sp. nov., isolated from roots of upland rice
An actinomycete strain, designated CP2R9-1T, was isolated from root internal tissues of upland rice (Oryza sativa). Based on a polyphasic approach, strain CP2R9-1T was characterized as a member of the genus Micromonospora. meso-Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids. Predominant menaquinones were MK-9(H4), MK-9(H6) and MK-10(H4). Whole-cell sugars consisted of ribose, xylose, arabinose and glucose. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence suggested that strain CP2R9-1T was closely related to Micromonospora haikouensis 232617T (99.32 % similarity), Micromonospora carbonacea DSM 43168T (99.18 %) and Micromonospora krabiensis MA-2T (99.16 %). Strain CP2R9-1T was distinct from its closest relatives based on low levels of DNA–DNA relatedness (21.3 ± 0.1–41.7 ± 0.7 %) and phenotypic differences. The results presented in this study showed that strain CP2R9-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora oryzae sp. nov. is proposed. The type strain is CP2R9-1T ( = BCC 67266T = NBRC 110007T).
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Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter
Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042T, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2-Ac034T, and 99.0 % and 97.4–97.7 % respectively for strain LIPI11-2-Ac042T. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034T was MK-9(H4) while that of strain LIPI11-2-Ac042T was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0 for strain LIPI11-2-Ac034T, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 for strain LIPI11-2-Ac042T. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034T and LIPI11-2-Ac042T were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA–DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034T and LIPI11-2-Ac042T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034T = InaCC A459T = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042T = InaCC A458T = NBRC 110974T) are proposed.
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Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively
More LessTwo Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).
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Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant
More LessA novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15–40 °C, pH 6–9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA–DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).
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Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer
More LessThree Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T = DSM 27158T = CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T = KACC 14220T = JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T = DSM 27159T = CIP 110720T), and to emend the description of Leucobacter celer Shin et al. 2011 .
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Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave
More LessA Gram-reaction-positive, high DNA G+C content, non-motile actinobacterium, strain D7-21T, was isolated from dried bat dung inside a natural cave and its taxonomic status was examined by using a polyphasic approach. The 16S rRNA gene sequence study showed that the isolate belonged to the genus Rhodococcus and formed a cluster with Rhodococcus defluvii (98.98 % gene similarity), Rhodococcus equi (98.62 %) and Rhodococcus kunmingensis (97.66 %). Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phosphoglycolipid and an unknown glycolipid. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. The DNA G+C content was 70.1 mol%. A battery of phenotypic features and DNA–DNA relatedness data support that strain D7-21T ( = KCTC 29469T = DSM 46727T) represents a novel species of the genus Rhodococcus, for which Rhodococcus antrifimi sp. nov. is proposed.
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Nonomuraea flavida sp. nov., a novel species of soil actinomycete isolated from Aconitum napellus rhizosphere
More LessA novel actinomycete strain, YN-5-1T, isolated from the rhizosphere soil of a medicinal plant, Aconitum napellus, was characterized by a polyphasic approach to determine its taxonomic position. The strain showed highest 16S rRNA gene sequence similarities of 97.3, 97.2 and 97.1 % to Nonomuraea turkmeniaca DSM 43926T, Nonomuraea ferruginea DSM 43553T and Nonomuraea candida DSM 45086T, respectively. A wide range of genotypic and phenotypic characteristics, as well as levels of DNA–DNA relatedness between strain YN-5-1T and N. turkmeniaca DSM 43926T (57.46 %), N. ferruginea DSM 43553T (53.50 %) and N. candida DSM 45086T (48.80 %), distinguished the novel isolate from its closest phylogenetic neighbours. The morphological characteristics of strain YN-5-1T were typical of the genus Nonomuraea. Chemotaxonomic characteristics, such as diagnostic diamino acid of the peptidoglycan, whole-cell sugars, phospholipid type, major menaquinone and major fatty acids, further supported the assignment of strain YN-5-1T to the genus Nonomuraea. The G+C content of the genomic DNA was 72.1 mol%. Based on the above data, strain YN-5-1T is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea flavida sp. nov. is proposed. The type strain is YN-5-1T ( = CCTCC AB 2012909T = KCTC 29143T).
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Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water
More LessA Gram-stain-positive, aerobic, non-motile, curved (selenoid), rod-shaped actinobacterium, designated KNCT, was isolated from the 0.2 μm-filtrate of river water in western Japan. Cells of strain KNCT were ultramicrosized (0.04–0.05 μm3). The strain grew at 15–37 °C, with no observable growth at 10 °C or 40 °C. The pH range for growth was 7–9, with weaker growth at pH 10. Growth was impeded by the presence of NaCl at concentrations greater than 1 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KNCT showed relatively high sequence similarity (97.2 %) to Alpinimonas psychrophila Cr8-25T in the family Microbacteriaceae. However, strain KNCT formed an independent cluster with cultured, but as-yet-unidentified, species and environmental clones on the phylogenetic tree. The major cellular fatty acids were anteiso-C15 : 0 (41.0 %), iso-C16 : 0 (21.8 %), C16 : 0 (18.0 %) and anteiso-C17 : 0 (12.9 %), and the major menaquinones were MK-11 (71.3 %) and MK-12 (13.6 %). The major polar lipids were phosphatidylglycerol and two unknown glycolipids. The cell-wall muramic acid acyl type was acetyl. The peptidoglycan was B-type, and contained 3-hydroxyglutamic acid, glutamic acid, aspartic acid, glycine, alanine and lysine, with the latter being the diagnostic diamino acid. The G+C content of the genome was unusually low for actinobacteria (52.1 mol%), compared with other genera in the family Microbacteriaceae. Based on the phenotypic characteristics and phylogenetic evidence, strain KNCT represents a novel species of a new genus within the family Microbacteriaceae, for which the name Aurantimicrobium minutum gen. nov., sp. nov. is proposed. The type strain of the type species is KNCT ( = NBRC 105389T = NCIMB 14875T).
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Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil
The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).
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Georgenia subflava sp. nov., isolated from a deep-sea sediment
More LessA Gram-stain-positive, aerobic, motile and non-spore-forming actinobacterium, strain Y32T, 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 Georgenia. Strain Y32T shared highest 16S rRNA gene sequence similarity of 97.8 % with Georgenia muralis 1A-CT, followed by Georgenia thermotolerans TT02-04T (97.4 %), Georgenia daeguensis 2C6-43T (97.2 %), Oceanitalea nanhaiensis JLT1488T (97.2 %), Georgenia ruanii YIM 004T (97.0 %) and Georgenia soli CC-NMPT-T3T (97.0 %). The organism grew in the presence of 0–10 % (w/v) NaCl, at 4–40 °C and at pH 6–11, with optimal growth occurring at 30–35 °C, at pH 7 and in the presence of 3.5 % (w/v) NaCl. The polar lipid profile of strain Y32T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. Strain Y32T contained MK-8(H4) and MK-7(H4) as the major components of the menaquinone system, and anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0 as the predominant fatty acids. Galactose was detected as the cell-wall sugar. The G+C content of the DNA was 71.2 mol%. Based on the results of phenotypic, genotypic and phylogenetic analyses, it is considered that strain Y32T represents a novel species of the genus Georgenia, for which the name Georgenia subflava sp. nov. is proposed. The type strain is Y32T ( = LMG 28101T = CGMCC 1.12782T = JCM 19765T = MCCC 1A09955T).
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Description of Streptomyces fabae sp. nov., a producer of antibiotics against microbial pathogens, isolated from soybean (Glycine max) rhizosphere soil
More LessAn actinomycete, designated strain T66T and isolated from soybean rhizosphere soil at Gyeonggi Siheung Sorae in the Republic of Korea, has antibiotic activity against a broad range of microbial pathogens. The strain was determined to be closely related to several known species in the genus Streptomyces on the basis of 16S rRNA gene sequence data (97.73–98.07 % similarity). The strain exhibited cell-wall chemotype I and phospholipid type II. The menaquinones present were MK-9 (H6), MK-9 (H8) and MK-10 (H2). Major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, and anteiso-C17 : 0. The level of DNA–DNA relatedness between strain T66T and closely related type strains was determined to be below 40 %. Strain T66T had spiral spore chains and a rugose spore surface that is different from its closest relatives. Comparison of the genotypic and phenotypic features confirmed that strain T66T ( = KEMB 9005-219T = KACC 18226T = NBRC 110902T) should be considered as the type strain of a novel species in the genus Streptomyces, for which the name Streptomyces fabae sp. nov. is proposed.
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Sphaerisporangium aureirubrum sp. nov., an actinomycete isolated from soil
A novel actinomycete, designated strain NEAU-GQTH1-3T, was isolated from muddy soil collected from a stream in Qitaihe, Heilongjiang Province, north-east China and characterized using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Sphaerisporangium and forms a stable clade with its closest relative Sphaerisporangium rubeum JCM 13067T (98.2 % 16S rRNA gene sequence similarity). Moreover, morphological and chemotaxonomic properties of strain NEAU-GQTH1-3T also confirmed the affiliation of the isolate to the genus Sphaerisporangium. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, galactose, madurose, mannose and ribose. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The major menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The predominant cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. Mycolic acids were absent. The DNA G+C content was 70.4 mol%. However, the low level of DNA–DNA relatedness and some phenotypic characteristics allowed the isolate to be differentiated from its closest relative. Therefore, it is concluded that strain NEAU-GQTH1-3T represents a novel species of the genus Sphaerisporangium, for which the name Sphaerisporangium aureirubrum sp. nov. is proposed. The type strain is NEAU-GQTH1-3T ( = CGMCC 4.7199T = JCM 30346T).
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Kutzneria chonburiensis sp. nov., isolated from soil
More LessA novel actinomycete strain, SMC 256T, which developed small, globose sporangia at the ends of long sporangiophores on aerial mycelium, was isolated from soil collected in a mountain forest of Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 256T belonged to the genus Kutzneria, and the closest phylogenetically related species were Kutzneria buriramensis BCC 29373T (98.9 % 16S rRNA gene sequence similarity), Kutzneria kofuensis ATCC 27102T (98.2 %), Kutzneria albida ATCC 25243T (97.9 %) and Kutzneria viridogrisea ATCC 25242T (97.4 %). The DNA–DNA relatedness values that distinguished strain SMC 256T from previously described members of the genus Kutzneria were significantly below 70 %. The G+C content of the genomic DNA was 71.8 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of rhamnose, ribose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. The diagnostic phospholipids were hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, unidentified phosphoglycolipids, unidentified phospholipids and an unidentified lipid. The predominant cellular fatty acids were iso-C16 : 0, C17 : 1 and C17 : 0 10-methyl. Following the evidence of phenotypic, chemotaxonomic and genotypic studies, it is proposed that strain SMC 256T represents a novel species in the genus Kutzneria, namely Kutzneria chonburiensis sp. nov. The type strain is SMC 256T ( = BCC 72675T = NBRC 110610T).
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Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch
A Gram-stain-positive bacterial strain, designated as NR2T, isolated from noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a representative of a member of the genus Brachybacterium, to which the most closely related neighbours were Brachybacterium squillarum M-6-3T (97.90 % similarity), Brachybacterium faecium DSM 4810T (97.50 %), Brachybacterium sacelli LMG 20345T (97.41 %), Brachybacterium phenoliresistens phenol-AT (97.36 %), Brachybacterium nesterenkovii DSM 9573T (97.36 %) and Brachybacterium rhamnosum LMG 19848T (97.32 %). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Strain NR2T was clearly distinguishable from the type strains of related species on the basis of phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data analysis and a range of physiological and comparison of biochemical characteristics. It is evident from the genotypic and phenotypic data that strain NR2T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium hainanense sp. nov. is proposed. The type strain is NR2T ( = DSM 29535T = CICC 10874T).
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Pseudoclavibacter terrae sp. nov. isolated from rhizosphere soil of Ophiopogon japonicus
More LessStrain THG-MD12T, a Gram-reaction-positive, aerobic, non-motile, rod-shaped bacterium was isolated from rhizosphere soil of Ophiopogon japonicus in PR China. THG-MD12T was closely related to members of the genus Pseudoclavibacter and showed the highest 16S rRNA gene sequence similarities with Pseudoclavibacter helvolus KCTC 19531T (98.8 %) and Pseudoclavibacter chungangensis KCTC 22691T (96.9 %). DNA–DNA hybridization showed 41.9 ± 2.1 % and 12.4 ± 0.9 % DNA reassociation with P. helvolus KCTC 19531T and P. chungangensis KCTC 22691T, respectively. Chemotaxonomic analyses revealed that strain THG-MD12T possesses menaquinone-9 as the predominant respiratory quinone, 2,4-diaminobutyric acid as the diamino acid in the peptidoglycan and anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The polar lipid profile was found to consist of diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and two unknown lipids. These data corroborated the affiliation of THG-MD12T to the genus Pseudoclavibacter. Thus, the isolate represents a novel species, for which the name Pseudoclavibacter terrae sp. nov. is proposed, with THG-MD12T as the type strain ( = CCTCC AB 2015124T = KCTC 39562T).
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Rhodococcus lactis sp. nov., an actinobacterium isolated from sludge of a dairy waste treatment plant
More LessA Gram-stain-positive, non-motile and aerobic bacterium, designated strain DW151BT, was isolated from a sludge sample of a dairy industry effluent treatment plant. 16S rRNA gene sequence analysis of strain DW151BT placed it within the genus Rhodococcus. It displayed significant similarity with recognized species of the genus: Rhodococcus pyridinivorans PDB9T (98.8 %), Rhodococcus gordoniae W 4937T (98.6 %), Rhodococcus rhodochrous DSM 43241T (98.5 %) and Rhodococcus artemisiae YIM 65754T (97.5 %). However, strain DW151BT differed from phylogenetically closely related species in various phenotypic properties. The cellular polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylinositol (PI) as major lipids, MK-8(H2) was the major menaquinone and meso-diaminopimelic acid was the cell-wall peptidoglycan. The fatty acid profile consisted of C16 : 0, C18 : 1 cis9 and C16 : 1 cis9 as main components. The presence of C16 : 0 and diphosphatidylglycerol as major fatty acid and polar lipid, respectively, was in accordance with chemotaxonomic markers of the genus Rhodococcus. The DNA G+C content of strain DW151BT was 69.9 mol%, a value within the limits reported for the members of this genus. Furthermore, strain DW151BT showed low similarity at the whole genome level in DNA–DNA hybridization experiments with phylogenetically closely related strains. Considering the low similarity at the genome level and differences in phenotypic properties, strain DW151BT is considered to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus lactis sp. nov. is proposed. The type strain is DW151BT ( = MTCC 12279T = DSM 45625T).
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Actinoplanes luteus sp. nov., isolated from soil
More LessA novel filamentous bacterial strain, A-T 5190T, which developed irregular sporangia at the end of sporangiophores on substrate mycelia, was isolated from dry evergreen forest soil collected in Thailand. The 16S rRNA gene sequence and phylogenetic analysis indicated that strain A-T 5190T belonged to the genus Actinoplanes and was related most closely to Actinoplanes palleronii NBRC 14916T (98.88 % similarity) and Actinoplanes rectilineatus NBRC 13941T (98.54 %). DNA–DNA relatedness values between strain A-T 5190T and its closest relatives were below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained rhamnose, ribose, galactose and xylose. The predominant menaquinone was MK-9(H4). The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were unsaturated fatty acid C17 : 1 and branched fatty acids iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 71.9 mol%. Evidence from phenotypic, chemotaxonomic and genotypic studies indicate that strain A-T 5190T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes luteus sp. nov. is proposed. The type strain is A-T 5190T ( = BCC 41582T = NBRC 109644T).
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Paraglycomyces xinjiangensis gen. nov., sp. nov., a halophilic actinomycete
More LessA novel halophilic actinobacterium, designated strain TRM 49201T, was isolated from a hypersaline soil in Xinjiang Province, north-west China. The strain was aerobic, Gram-stain-positive and halophilic. The aerial mycelium was chaotic with irregular branches, and spherical sporangia containing several spherical spores developed at mycelial aggregations. The strain had an optimum NaCl concentration for growth of 8–13 % (w/v). The whole-cell sugar pattern of strain TRM 49201T consisted of xylose and ribose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 70 mol%. Phylogenetic analysis showed that strain TRM 49201T can be distinguished from representatives of Glycomyces, Stackebrandtia and Haloglycomyces, the three existing genera in the family Glycomycetaceae, based on low 16S rRNA gene sequence similarities ( < 94.42 %). Strain TRM 49201T is thus considered to represent a novel species of a new genus in the family Glycomycetaceae, for which the name Paraglycomyces xinjiangensis gen. nov., sp. nov. is proposed. The type strain of Paraglycomyces xinjiangensis is TRM 49201T ( = NRRL B-24926T = CCTCC AA 2013002T = KACC 17683T).
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- Firmicutes and related organisms
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Multilocus sequence analysis of the genus Kurthia, and a description of Kurthia populi sp. nov.
Four novel bacterial strains belonging to the genus Kurthia were isolated from the surface of a weevil of the family Curculionidae (strain 10y-14T), and from bark samples of hybrid poplar, Populus × euramericana (strains 6-3, 2-5 and 06C10-3-14), in Puyang, Henan Province, China. Phylogenetic analyses of the 16S rRNA gene and multilocus sequence analysis (MLSA) data showed that the four strains form a distinct cluster in the genus Kurthia, indicating that they all belong to a single taxon within the genus. DNA–DNA hybridization levels between strain 10y-4T and Kurthia huakuii LAM0618T and Kurthia massiliensis DSM 24639T were 58.31 and 53.92 %, respectively. This indicates that the four novel strains represent a species distinct from these two closely related species. The DNA G+C content of the novel strains was 42.1–42.6 %. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and unidentified aminophospholipids. The predominant menaquinones were MK-7 (90 %) and MK-6 (10 %). The major cell-wall amino acids were lysine, alanine, glutamic acid and glycine. On the basis of the MLSA and 16S rRNA gene sequence phylogenetic analyses, DNA–DNA reassociation values, DNA base composition, and biochemical and phenotypic characteristics, the four strains are considered to represent a novel species within the genus Kurthia, for which the name Kurthia populi sp. nov. is proposed. The type strain is 10y-14T ( = CFCC 11600T = KCTC 33522T).
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Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment
A Gram-staining-positive, coccoid, halotolerant bacterial strain, designated SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurred at temperatures in the range 25–37 °C (optimum 30 °C), at pH 7.0–11.0 (optimum pH 8.0) and at NaCl concentrations of up to 25.0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. The draft genome of strain SV-16T consisted of 2 591 284 bp with a DNA G+C content of 48.7 mol%. On the basis of the phenotypic characteristics and genotypic distinctiveness of strain SV-16T, it should be classified within a novel species of the genus Salinicoccus, for which the name Salinicoccus sediminis sp. nov. is proposed. The type strain is SV-16T ( = MTCC 11832T = DSM 28797T).
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Bacillus formosensis sp. nov., isolated from pesticide wastewater
More LessA Gram-stain-positive, endospore-forming rod (designated strain CC-LY275T) was isolated from a pesticide wastewater sample. The isolate grew at a temperature 20–45 °C, at pH 7.0–8.0 and tolerated NaCl 6 % (w/v). The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus horneckiae (97.1 %) and Bacillus oceanisediminis (96.8 %), respectively. The G+C content of the genomic DNA was 37.9 mol%. Strain CC-LY275T was determined to possess iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 as predominant fatty acids. The major polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Cell-wall peptidoglycan contained meso-diaminopimelic acid; menaquinone (MK-7) was the predominant respiratory quinone. According to the distinct phylogenetic, phenotypic and chemotaxonomic properties, the name Bacillus formosensis sp. nov. (type strain CC-LY275T = BCRC 80443T = JCM 18448T) is proposed.
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Paenibacillus yunnanensis sp. nov., isolated from Pu'er tea
A novel Gram-staining-positive, aerobic, endospore-forming, rod-shaped bacterial strain, YN2T, was isolated from ripened Pu'er tea. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain represented a novel species of the genus Paenibacillus. The strains most closely related to strain YN2T were Paenibacillus vulneris JCM 18268T and Paenibacillus rigui JCM 16352T, with 16S rRNA similarities of 98.6 and 95.5 %, respectively. Chemotaxonomic data supported the affiliation of the new isolate to the genus Paenibacillus, including MK-7 as the major menaquinone, DNA G+C content of 51 mol%, cell-wall type A1γ (meso-diaminopimelic acid as the diagnostic diamino acid) and anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and phospholipid. Strain YN2T could be differentiated from recognized species of the genus Paenibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of evidence from this polyphasic study, Paenibacillus yunnanensis sp. nov., is proposed, with strain YN2T ( = CGMCC 1.12968T = JCM 30953T) as the type strain.
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Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.)
A Gram-stain-variable, short-rod-shaped, endospore-forming, strictly aerobic, non-motile, chitinolytic and endophytic bacterium, designated strain CC-Alfalfa-19T, exhibiting unusual bipolar appendages was isolated from a root nodule of alfalfa (Medicago sativa L.) in Taiwan and subjected to a polyphasic taxonomic study. Based on 16S rRNA gene sequence analysis, strain CC-Alfalfa-19T was found to be most closely related to Paenibacillus puldeungensis CAU 9324T (95.2 %), whereas other species of the genus Paenibacillus shared ≤ 95.0 % sequence similarity. The phylogenetic analysis revealed a distinct phyletic lineage established by strain CC-Alfalfa-19T with respect to other species of the genus Paenibacillus. Fatty acids comprised predominantly anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. Menaquinone 7 (MK-7) was identified as the sole respiratory quinone and the genomic DNA G+C content was 42.7 mol%. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the polyphasic taxonomic evidence that was in line with the genus Paenibacillus and additional distinguishing characteristics, strain CC-Alfalfa-19T is considered to represent a novel species, for which the name Paenibacillus medicaginis sp. nov. (type strain CC-Alfalfa-19T = BCRC 80441T = JCM 18446T) is proposed.
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Bacillus hisashii sp. nov., isolated from the caeca of gnotobiotic mice fed with thermophile-fermented compost
A taxonomic study was performed on 15 bacterial isolates from the caeca of gnotobiotic mice that had been fed with thermophile-fermented compost. The 15 isolates were thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming bacteria, and were most closely related to Bacillus thermoamylovorans CNCM I-1378T. The 16S rRNA gene sequence of strain N-11T, selected as representative of this new group, showed a similarity of 99.4 % with Bacillus thermoamylovorans CNCM I-1378T, 94.7 % with Bacillus thermolactis R-6488T, and 94.4 % with Bacillus kokeshiiformis MO-04T. The isolates were then classified into two distinct groups based on a (GTG)5-fingerprint analysis. Two isolates, N-11T and N-21, were the representatives of these two groups, respectively.` The N-11T and N-21 isolates showed 66–71 % DNA–DNA relatedness with one other, but had less than 37 % DNA–DNA relatedness with B. thermoamylovorans LMG 18084T. The other 13 isolates showed DNA–DNA relatedness values above 74 % with the N-11T isolate. All 15 isolates grew at 25–60 °C (optimum 50 °C), pH 6–8 (optimum pH 7) and were capable of growing on a medium containing 6 % (w/v) NaCl (optimum 0.5 %). The 15 isolates could be distinguished from B. thermoamylovorans LMG 18084T because they showed Tween 80 hydrolysis activity and did not produce acid from melibiose. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The menaquinone was MK-7. The DNA G+C content was 37.9 mol%. Based on the phenotypic properties, the 15 strains represent a novel species of the genus Bacillus, for which the name Bacillus hisashii sp. nov. is proposed. The type strain is N-11T ( = NRBC 110226T = LMG 28201T).
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Aureibacillus halotolerans gen. nov., sp. nov., isolated from marine sediment
More LessA Gram-staining-positive, strictly aerobic, spore-forming and rod-shaped motile bacterium with peritrichous flagellae, designated strain S1203T, was isolated from the sediment of the northern Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S1203T formed a lineage within the family Bacillaceae that was distinct from the most closely related genera Bacillus, Bhargavaea, Planomicrobium and Virgibacillus with gene sequence similarities ranging from 86.2 to 93.76 %. Optimal growth occurred in the presence of 4–8 % (w/v) NaCl, at pH 7.0–8.0 and 25–32 °C. The cell-wall peptidoglycan was based on meso-diaminopimelic acid and unsaturated menaquinone with seven isoprene units (MK-7) as the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0.The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The DNA G+C content of strain S1203T was 47.7 mol%. On the basis of polyphasic analysis, strainS1203T was considered to represent a novel species in a new genus of the family Bacillaceae, for which the name Aureibacillus halotolerans gen. nov., sp. nov. is proposed; the type strain of Aureibacillus halotolerans is S1203T ( = DSM 28697T = JCM 30067T = MCCC 1K00259T).
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Paenibacillus kyungheensis sp. nov., isolated from flowers of magnolia
More LessA Gram-staining-positive, catalase-positive, oxidase-negative, facultatively anaerobic, rod-shaped bacterium designated strain DCY88T, was isolated from flowers of magnolia. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus that was closely related to Paenibacillus hordei RH-N24T (97.8 %). The other most closely related species were Paenibacillus illinoisensis NRRL NRS-1356T (94.3 %), Paenibacillus hunanensis DSM 22170T (94.2 %), Paenibacillus peoriae DSM 8320T (93.9 %), Paenibacillus kribbensis Am49T (93.8 %) and the type species of the genus, Paenibacillus polymyxa ATCC 842T (93.3 %). Cells of the strain were endospore-forming and motile by peritrichous flagella. Strain DCY88T formed pink-pigmented colonies on trypticase soy agar and R2A agar medium. Growth of strain DCY88T occurs at temperatures 5–37 °C, at pH 4–9 and 0.5–5.5 % NaCl (w/v). The menaquinone was MK-7.The cell wall peptidoglycan of strain DCY88T contained meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 (61.0 %) and C16 : 0 (11.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified polar lipid. The strain DCY88T contained spermidine as the major polyamine. The DNA G+C content was 51.6 mol%. The DNA–DNA hybridization relatedness between strain DCY88T and P. hordei RH-N24T was 48 ± 2 %. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain DCY88T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus kyungheensis sp. nov. is proposed. The type strain is DCY88T ( = JCM 19886T = KCTC 33429T).
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Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil
More LessA mesophilic, aerobic, Gram-stain-positive, filamentous bacterial strain, designated ZYf1a3T, was isolated from rice paddy soil in Japan. This strain grew on a solid medium with formation of substrate mycelium; endospores were produced singly along the mycelium. Formation of aerial mycelium was not observed on any of the media tested. This strain produced a characteristic saffron yellow soluble pigment. Cloned 16S rRNA gene sequences of strain ZYf1a3T yielded three different copies (similarity between the three sequences: 99.8–99.9 %). One of these sequences had one base deletion. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYf1a3T belongs to an independent phylogenetic lineage of the family Thermoactinomycetaceae. The cell wall of strain ZYf1a3T contained meso-diaminopimelic acid, alanine and glutamic acid, but no characteristic sugars. It contained menaquinone 7 as the sole menaquinone. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-N-methylethanolamine and unidentified aminophospholipids. The DNA G+C content was 42.5 mol%. From phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, this strain is considered to represent a novel species in a new genus, for which the name Croceifilum oryzae gen. nov., sp. nov. is proposed. The type strain of Croceifilum oryzae is ZYf1a3T ( = JCM 30426T = CCUG 66446T = DSM 46876T).
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Bacillus solani sp. nov., isolated from rhizosphere soil of a potato field
A novel Gram-stain-positive, endospore-forming bacterium, designated strain FJAT-18043T, was isolated from a soil sample of a potato field in Xinjiang Autonomous Region, China. Cells were rods that were catalase-positive and motile by peritrichous flagella. The strain grew at 20–45 °C (optimum 35 °C), at pH 6.0–10.0 (optimum pH 9) and with 0–10 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FJAT-18043T belonged to the genus Bacillus and exhibited similarities of 97.7, 97.6, 97.2 and 97.2 % with Bacillus eiseniae A1-2T, Bacillus horneckiae DSM 23495T, Bacillus gottheilii WCC 4585T and Bacillus purgationiresistens DS22T, respectively. DNA–DNA relatedness between strain FJAT-18043T and B. eiseniae A1-2 T was lower than 70 % (36.1 %). The menaquinone was identified as MK-7 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0, C16 : 0 and iso-C14 : 0. The DNA G+C content was 48.8 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate FJAT-18043T represents a novel species within the genus Bacillus, for which the name Bacillus solani sp. nov. is proposed. The type strain is FJAT-18043T ( = DSM 29501T = CCTCC AB 2014277T).
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Paenibacillus panaciterrae sp. nov., isolated from ginseng-cultivated soil
More LessA novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis, this isolate was assigned to the genus Paenibacillus and found to be closely related to Paenibacillus sacheonensis SY01T (97.1 % 16S rRNA gene sequence similarity) and Paenibacillus taihuensis THMBG22T (96.4 %). The partial gyrB gene of DCY95T possessed 69.6–83.9 % sequence identity to those of other members of the genus Paenibacillus. Strain DCY95T was Gram-reaction-negative, catalase-negative, oxidase-positive, strictly aerobic, rod-shaped and motile by means of peritrichous flagella. Ellipsoidal free spores or subterminal endospores were produced in sporangia. MK-7 was the diagnostic menaquinone. The cell-wall peptidoglycan contained meso-diamonopimelic acid as the diamino acid. Whole-cell sugars comprised ribose, mannose and glucose. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, and two unidentified phospholipids. The genomic DNA G+C content was 60.7 ± 0.9 mol%. Phenotypic and chemotaxonomic results placed strain DCY95T within the genus Paenibacillus. However, DNA–DNA relatedness values between strain DCY95T and P. sacheonensis KACC 14895T or P. taihuensis NBRC 108766T were lower than 36 %. The low DNA relatedness data in combination with phylogenetic and (GTG)5-PCR analyses, as well as biochemical tests, indicated that strain DCY95T could not be assigned to any recognized species. In conclusion, the results in this study support the classification of strain DCY95T as a representative of a novel species within the genus Paenibacillus, for which the name Paenibacillus panaciterrae is proposed. The type strain is DCY95T ( = KCTC 33581T = DSM 29477T).
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Tumebacillus luteolus sp. nov., isolated from soil
More LessTwo strains of Gram-stain-positive, aerobic, spore-forming and rod-shaped bacteria, designated U13T and U14, were isolated from soil of the Ukraine. Comparative analysis of the 16S rRNA gene sequences indicated that these strains belong to the genus Tumebacillus, with the highest 16S rRNA gene sequence similarity with Tumebacillus ginsengisoli Gsoil 1105T (95.48 % and 95.49 %, respectively). Strains U13T and U14 had iso-C15 : 0 and summed features 1 and 4 as the main fatty acids, and were able to grow at pH ranging from pH 5.0 to 9.0 (optimum pH 6.0–7.0), temperatures ranging from 25 to 42 °C (optimum 28–37 °C) and with 0–1 % (w/v) NaCl (optimum 0 %, w/v) on R2A agar medium. Chemotaxonomic data revealed that the cell-wall peptidoglycan type of the two strains was type A1γ (meso-diaminopimelic acid). On the basis of the evidence from this study, strains U13T and U14 represent a novel species of the genus Tumebacillus, for which the name Tumebacillus luteolus sp. nov. is proposed. The type strain is U13T ( = KEMB 7305-100T = JCM 19866T) and a second strain is U14 ( = KEMB 7305-101 = JCM 19867).
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Bacillus gossypii sp. nov., isolated from the stem of Gossypium hirsutum
More LessA Gram-stain-positive, facultatively anaerobic, endospore-forming organism, isolated from the stem of Gossypium hirsutum, was studied to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain JM-267T was grouped in the genus Bacillus, related most closely to the type strains of Bacillus simplex and Bacillus huizhouensis (both 97.8 %), Bacillus muralis (97.7 %), Bacillus butanolivorans and Bacillus psychrosaccharolyticus (both 97.3 %). 16S rRNA gene sequence similarity to the sequences of the type strains of other Bacillus species was < 97.0 %. The fatty acid profile supported the grouping of the strain to the genus Bacillus. As major fatty acids, anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0 were detected. The polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major quinone was menaquinone 7 (MK-7). DNA–DNA hybridizations with B. simplex DSM 1321T, B. huizhouensis GSS03T, B. muralis LMG 20238T, B. butanolivorans LMG 23974T and B. psychrosaccharolyticus DSM 6T resulted in values clearly below 70 %. In addition, physiological and biochemical test results allowed the clear phenotypic differentiation of strain JM-267T from the most closely related species. Hence, strain JM-267T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus gossypii sp. nov. is proposed. The type strain is JM-267T ( = DSM 100034T = LMG 28742T).
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Lysinibacillus cresolivorans sp. nov., an m-cresol-degrading bacterium isolated from coking wastewater treatment aerobic sludge
More LessA Gram-stain-positive, rod-shaped, facultatively anaerobic, endospore-forming bacterium (designated strain SC03T) was isolated from the aerobic treatment sludge of a coking plant (Shaoguan City, China). The optimal pH and temperature for growth were pH 7.0 and 35 °C. On the basis of 16S rRNA gene sequence analysis, strain SC03T was related to the genus Lysinibacillus and the similarity between strain SC03T and the most closely related type strain, Lysinibacillus macroides LMG 18474T, was 94.4 %. The genomic G+C content of the DNA of strain SC03T was 41.2 mol%. Chemotaxonomic data supported the affiliation of strain SC03T to the genus Lysinibacillus. These properties include MK-7 as the predominant menaquinone; iso-C15 : 0 and iso-C16 : 0 as major fatty acids; A4α (l-Lys–d-Asp) as the cell-wall peptidoglycan type; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine plus three unknown phospholipids as polar lipids. The phenotypic, phylogenetic and chemotaxonomic characters enable the differentiation of strain SC03T from recognized Lysinibacillus species. Thus, strain SC03T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus cresolivorans sp. nov. is proposed. The type strain is SC03T ( = NRRL B-59352T = CCTCC M 208210T).
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Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo
Investigation of the microbial diversity of Ntoba Mbodi, an African food made from the alkaline fermentation of cassava leaves, revealed the presence of a Gram-positive, catalase-positive, aerobic, motile and rod-shaped endospore-forming bacterium (NM73) with unusual phenotypic and genotypic characteristics. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Lysinibacillus meyeri WS 4626T (98.93 %), Lysinibacillus xylanilyticus XDB9T (96.95 %) and Lysinibacillus odysseyi 34hs-1T (96.94 %). The DNA–DNA relatedness of the isolate with L. meyeri LMG 26643T, L. xylanilyticus DSM 23493T and L. odysseyi DSM 18869T was 41 %, 16 % and 15 %, respectively. The internal transcribed spacer-PCR profile of the isolate was different from those of closely related bacteria. The cell-wall peptidoglycan type was A4α, l-Lys-d-Asp and the major fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 and iso-C17 : 1ω10c. The polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipid, two phospholipids and two unknown lipids. The predominant menaquinones were MK-7 and MK-6. Ribose was the only whole-cell sugar detected. The DNA G+C content was 38 mol%. Based on the results of the phenotypic and genotypic characterization, it was concluded that the isolate represents a novel species of the genus Lysinibacillus, for which the name of Lysinibacillus louembei sp. nov. is proposed. NM73T ( = DSM 25583T = LMG 26837T) represents the type strain.
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Salibacterium halotolerans gen. nov., sp. nov., a bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.
Two novel Gram-stain-positive, rod-shaped, non-motile, non-endospore-forming bacterial strains, S7T and IB5, were isolated from Khavda, India. Based on 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae, and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strains S7T and IB5 might not be members of the genus Bacillus. The DNA–DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 ± 0.8. The cell-wall peptidoglycan of strains S7T and IB5 contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. anteiso-C15 : 0 was the predominant fatty acid. The results of the phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, suggesting that they represent a novel member of the family Bacillaceae, for which the name Salibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of Salibacterium halotolerans is S7T ( = KCTC 33658T = CGMCC 1.15324T). Based on the results of the present study, it is also suggested that B. qingdaonensis and B. halochares should be transferred to this novel genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.
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- Proteobacteria
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Cavicella subterranea gen. nov., sp. nov., isolated from a deep mineral-water aquifer, and emended description of the species Perlucidibaca piscinae
More LessOne strain designated W2.09-231T was isolated from an aquifer through a 150-metre-deep borehole feeding a mineral-water bottling plant in Central Portugal. Based on 16S rRNA gene sequence analysis, the novel organism is most closely related to the species of the genera Perlucidibaca and Paraperlucidibaca, belonging to the family Moraxellaceae, with 16S rRNA gene pairwise sequence similarity of 94.5 and 93.1 %, respectively. The strain was not pigmented and formed Gram-stain-negative, non-motile, short rod-shaped cells. The organism was strictly aerobic, and oxidase- and catalase-positive. Strain W2.09-231T was organotrophic, but grew only on a very limited number of single carbon sources. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one major unknown phospholipid. Ubiquinone 12 (U-12) was the major respiratory quinone. The DNA G+C content of strain W2.09-231T was 62.0 mol%. Based on phylogenetic, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain W2.09-231T ( = CECT 8582T = LMG 28332T) for which we propose the name Cavicella subterranea gen. nov., sp. nov. We also propose to emend the description of the species Perlucidibaca piscinae to reflect new results obtained in this study.
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Halocynthiibacter arcticus sp. nov., isolated from Arctic marine sediment
A Gram-staining-negative, oxidase- and catalase-positive, non-motile, aerobic and rod-shaped bacterium producing white colonies, PAMC 20958T, was isolated from a marine sediment of the Arctic. PAMC 20958T grew at 10–27 °C (optimally at 21 °C), at pH 5.5–9.5 (optimally at pH 7.0–7.5) and in the presence of 0.5–7.5 % (w/v) (optimally at 2.0 %) NaCl. PAMC 20958T showed 97.5 % 16S rRNA gene sequence similarity with Halocynthiibacter namhaensis KCTC 32362T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain PAMC 20958T and H. namhaensis KCTC 32362T was 79.7 % and the genome-to-genome distance was 13.0 % on average. The genomic DNA G+C content calculated from the genome sequence was 53.2 mol%. The major fatty acids were C18 : 1ω7c and/or C18 : 1ω6c. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. On the basis of phylogenetic analysis and genotypic and phenotypic data obtained in this study, it is concluded that strain PAMC 20958T ( = KCTC 42129T = JCM 30530T) represents the type strain of a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacter arcticus sp. nov. is proposed.
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Marinibactrum halimedae gen. nov., sp. nov., a gammaproteobacterium isolated from a marine macroalga
More LessPhylogenetic and taxonomic characterization was performed for a bacterium, designated strain Q-192T, isolated from the surface of the green macroalga Halimeda sp., collected from the subtropical Ishigaki Island, Japan. The isolate was a polysaccharide-producing, Gram-stain-negative, aerobic, rod-shaped, motile bacterium with a polar flagellum. The isolate was slightly halophilic, required Na+, Mg2+ and Ca2+ ions for growth, but did not require growth factors. The only isoprenoid quinone was ubiquinone-8.The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0. The main hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 45.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the isolate in the class Gammaproteobacteria. The phylogenetically closest relatives with validly published names were Pseudomaricurvus alkylphenolicus KU41GT, Teredinibacter turnerae T7902T, Pseudoteredinibacter isoporae SW-11T and Simiduia agarivorans SA1T with sequence similarities of 94.5, 94.1, 93.7 and 93.6 %, respectively. The isolate was distinguished from members of these genera by a combination of DNA G+C content, chemotaxonomic characteristics (respiratory quinone system, fatty acid profile and polar lipid composition) and other phenotypic features. Based on phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics, strain Q-192T is considered to represent a novel species of a new genus, for which the name Marinibactrum halimedae gen. nov., sp. nov. is proposed. The type strain of Marinibactrum halimedae is Q-192T ( = NBRC 110095T = NCIMB 14932T).
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Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil
More LessStrain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18 : 1ω7c or C18 : 1ω6c and C16 : 0, and C18 : 0, C18 : 1ω9c, C10 : 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA–DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA–DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.
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Acinetobacter albensis sp. nov., isolated from natural soil and water ecosystems
More LessWe have studied the taxonomic position of a phenetically unique group of eight strains of the genus Acinetobacter which were isolated from soil and water samples collected in protected landscape areas in the Czech Republic. Each of the comparative sequence analyses of the 16S rRNA, gyrB and rpoB genes showed that the eight strains formed a cohesive and tight cluster (intracluster sequence identities of ≥ 99.9 %, ≥ 98.5 % and ≥ 97.7 %, respectively), which was clearly separated from all hitherto known species of the genus Acinetobacter ( ≤ 98.6 %, ≤ 84.5 % and ≤ 89.3 %, respectively). Congruent with these findings were the results of comparative sequence analysis of three additional housekeeping genes (gltA, pyrG and recA). This genotypic distinctness was mirrored by the uniqueness of the combination of a number of independent phenotypic markers including the whole-cell spectra produced by matrix-assisted laser desorption ionization time-of-flight (MALDI-ToF) MS and physiological and metabolic features. The most useful phenotypic features to differentiate the eight strains from all known species of the genus Acinetobacter were the ability to assimilate tricarballylate and the inability to grow at 35 °C or to assimilate ethanol or l-histidine. We conclude that the eight strains represent a novel environmental species for which the name Acinetobacter albensis sp. nov. is proposed. The type strain is ANC 4874T ( = CCUG 67281T = CCM 8611T).
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Labrys soli sp. nov., isolated from the rhizosphere of ginseng
In this study, we describe strain DCY64T that was isolated from the rhizosphere of three-year-old Korean ginseng root. Cells were Gram-reaction negative, oxidase- and catalase-positive, strictly aerobic, capsulated, non-motile, non-sporulating and spherical to short rod-shaped. Multiplicative budding cells were produced. Vesicles covered the surface of cells. Phylogenetic analysis placed strain DCY64T within the genus Labrys with the highest similarity to Labrys monachus VKM B-1479T (97.6 % 16S rRNA gene sequence similarity), followed by Labrys okinawensis MAFF 210191T (97.5 %), Labrys miyagiensis G24103T (97.4) and Labrys portucalensis F11T (97.0 %). The genomic DNA G+C content was 63 mol%. The presences of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 1 cyclo ω8c and C16 : 0 as major fatty acids; phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol as major polar lipids; ubiquinone Q-10 as the predominant quinone and sym-homospermidine as the dominant polyamine were found in strain DCY64T. These chemotaxonomic results were in accordance with those of members of the genus Labrys. However, the absence of C16 : 0 2-OH, C16 : 0 3-OH and C18 : 1 2-OH from the fatty acids profile and differences in minor polar lipids and phenotypic characteristics distinguished strain DCY64T from the closest type strains. The discrimination was also supported by unique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) fingerprints, as well as DNA–DNA hybridization values ( ≤ 48 %) between strain DCY64T and related type strains. Therefore, we propose that strain DCY64T represents a novel species of the genus Labrys. The name Labrys soli sp. nov. is proposed, with DCY64T ( = KCTC 32173T = JCM 19895T) as the type strain.
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Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter
More LessStrain D40PT, representing a novel Gram-stain-negative, obligately aerobic, bacteriochlorophyll a-containing bacterium of the α-4 subgroup of the phylum Proteobacteria, was isolated from permafrost soil of Kunlun mountains gap, Qinghai-Tibet plateau. Cells were non-motile rod–cocci and formed brown-pigmented colonies. According to the absorption spectrum, carotenoids and two different photosynthetic light-harvesting complexes, an LHI complex and a B800-835-type peripheral LHII complex, were present in the cells. The strain was oxidase-negative and catalase-positive. The predominant fatty acids of strain D40PT were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, two glycolipids and sphingoglycolipid. The major respiratory quinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The 16S rRNA gene sequence similarity to the closest phylogenetic relative, Polymorphobacter multimanifer JCM 18140T, was 97.5 %. DNA–DNA relatedness (ΔT m) between strain D40PT and P. multimanifer was 12.4 °C. The G+C content of the genomic DNA of strain D40PT was 67.4 mol%. Accordingly, the strain represents a novel species, for which the name Polymorphobacter fuscus sp. nov. is proposed. The type strain is D40PT ( = CGMCC 1.12714T = JCM 19740T). An emended description of the genus Polymorphobacter is also proposed.
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Thiorhodococcus fuscus sp. nov., isolated from a lagoon
More LessA brown, moderately halophilic, photoautotrophic bacterium designated strain JA363T was purified from a photoheterotrophic enrichment obtained from sediment from Chilika lagoon, Odisha, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. Strain JA363T had an obligate requirement for NaCl and could tolerate up to 7 % (w/v) NaCl. Strain JA363T had complex growth factor requirements. Internal photosynthetic membranes were present as vesicles. Strain JA363T contained bacteriochlorophyll a and spirilloxanthin series carotenoids with rhodopin as a major (>85 %) component. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c and C16 : 0 were the major fatty acids and phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. Q8 was the predominant quinone system of strain JA363T. The DNA G+C content was 64 mol%. The highest 16S rRNA gene sequence similarity of strain JA363T was found with the type strains of Thiorhodococcus kakinadensis (98.7 %), Thiohalobacter thiocyanaticus (98.2 %), Thiophaeococcus fuscus (97.4 %) and Thiorhodococcus bheemlicus (96.3 %). However, the phylogenetic trees generated firmly placed strain JA363T in the genus Thiorhodococcus, which was further supported by phenotypic and chemotaxonomic evidence. Consequently, strain JA363T is described as representing a novel species of the genus Thiorhodococcus as Thiorhodococcus fuscus sp. nov. The type strain is JA363T ( = KCTC 5701T = NBRC 104959T).
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Primorskyibacter insulae sp. nov., isolated from the junction between the ocean and a freshwater spring
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated SSK3-2T, was isolated from the locality where the ocean and a freshwater spring meet at Jeju island, South Korea, and subjected to a polyphasic taxonomic study. Strain SSK3-2T 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 revealed that strain SSK3-2T clustered with the type strain of Primorskyibacter sedentarius, with which it exhibited 97.3 % sequence similarity. Strain SSK3-2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain SSK3-2T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain SSK3-2T was 60.6 mol% and its mean DNA–DNA relatedness value with P. sedentarius JCM 16874T was 19 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK3-2T is separated from P. sedentarius. On the basis of the data presented, strain SSK3-2T is considered to represent a novel species of the genus Primorskyibacter, for which the name Primorskyibacter insulae sp. nov. is proposed. The type strain is SSK3-2T ( = KCTC 42602T = CECT 8871T).
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Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol
More LessPseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name ‘Pseudomonas alkylphenolia’ was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T with the Pseudomonas putida group, with Pseudomonas vranovensis DSM 16006T as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, gyrB, rpoD and rpoB partial gene sequences showed that isolate KL28T could be differentiated from P. vranovensis DSM 16006T (sequence similarity 93.7 %). Genomic comparisons of strain KL28T with the type strains of the species in the P. putida group using average nucleotide index based on blast (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with P. vranovensis DSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T ( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, ‘P. alkylphenolia’, is correctly latinized as Pseudomonas alkylphenolica sp. nov.
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Sphingomonas hylomeconis sp. nov., isolated from the stem of Hylomecon japonica
A yellow-pigmented bacterium, designated strain GZJT-2T, was isolated from the stem of Hylomecon japonica (Thunb.) Prantl et Kündig collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain GZJT-2T were Gram-reaction-negative, strictly aerobic, rod-shaped, non-spore-forming and non-motile. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GZJT-2T was a member of the genus Sphingomonas, with sequence similarities of 92.1–96.9 % to type strains of recognized species of the genus Sphingomonas (92.1 % to Sphingomonas oligoaromativorans SY-6T and 96.9 % to Sphingomonas oligophenolica JCM 12082T). Strain GZJT-2T contained ubiquinone-10 (Q-10) as the predominant respiratory quinone and sym-homospermidine as the major polyamine. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 2-OH. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, four unidentified phospholipids, an unidentified aminolipid and four unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 62.5 ± 0.3 mol%. On the basis of data from phenotypic, phylogenetic and DNA–DNA relatedness studies, strain GZJT-2T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas hylomeconis sp. nov. is proposed. The type strain is GZJT-2T ( = CCTCC AB 2013304T = KCTC 42739T).
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Reclassification of Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus as Archangium disciforme comb. nov., Archangium minus comb. nov. and Archangium violaceum comb. nov., unification of the families Archangiaceae and Cystobacteraceae, and emended descriptions of the families Myxococcaceae and Archangiaceae
More LessThe species Archangium gephyra, Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus are currently classified in three different genera of the order Myxococcales. The 16S rRNA gene sequences of the respective type strains show a similarity higher than 98.4 % and form a tight phylogenetic group. A dendrogram calculating the similarity of MALDI-TOF spectra confirmed the close relatedness of the four species that grouped in a monophyletic cluster in the neighbourhood of other species of the genus Cystobacter. The type strains shared similar fatty acid patterns of high complexity with iso-C15 : 0, C16 : 1ω5c and iso-C14 : 0 3-OH as the major components. The vegetative cells of these species are uniformly long needle-shaped rods, and the myxospores are short rods, ovoid or irregularly spherical thus differing from the myxospores of species related to Cystobacter fuscus, the type species of this genus. Some enzymic and hydrolysing reactions of the type strains are described. As a result of the high relatedness and similarity of the four species, it is proposed to place them into one genus, and due to phylogenetic and morphological distinctness, the species should be classified in a genus distinct from the genus Cystobacter as Archangium gephyra (type strain M18T = DSM 2261T = ATCC 25201T = NBRC 100087T), Archangium disciforme comb. nov. (type strain CMU 1T = DSM 52716T = ATCC 33172T), Archangium minus comb. nov. (proposed neotype strain Cb m2 = DSM 14751 = JCM 12627) and Archangium violaceum comb. nov. (type strain Cb vi61T = DSM 14727T = CIP 109131T = JCM 12629T). Since the family Archangiaceae Jahn 1924 AL has priority over the family Cystobacteraceae McCurdy 1970 AL, it is proposed to assign the genera Archangium, Anaeromyxobacter, Cystobacter, Hyalangium, Melittangium and Stigmatella to the family Archangiaceae. Emended descriptions of the families Myxococcaceae and Archangiaceae are also provided.
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Roseomonas wooponensis sp. nov., isolated from wetland freshwater
More LessA non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram-stain-negative, catalase- and oxidase-positive. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0.The predominant quinone and polyamine were ubiquinone 10 (Q-10) and spermidine, respectively. The DNA G+C content was 71 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WW53T belongs to the family Acetobacteraceae, and is related to the genus Roseomonas. Strain WW53T was most closely related to Roseomonas stagni HS-69T (95.3 % 16S rRNA gene sequence similarity). Results of a polyphasic taxonomy study suggested that the isolate represents a novel species in the genus Roseomonas, for which the name Roseomonas wooponensis sp. nov. is proposed. The type strain is WW53T ( = KCTC 32534T = JCM 19527T).
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Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays
More LessA beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA–DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA–DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).
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Thalassocola ureilytica gen. nov., sp. nov., of the family Phyllobacteriaceae isolated from seawater
A Gram-stain-negative, aerobic, rod-shaped, non-flagellated marine bacterium, designated strain LS-861T, was isolated from seawater of the South China Sea (Taiwan). Strain LS-861T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity (91.5 % each) with ‘Nitratireductor shengliensis’ CGMCC 1.12519 and Hoeflea halophila JG120-1T and lower sequence similarity ( < 91.5 %) with other species. Phylogenetic analyses based on 16S rRNA gene sequences revealed a distinct taxonomic position attained by strain LS-861T within the clade that accommodated members of the family Phyllobacteriaceae. The major fatty acids were C16 : 0, iso-C17 : 1ω10c, C18 : 0 3-OH and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile was relatively simple as compared with other representatives of Phyllobacteriaceae, by having major amounts of diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid, and moderate amounts of three unidentified phospholipids and an unidentified aminolipid. The DNA G+C content was 61.2 mol%. The predominant quinone system was ubiquinone-10 (Q-10). The data in general and phylogenetic and polar lipid data in particular clearly distinguish the novel strain from related species at the genus level. Thus, strain LS-861T is suggested to represent a novel species of a new genus of the family Phyllobacteriaceae, for which the name Thalassocola ureilytica gen. nov., sp. nov. is proposed. The type strain of Thalassocola ureilytica is LS-861T ( = BCRC 80818T = JCM 30682T).
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Undibacterium aquatile sp. nov., isolated from a waterfall
More LessA Gram-stain-negative, aerobic, motile and rod-shaped strain, THG-DN7.3T, was isolated from a waterfall. Strain THG-DN7.3T grew well at 18–28 °C and at pH 6.0–7.5 on Reasoner's 2A agar. Based on 16S rRNA gene sequence comparisons, strain THG-DN7.3T was most closely related to Undibacterium jejuense JS4-4T (97.3 % 16S rRNA gene sequence similarity) and Undibacterium seohonense SHS5-24T (96.5 %). The G+C content of the genomic DNA was 57.4 mol%. The mean DNA–DNA relatedness of strain THG-DN7.3T with U. jejuense KACC 12607T was 40 ± 1 % (reciprocal 50 ± 2.1 %). The major cellular fatty acids of strain THG-DN7.3T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (47.4 %), C16 : 0 (30.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (6.8 %) and C12 : 0 (6.2 %). The predominant isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of the DNA–DNA hybridization and genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-DN7.3T represents a novel species of the genus Undibacterium, for which the name Undibacterium aquatile sp. nov. is proposed. The type strain is THG-DN7.3T ( = KCTC 42243T = CCTCC AB 2015119T).
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Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater
An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).
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Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater
More LessA Gram-stain-negative, non-motile, aerobic bacterium, strain 13-93-B1T, was isolated from seawater off Jeju Island, Republic of Korea, and was subjected to polyphasic taxonomic study. Cells formed ivory colonies and were ovoid to rod-shaped. The strain was catalase-positive, oxidase-negative and grew optimally at 30 °C, in the presence of 1–2 % (w/v) NaCl and at pH 7.0–7.5. It did not synthesize bacteriochlorophyll a. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain 13-93-B1T clustered with the type strain Donghicola eburneus SW-277T (97.0 % 16S rRNA gene sequence similarity). DNA–DNA hybridization between strain 13-93-B1T and D. eburneus KCTC 12735T was 33.1 ± 1.4 % (35.2 ± 2.8 % in a reciprocal experiment). The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 76.9 %). The major respiratory quinone was ubiquinone Q-10 and polar lipids detected in strain 13-93-B1T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified aminolipid and unidentified lipids. The DNA G+C content of strain 13-93-B1T was 60.4 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain 13-93-B1T is considered to represent a novel species of the genus Donghicola, for which the name Donghicola tyrosinivorans sp. nov. is proposed. The type strain is 13-93-B1T ( = DSM 100212T = KCTC 42571T)
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Marinibacterium profundimaris gen. nov., sp. nov., isolated from deep seawater
More LessA taxonomic study was carried out on strain 22II1-22F33T, which was isolated from deep seawater of the Atlantic Ocean. The bacterium was Gram-stain-negative, oxidase-positive and weakly catalase-positive, oval in shape without flagellum. Growth was observed at salinities of 0–12 % and at temperatures of 4–41 °C. The isolate was capable of hydrolysing aesculin and Tween 80 and reduction of nitrate to nitrite, but unable to hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II1-22F33T belongs to the family Rhodobacteraceae, with highest sequence similarity to Pseudooceanicola marinus AZO-CT (96.5 %). The principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ω6c) (73.8 %). The G+C content of the genomic DNA was 66.2 mol%. The respiratory quinone was Q-10 (100 %). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids (ALs), six unidentified phospholipids (PLs) and one unidentified lipid (L) were present. The combined genotypic and phenotypic data show that strain 22II1-22F33T represents a novel species within a new genus, for which the name Marinibacterium profundimaris gen. nov., sp. nov. is proposed. The type strain of Marinibacterium profundimaris is 22II1-22F33T ( = LMG 27151T = MCCC 1A09326T).
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Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province
More LessA Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY2–5T, was isolated from surface sediment of Pacific Clarion-Clipperton Fracture Zone (CCFZ). Growth occurred at 0–37 °C (optimum 28 °C), pH 6.5–9.0 (optimum pH 7.0–7.5) and in the presence of 1–11 % (w/v) NaCl (optimum 3–4 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain was most closely related to Celeribacter halophilus ZXM137T with 96.13 % sequence similarity, and had 16S rRNA gene sequence similarities in the range 93.89–95.87 % with other species of the genus Celeribacter. The dominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipids of strain DY2–5T comprised phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major respiratory quinone was ubiquinone–10 (Q–10). The DNA G+C content of strain DY2–5T was 64.8 mol%. On the basis of the phenotypic, genotypic and physiological evidence, strain DY2–5T represents a novel species of the genus Celeribacter, for which the name Celeribacter manganoxidans sp. nov. is proposed. The type strain is DY2–5T ( = JCM 19384T = KCTC 32473T).
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Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015
More LessA Gram-staining-negative, aerobic and moderately halophilic bacterium, designated strain NS6T, was isolated from sea-tidal-flat sediment of the South Sea in Korea. Cells were motile rods with a single flagellum showing positive catalase and oxidase activities. Strain NS6T grew at 15–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 1–5 % (w/v) NaCl (optimum, 2 %). Ubiquinone-10 was identified as the only isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c/ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C10 : 0 3-OH were the major fatty acids. Strain NS6T contained phosphatidylglycerol, sulfoquinovosyldiacylglycerol, an unidentified amino lipid and an unidentified lipid as the major polar lipids. An unidentified phospholipid and three unidentified lipids were also detected as the minor polar lipids. The G+C content of the genomic DNA was 64.5 mol%. Strain NS6T was most closely related to Confluentimicrobium lipolyticum SSK1-4T with a 96.8 % 16S rRNA gene sequence similarity, and the phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS6T formed a tight phylogenetic lineage with C. lipolyticum SSK1-4T. The physiological, chemotaxonomic and phylogenetic properties suggest that strain NS6T represents a novel species of the genus Confluentimicrobium, for which the name Confluentimicrobium naphthalenivorans sp. nov. is proposed. The type strain is NS6T ( = KCTC 18418T = JCM 30828T). An emended description of the genus Confluentimicrobium is also proposed.
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Alteromonas naphthalenivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from tidal-flat sediment
More LessA Gram-staining-negative and halotolerant bacterium, designated SN2T, capable of biodegrading polycyclic aromatic hydrocarbons, was isolated from a tidal flat contaminated with crude oil in Korea. Cells were strictly aerobic, catalase- and oxidase-positive, motile rods, with a single polar flagellum. Growth was observed at 4–37 °C (optimum, 25–30 °C) at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–9.0 % (w/v) NaCl (optimum, 2.0 %). Only ubiquinone 8 was detected as the isoprenoid quinone, and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C12 : 0 were observed as the major cellular fatty acids. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, an aminolipid and three unidentified lipids. The DNA G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SN2T formed a phylogenetic lineage with Alteromonas stellipolaris and Alteromonas addita within the genus Alteromonas, which was consistent with multilocus phylogenetic and MALDI-TOF MS analyses. Strain SN2T was most closely related to the type strains of A. stellipolaris, A. addita and Alteromonas macleodii, with 16S rRNA gene sequence similarities of 99.5, 99.3 and 98.4 % and DNA–DNA relatedness of 48.7 ± 6.6, 24.9 ± 7.5 and 27.9 ± 8.4 %, respectively. In conclusion, strain SN2T represents a novel species of the genus Alteromonas, for which the name Alteromonas naphthalenivorans sp. nov. is proposed. The type strain is SN2T ( = KCTC 11700BPT = JCM 17741T = KACC 18427T).
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Umboniibacter roseus sp. nov., isolated from coastal seawater
More LessA Gram-reaction-negative, non-motile, strictly aerobic, dark pink-pigmented and rod-shaped bacterial isolate, designated 14-121-B13T, was isolated from surface seawater off the coast of the South Sea at Namhae-gun, Republic of Korea. Cells were catalase- and oxidase-positive and required NaCl for growth. Strain 14-121-B13T grew optimally at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7.5–8.0.Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain 14-121-B13T clustered with the type strain of Umboniibacter marinipuniceus, with which it exhibited 96.7 % sequence similarity. The DNA G+C content of strain 14-121-B13T was 48.9 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major respiratory quinone was ubiquinone Q-7 and the polar lipids detected in strain 14-121-B13T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, unidentified phospholipids, unidentified aminophospholipids and unidentified lipids. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain 14-121-B13T is considered to represent a novel species of the genus, Umboniibacter for which the name Umboniibacter roseus sp. nov. is proposed. The type strain is 14-121-B13T ( = DSM 29882T = KCTC 42467T).
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- Bacteroidetes
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Epilithonimonas psychrotolerans sp. nov., isolated from alpine permafrost
More LessA bacterial strain, designated TSBY 57T, was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China, and was classified by means of a polyphasic taxonomic approach. The novel strain was found to belong to the genus Epilithonimonas and was distinguished from recognized species of this genus. Strain TSBY 57T grew aerobically, at 0–30 °C, with 0–1.5 % (w/v) NaCl and at pH 6–8.Cells were Gram-stain-negative, non-motile, non-spore-forming rods. Compared with the reference strains, the novel strain was psychrotolerant. The predominant fatty acids were summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and iso-C15 : 0.The sole respiratory quinone was MK-6.Phosphatidylethanolamine was predominant in the polar lipid profile of strain TSBY 57T. These chemotaxonomic traits were in good agreement with the characteristics of the genus Epilithonimonas. On the basis of 16S rRNA gene sequence similarity, strain TSBY 57T was a member of the genus Epilithonimonas and was closely related to Epilithonimonas tenax DSM 16811T (99.0 %), Epilithonimonas ginsengisoli DCY78T (98.6 %) and Epilithonimonas lactis H1T (98.5 %). However, DNA–DNA reassociation values between strain TSBY 57T and E. tenax DSM 16811T, E. ginsengisoli DCY78T and E. lactis H1T were 39.5 ± 2.6, 37.7 ± 1.0 and 37.3 ± 1.1 %, respectively. The G+C content of the DNA was 34.4 ± 0.2 mol%. Based on data from this polyphasic taxonomic study, strain TSBY 57T represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas psychrotolerans sp. nov. is proposed. The type strain is TSBY 57T ( = NRRL B-51307T = CCTCC AB 207182T).
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Pedobacter alpinus sp. nov., isolated from a plateau lake
More LessTwo Gram-staining-negative, aerobic, non-motile, red-pigment and rod-shaped bacterial strains, designated RSP19T and RSR28, were isolated from lake water and subjected to polyphasic taxonomic studies. Based on 16S rRNA gene sequence analysis, strains RSP19T and RSR28 exhibited 91.4–95.7 % similarity to the type strains of existing species of the genus Pedobacter. The species most closely related phylogenetically were Pedobacter daechungensis (95.7 % sequence similarity), Pedobacter lentus (95.4 %), Pedobacter glucosidilyticus (94.5 %), Pedobacter panaciterrae (94.5 %) and Pedobacter terricola (94.2 %). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and several unidentified polar lipids. The predominant fatty acids were C16 : 1ω7c, iso-C15 : 0 and iso-C17 : 0 3-OH. The genomic DNA G+C contents were 34.3 and 33.9 mol% for strains RSP19T and RSR28, respectively. Based on the phenotypic characteristics, biochemical properties and genetic analysis, strains RSP19T and RSR28 clearly represent a novel species of the genus Pedobacter, for which the name Pedobacter alpinus is proposed. The type strain is RSP19T ( = CGMCC 1.14040T = KCTC 42456T = NBRC 110967T).
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Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica
A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28T, was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 °C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter alluvionis NWER-II11T (95.6 %) and Pedobacter terrae DS-57T (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28T to the genus Pedobacter. Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28T from species of the genus Pedobacter with validly published names. Therefore, strain R2-28T represents a novel species within the genus Pedobacter, for which the name Pedobacter ardleyensis sp. nov. is proposed. The type strain is R2-28T ( = CCTCC AB 2013365T = LMG 28255T).
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Flavobacterium endophyticum sp. nov., a nifH gene-harbouring endophytic bacterium isolated from maize root
More LessA novel Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain 522T, was isolated from surface-sterilized root tissue of maize planted in Fangshan District of Beijing, China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belonged to the genus Flavobacterium and showed less than 93.9 % similarity to the type strains of all recognized species of the genus Flavobacterium. The predominant respiratory quinone was menaquinone-6 and the polar lipid profile was composed of the major lipids phosphatidylethanolamine, phosphatidylserine and two unidentified amino lipids. The major fatty acids were C15 : 0, iso-C15 : 0, iso-C15 : 1 G and iso-C16 : 0.The G+C content of the DNA was 37.7 mol%. The results of physiological and biochemical tests and the differences in fatty acid profiles allowed the clear phenotypic differentiation of strain 522T from closely related species of the genus Flavobacterium. Strain 522T therefore represents a novel species within the genus Flavobacterium, for which the name Flavobacterium endophyticum sp. nov. is proposed. The type strain is 522T ( = ACCC 19708T = DSM 29537T).
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Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater
More LessA novel Gram-stain-negative, rod-shaped, yellow-pigmented, non-sporulating, non-motile bacterium, designated strain AK20T, was isolated from seawater collected from Kochi city, Kerala state, India. Colonies on marine agar were circular, yellow, shiny, translucent, 2–3 mm in diameter, convex and with entire margin. Flexirubin-type pigment was present. The fatty acids were dominated by iso-branched units with a high abundance of iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C15 : 0 3-OH. Polar lipids included phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The DNA G+C content of strain AK20T was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK20T was closely related to Formosa spongicola A2T and Bizionia paragorgiae KMM 6029T (pair-wise sequence similarities of 95.9 and 95.7 %, respectively), forming a distinct branch within the family Flavobacteriaceae and clustering with the clade comprising species of the genus Bizionia. Based on phenotypic and chemotaxonomic characteristics and phylogenetic analysis, strain AK20T is different from the existing genera in the family Flavobacteriaceae, and is therefore considered to represent a novel species of a new genus, for which the name Xanthomarina gelatinilytica gen. nov., sp. nov. is proposed. The type strain of Xanthomarina gelatinilytica is AK20T ( = MTCC 11705T = JCM 18821T).
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Mucilaginibacter ginsengisoli sp. nov., isolated from a ginseng-cultivated soil
A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10–35 °C (optimum, 25 °C), at pH 3.0–11.0 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).
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Chryseobacterium echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla)
A Gram-stain-negative, aerobic, non-motile, rod-shaped, flexirubin-producing bacterium, designated strain CC-CZW010T, was isolated from the edible sea urchin Tripneustes gratilla in Penghu Island, Taiwan. The isolate grew optimally at pH 7.0 and 30 °C in the presence of 2 % (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were Chryseobacterium taihuense NBRC 108747T (97.6 %) and Chryseobacterium aquaticum KCTC 12483T (96.7 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed a distinct taxonomic position attained by strain CC-CZW010T with respect to other species of the genus Chryseobacterium. Strain CC-CZW010T possessed iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) and summed feature 9 (comprising C16 : 0 10-methyl/iso-C17 : 1ω9c) as predominant fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified lipids and five aminolipids. The polyamine pattern contained the major compound sym-homospermidine. Menaquinone 6 (MK-6) was the predominant respiratory quinone, and the G+C content of the genomic DNA was 36.4 mol%. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-CZW010T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium echinoideorum sp. nov. is proposed. The type strain is CC-CZW010T ( = BCRC 80786T = JCM 30470T).
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Lutibacter holmesii sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Lutibacter
More LessSeven Gram-staining-negative, strictly aerobic, pale-yellow-pigmented, rod-shaped and non-motile strains were isolated from the sea urchin Strongylocentrotus intermedius collected from Troitsa Bay, Sea of Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were affiliated with the family Flavobacteriaceae. The novel isolates showed 99.9–100 % 16S rRNA gene sequence similarity to each other and were closely related to the type strains of the recognized members of the genus Lutibacter with sequence similarities of 95.8–98.4 %. The G+C content of the genomic DNA was 35–36 mol%. DNA–DNA relatedness among the sea urchin isolates was 95–99 % and between strain KMM 6277T and its most closely related type strains, Lutibacter agarilyticus KCTC 23842T and Lutibacter litoralis JCM 13034T, was 38 and 27 %, respectively. The prevalent fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c fatty acids), iso-C15 : 1 and C15 : 0. The polar lipid profile was composed of the phosphatidylethanolamine, one unknown aminolipid and one unknown lipid. The main respiratory isoprenoid quinone was MK-6.The results of phylogenetic, phenotypic and genotypic analyses indicated that the novel strains represent a novel species within the genus Lutibacter, for which the name Lutibacter holmesii sp. nov. is proposed. The type strain is KMM 6277T ( = CCUG 62221T = LMG 26737T).
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Maribacter flavus sp. nov., isolated from a cyanobacterial culture pond
A Gram-stain-negative, yellow, non-spore-forming, strictly aerobic bacterium, designated C3T, was isolated from a cyanobacterial culture pond. Cells were halophilic, rod-shaped and able to move by gliding. Growth of strain C3T was observed at 15–30 °C (optimum 25 °C), pH 6.0–9.0 (optimum pH 7.5), and in the presence of 1–7 % (w/v) NaCl (optimum 2–3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain C3T formed a distinct lineage within the family Flavobacteriaceae and exhibited the highest similarity (95.21 %) to the type strains of Maribacter dokdonensis, Maribacter arcticus, Maribacter orientalis and Maribacter stanieri, and ‘Maribacter caenipelagi’ HD-44. The only isoprenoid quinone present within strain C3T was menaquinone 6 (MK-6). The G+C content of genomic DNA was 41.5 mol%. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. The predominant cellular fatty acids (>5 % of the total fatty acids) were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain C3T represents a novel species of the genus Maribacter, for which the name Maribacter flavus sp. nov. is proposed. The type strain is C3T ( = KCTC 42508T = CGMCC 1.15112T).
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Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system
More LessA Gram-stain-negative, yellow-pigmented bacterial strain, designated PR1012KT, was isolated from a motor car evaporator core collected in Korea. Cells of the strain were facultatively anaerobic, non-spore-forming and rod-shaped. The strain grew at 10–40 °C (optimum, 25 °C), at pH 6.5–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–1 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Spirosoma (97.50–90.74 % 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (97.50 %). Its predominant fatty acids included summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso B) and it had MK-7 as the major menaquinone. The polar lipids present included phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and five unknown polar lipids. The DNA G+C content of this strain was 54 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain PR1012KT represents a novel species in the genus Spirosoma, for which the name Spirosoma aerolatum sp. nov. is proposed. The type strain is PR1012KT ( = KACC 17939T = NBRC 110794T).
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Myroides indicus sp. nov., isolated from garden soil
More LessA novel aerobic, non-motile, rod-shaped, catalase- and oxidase-positive bacterial strain, designated UKS3T, was isolated from garden soil, and subjected to polyphasic taxonomic analysis. Strain UKS3T formed whitish, viscous colonies on nutrient agar and was Gram-staining negative. Phylogenetic analysis, based on 16S rRNA gene sequence, showed that maximum pairwise similarity occurs with representatives of the genus Myroides. The most closely related species include Myroides marinus JS-08T (92.7 % sequence similarity), Myroides phaeus MY15T (92.7 %), Myroides odoratus DSM 2801T (91.5 %) and Myroides odoratimimus CCUG 39352T (91.4 %). Strain UKS3T contained menaquinone-6 (MK-6) as the major respiratory quinone and iso-C15 : 0 (40.2 %), anteiso-C15 : 0 (9.4 %) and iso-C17 : 0 3-OH (8.5 %) as major fatty acids. Phosphatidylethanolamine, phospholipids and three aminolipids were the major polar lipids. The DNA G+C content of strain UKS3T was 36.8 ± 2.0 mol%. On the basis of phenotypic, chemotaxonomic and molecular analysis, strain UKS3T represents a novel species of the genus Myroides, for which the name Myroides indicus sp. nov., is proposed. The type strain is UKS3T ( = DSM 28213T = NCIM 5555T ).
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Chryseobacterium sediminis sp. nov., isolated from a river sediment
More LessA slightly yellow-pigmented strain (IMT-174T) isolated from a river sediment in Guyana was studied in detail for its taxonomic position. Cells of the isolate appeared rod-shaped and stained Gram-negative. Comparative 16S rRNA gene sequence analysis showed that the isolate had the highest sequence similarities to type strains of Chryseobacterium rhizoplanae (99.0 %), Chryseobacterium viscerum (98.9 %), Chryseobacterium lactis (98.8 %) and Chryseobacterium indologenes (98.6 %). The 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98.5 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of members of the genus Chryseobacterium, with fatty acids iso-C15 : 0, iso-C15 : 0 2-OH, iso-C17 : 1ω9c and iso-C17 : 0 3-OH as major compounds. The polyamine pattern contained predominantly sym-homospermidine. The major quinone was menaquinone MK-6 and the only lipid identified in the polar lipid profile was phosphatidylethanolamine. In addition, 13 unidentified lipids were detected in moderate to major amounts. DNA–DNA hybridizations with type strains of C. rhizoplanae, C. viscerum, C. lactis and C. indologenes resulted in values below 70 %. In addition to the genotypic differences, differentiating biochemical and chemotaxonomic properties confirmed that isolate IMT-174T represents a novel species, for which the name Chryseobacterium sediminis sp. nov. (type strain IMT-174T = LMG 28695T = CIP 110895T) is proposed.
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Muricauda pacifica sp. nov., isolated from seawater of the South Pacific Gyre
More LessA Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, rod-shaped and orange-pigmented bacterium with appendages, designated strain SW027T, was isolated from a surface seawater sample collected from the South Pacific Gyre (26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW027T shared the highest sequence similarity with members of the genus Muricauda (94.3–92.7 %), exhibiting 94.3 % sequence similarity to Muricauda flavescens SW-62T. Optimal growth occurred in the presence of 3 % (w/v) NaCl, at pH 7.0 and at 37 °C. The DNA G+C content of strain SW027T was 42.7 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Enzymic activity profiles, cell morphology and DNA G+C content differentiated the novel bacterium from the most closely related members of the genus Muricauda. On the basis of the polyphasic analyses, strain SW027T is considered to represent a novel species of the genus Muricauda, for which the name Muricauda pacifica sp. nov. is proposed. The type strain is SW027T ( = JCM 17861T = LMG 26637T).
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Hymenobacter mucosus sp. nov., isolated from a karst cave soil sample
A novel Gram-stain-negative, non-motile, rod-shaped and watermelon-red-pigmented aerobic bacterial strain, designated YIM 77969T, was isolated from a soil sample of Jiuxiang cave, a tourism cave located in Yiliang county, Yunnan province, south-west China. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77969T belongs to the genus Hymenobacter, and was closely related to Hymenobacter tibetensis XTM003T (96.58 %), Hymenobacter gelipurpurascens Txg1T (96.02 %) and Hymenobacter xinjiangensis X2-1gT (95.80 %). Growth of strain YIM 77969T occurred at 5–35 °C, at pH 5.0–9.0 and in the presence of 0–1 % (w/v) NaCl. The predominant menaquinone was MK-7. The major fatty acids were iso-C15 : 0, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profiles consisted of the major compound phosphatidylethanolamine, two unknown aminolipids, three unknown aminophospholipids, one glycolipid and one unknown polar lipid. Pigment analysis showed that the pigment belonged to the plectaniaxanthin series of carotenoid pigments. The genomic DNA G+C content was 55.2 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM 77969T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter mucosus sp. nov. is proposed. The type strain is YIM 77969T ( = KCTC 32567T = DSM 28041T).
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Chitinophaga barathri sp. nov., isolated from mountain soil
More LessA Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium, designated strain YLT18T, was isolated from mountain cliff soil of Enshi Grand Canyon in China. The major menaquinone was menaquinone 7 (MK-7) and the predominant fatty acids (>5 %) were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH) and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unknown aminophospholipids, two unknown aminolipids and two unknown polar lipids. The DNA G+C content was 55.4 mol%. According to phylogenetic analysis based on 16S rRNA gene sequences, strain YLT18T was related most closely to Chitinophaga niabensis JS13-10T ( = DSM 24787T) and Chitinophaga cymbidii R156-2T ( = KCTC 23738T), with similarities of 96.7 and 96.2 %, respectively. In addition, strain YLT18T showed obvious differences from the closely related species in terms of esterase (C4) activity, acid production from fructose and rhamnose, and sole carbon source utilization by arabinose and rhamnose. The results from this polyphasic taxonomic study revealed that strain YLT18T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga barathri sp. nov. is proposed. The type strain is YLT18T ( = KCTC 42472T = CCTCC AB 2015054T).
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Roseivirga marina sp. nov., isolated from seawater
Jie Pan, Cong Sun, Rui-Jun Wang and Min WuStrain PSRT was isolated from seawater of the Pacific Ocean. Cells of the strain were Gram-stain-negative, strictly aerobic, rod-shaped and motile by gliding. Growth was observed at 4–40 °C (optimum 25–30 °C), at pH 6.0–9.5 (optimum pH 7.0–7.5) and with 0.5–8 % (w/v) NaCl (optimum 2–3 %). The major fatty acids were iso-C15 : 1 G (18.9 %), iso-C15 : 0 (26.3 %) and iso-C17 : 0 3-OH (17.9 %). The predominant isoprenoid quinone was MK-7, and the DNA G+C content was 49.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PSRT was most closely related to Roseivirga spongicola UST030701-084T (96.9 % 16S rRNA gene sequence similarity), and they formed a distinct clade in neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees with significant bootstrap supports. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain PSRT represents a novel species of the genus Roseivirga, for which the name Roseivirga marina sp. nov. is proposed. The type strain is PSRT ( = MCCC 1K00459T = KCTC 42444T).
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Gramella aquimixticola sp. nov., isolated from water of an estuary environment
More LessA Gram-stain-negative, aerobic, non-spore-forming bacterial strain, motile by gliding and with rod-shaped or ovoid cells, was isolated from water of an estuary environment at Hwajinpo, South Korea. The strain was designated HJM-19T and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain HJM-19T belongs to the genus Gramella. It exhibited 16S rRNA gene sequence similarity values of 97.2–98.1 % to the type strains of Gramella portivictoriae, Gramella aestuariivivens, Gramella marina, Gramella echinicola and Gramella aestuarii, and of 93.9–96.5 % to the type strains of the other species of the genus Gramella with validly published names. Strain HJM-19T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c and C17 : 0 2-OH as the major fatty acids. The major polar lipids of strain HJM-19T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain HJM-19T was 48.0 mol%, and its DNA–DNA relatedness values with the type strains of the five phylogenetically closely related species of the genus Gramella were 11–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HJM-19T is separated from other species of the genus Gramella. On the basis of the data presented, strain HJM-19T is considered to represent a novel species of the genus Gramella, for which the name Gramella aquimixticola sp. nov. is proposed. The type strain is HJM-19T ( = KCTC 42706T = NBRC 111224T).
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- Other bacteria
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Borrelia yangtzensis sp. nov., a rodent-associated species in Asia, is related to Borrelia valaisiana
Twenty-nine isolates of Lyme borreliosis (LB) group spirochaetes collected from ticks and rodents in China and Japan were included in a multilocus sequence analysis (MLSA). Using a different typing system, three of these strains had previously been identified as being divergent from other LB spirochaete species and the name ‘Borrelia yangtze’ sp. nov. was proposed. The data presented here confirm that the genetic distance, calculated using sequences of MLSA housekeeping genes, to other known LB group spirochaete species was < 95 % and to Borrelia valaisiana was 96.67 % (which represents the most closely related species within the group of LB spirochaetes). This and the fact that these strains are ecologically distinct from B. valaisiana (rodent-transmitted vs bird-transmitted) provide strong support for the validation of the proposed species status. We suggest the name Borrelia yangtzensis sp. nov. The type strain is Okinawa-CW62T ( = DSM 24625T = JCM 17189T).
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Spirochaeta sinaica sp. nov., a halophilic spirochaete isolated from a cyanobacterial mat
A strain of free-living obligately anaerobic, halophilic spirochaete, SLT, was isolated from a sample of a cyanobacterial mat of the hypersaline Solar Lake, Sinai shore. The strain had motile helical cells, 0.35–0.40 × 6–10 μm. Strain SLT exhibited high resistance to NaCl among known halophilic spirochaetes growing at NaCl concentrations from 2 to 12 % (optimum growth at 7 %). The strain grew at temperatures from 10 to 32 °C (optimum at 28 °C) and pH from 6 to 8.5 (optimum at pH 7.0–7.5). Carbohydrates, but not alcohols, organic acids or nitrogenous compounds (peptone, yeast extract and amino acids), were used as energy substrates for growth. Ethanol, acetate, lactate, H2 and CO2 were the products of glucose fermentation. Sulfide was produced in the presence of S0 or thiosulfate in the medium. The DNA G+C content was 44.7 mol%. Based on 16S rRNA gene sequence analysis, strain SLT clustered within the genus Spirochaeta, exhibiting 94.2 and 93.7 % similarity with its closest relatives, Spirochaeta bajacaliforniensis DSM 160554T and Spirochaeta smaragdinae DSM 11293T, respectively; similarity with other species did not exceed 86 %. The phenotypic and chemotaxonomic characteristics of the strain, as well as the results of phylogenetic analysis support the classification of strain SLT as representing a novel species of the genus Spirochaeta, for which the name Spirochaeta sinaica sp. nov. is proposed. The type strain is SLT ( = DSM 14994 = UNIQEM U 783).
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Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates
Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).
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Lentisphaera profundi sp. nov., isolated from deep-sea water
More LessA Gram-staining-negative, aerobic, non-motile, coccus-shaped bacterium, designated SAORIC-696T, was isolated from deep-sea water at a depth of 1700 m in the western North Pacific Ocean. Optimal growth of strain SAORIC-696T was observed at 15 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Strain SAORIC-696T formed a robust phylogenetic clade with members of the genus Lentisphaera. The 16S rRNA gene sequence similarity showed that strain SAORIC-696T was most closely related to Lentisphaera marina (98.0 % similarity) and Lentisphaera araneosa (97.3 %). The DNA–DNA relatedness between SAORIC-696T and two species of the genus Lentisphaera was only 27–42 %. The DNA G+C content of strain SAORIC-696T was 43.1 mol% and predominant cellular fatty acids were C16 : 1ω9c (36.8 %), C14 : 0 (22.5 %) and C14 : 0 3-OH and/or iso-C16 : 1 I (10.8 %). Strain SAORIC-696T contained MK-7 as the only respiratory quinone. On the basis of taxonomic data collected in this study, it was concluded that strain SAORIC-696T represents a novel species of the genus Lentisphaera, for which the name Lentisphaera profundi sp. nov. is proposed, with the type strain SAORIC-696T ( = NBRC 110692T = KCTC 42681T).
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- Evolution, Phylogeny and Biodiversity
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Evolutionary relationships of completely sequenced Clostridia species and close relatives
More LessThe class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.
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- TAXONOMIC NOTES
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Proposal to change Recommendation 12c of the International Code of Nomenclature of Prokaryotes
More LessWe propose changing Recommendation 12c of the International Code of Nomenclature of Prokaryotes to clarify the ways species and subspecies can be named to honour persons.
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Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes
The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.
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- CORRIGENDUM
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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 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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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 32 (1982)
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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)