- Volume 69, Issue 1, 2019
Volume 69, Issue 1, 2019
- Editorial
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Preparation of the Validation Lists and the role of the List Editors
More LessRecently a number of queries were received about the ways in which requests for validation of names of taxa effectively published in journals other than the IJSEM are approved or denied and about the criteria used by the List Editors of the journal when deciding whether or not a validation request can be approved. As this process may be unclear to some authors of proposals, we would like to clarify the nature of the validation process and the role of the List Editors.
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- Validation List
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- Notification List
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- List of Changes in Taxonomic Opinion
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- New Taxa
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- Actinobacteria
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Nocardioides silvaticus sp. nov., isolated from forest soil
More LessA Gram-stain-positive, non-motile, rod-shaped bacterial strain S-34T was isolated from forest soil. According to 16S rRNA gene sequence analysis, strain S-34T was related to Nocardioides members and showed the highest similarities to Nocardioides thalensis NCCP-696T (97.3 %) and Nocardioides panacisoli Gsoil 346T (97.0 %), Nocardioides litorisoli X-2T (96.5 %) and Nocardioides immobilis FLL521T (96.4 %). Phylogenetic trees showed that strain S-34T fell within the cluster containing strain S-34T and N. immobilis FLL521T. The levels of DNA–DNA relatedness between strain S-34T and N. thalensis CCTCC AB 2016296T and between strain S-34T and N. panacisoli KCTC 19470T were 50.6 and 58.8 %, respectively. The genome orthoANI value between strain S-34T and N. immobilis CCTCC AB 2017083T was 82.4 %. Strain S-34T had ll-diaminopimelic acid in the cell-wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol, four unknown phospholipids and one unknown lipid as the polar lipids, meanquinone-8(H4) as the only respiratory quinone and iso-C16 : 0, C17:1 ω8c, C17:1 ω6c, C17 : 0 and C17 : 0 10-methyl (tbsa) as the major fatty acids. The genome length of strain S-34T was 4.53 Mb containing 52 contigs and with a DNA G+C content of 71.2 mol%. Strain S-34T could be distinguished from the other Nocardioides members mainly based on the data of phylogenetic analyses, DNA–DNA hybridization, polar lipids and some biochemical differences. Therefore, strain S-34T represents a novel species of the genus Nocardioides , for which the name Nocardioides silvaticus sp. nov. is proposed. The type strain is S-34T (=KCTC 49137T=CCTCC AB 2018079T).
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Streptomyces reniochalinae sp. nov. and Streptomyces diacarni sp. nov., from marine sponges
More LessTwo marine actinomycete strains, LHW50302T and LHW51701T, were isolated from marine sponges collected in Sansha, Hainan Province, China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with their classification in the genus Streptomyces . The strains formed hooked and looped chains of arthrospores with smooth surfaces. The cell-wall hydrolysates of the strains contained ll-diaminopimelic acid as the diagnostic diamino acid. MK-9(H8) was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Major fatty acids of the strains were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The 16S rRNA gene sequences indicated that the strains clustered together with Streptomyces albus CGMCC 4.1640T and Streptomyces qinglanensis CGMCC 4.6825T. Multilocus sequence analysis (MLSA) confirmed their relationship. Genome relatedness in forms of average nucleotide identity, digital DNA–DNA hybridization value and MLSA evolutionary distance between each of the strains and its closest relatives showed that they belonged to distinct species. On the basis of these results, strains LHW50302T and LHW51701T belong to two novel species in the genus Streptomyces , for which the names Streptomyces reniochalinae sp. nov. (type strain LHW50302T=CCTCC AA 2018013T=DSM 106194T) and Streptomyces diacarni sp. nov. (type strain LHW51701T=CCTCC AA 2018017T=DSM 106126T) are proposed, respectively.
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Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum
More LessThe taxonomic position of an actinobacterium, designated CPCC 204380T, which was isolated from a rhizosphere soil sample of the plant Calligonum mongolicum collected from Xinjiang Province, China, was established using a polyphasic approach. Vegetative hyphae developed well and globose bodies formed from aged hyphae. Spore chains that differentiated from the vegetative hyphae contained non-motile rod-shaped spores. The peptidoglycan contained meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid as the diagnostic amino acids. The acyl type of the peptidoglycan was glycolyl. Glucose, mannose, ribose and xylose were detected in whole-cell hydrolysates. The predominant menaquinone was MK-10(H8), followed by MK-10(H6) and MK-10(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C17 : 1ω9c. The genomic G+C content was 64.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204380T should be placed in the family Micromonosporaceae , in which it formed a distinct lineage next to the genera Rhizocola , Catellatospora , Catelliglobosispora , Hamadaea and Allocatelliglobosispora. It shared the highest 16S rRNA gene sequence similarities with Rhizocola hellebori K12-0602T (96.1 %), Catellatospora chokoriensis 2-25/1T (95.9 %), Catelliglobosispora koreensis DSM 44566T (95.9 %), Hamadaea tsunoensis DSM 44101T (95.3 %) and Allocatelliglobosispora scoriae Sco-B14 T (94.2 %), and less than 94.0 % sequence similarity with other validly described species. The combination of phylogenetic analysis and phenotypic characteristics supported the proposal of strain CPCC 204380T as representing a novel species of a new genus in the family Micromonosporaceae , for which the name Allorhizocola rhizosphaerae gen. nov., sp. nov. is proposed. CPCC 204380T (=DSM 102292T=KCTC 39746 T) is the type strain of the type species.
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Thermocatellispora soli sp. nov., isolated from hot spring soil
More LessAn aerobic, spore-forming, actinomycete, designated strain CHM3-46T, was isolated from soil in a hot spring pond located in Chiangmai province, Thailand. The strain exhibited taxonomic characteristics consistent with the genus Thermocatellispora . Strain CHM3-46T produced short, straight chains of warty spores on aerial mycelia. The presence of meso-diaminopimelic acid was observed in the cell-wall peptidoglycan. The whole-cell reducing sugars were glucose, mannose, galacose and ribose. The phospholipids comprised phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, four phosphoglycolipids and three unidentified phospholipids. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). 10-methyl C17 : 0, C16 : 0, C17 : 0 and iso-C16 : 0 were identified as the main cellular fatty acids. The G+C content of the genomic DNA was 73.2 mol%. Analysis of the 16S rRNA gene sequence showed that strain CHM3-46T belonged to the genus Thermocatellispora , exhibiting the highest similarity to Thermocatellispora tengchongensis YIM 77521T (98.5 %). Furthermore, a low DNA relatedness value (23.4 %±0.8) and several physiological and biochemical characteristic differences were detected between strain CHM3-46T and its closest relative. Based on the taxonomic data, strain CHM3-46T could be readily distinguished from its closest phylogenetic relative and represents a novel species, for which the name Thermocatellispora soli sp. nov. is proposed. The type strain is CHM3-46T (=TBRC 7649T=NBRC 113148T).
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Nocardia aurea sp. nov., a novel actinobacterium isolated from a karstic subterranean environment
A novel actinobacterium, designated strain SYSU K10002T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K10002T was most closely related to the type strains of Nocardiaaltamirensis NBRC 108246T (99.0 % sequence similarity) and Nocardiatenerifensis NBRC 101015T (98.8 %) and is therefore considered to represent a member of the genus Nocardia . DNA–DNA hybridization values between strain SYSU K10002T and the closely related type strains of the genus Nocardia were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, ribose and galactose. The major isoprenoid quinone was MK-8(H4,ω-cycl), while the major fatty acids (>10 %) were C16 : 0, C18 : 1ω9c and C18 : 0 10-methyl. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified glycolipid. Mycolic acids were present. The genomic DNA G+C content of strain SYSU K10002T was 67.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10002T represents a novel species of the genus Nocardia , for which the name Nocardia aurea sp. nov. is proposed. The type strain is SYSU K10002T (=KCTC 39849T=DSM 103986T).
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Nakamurella deserti sp. nov., isolated from rhizosphere soil of Reaumuria in the Taklamakan desert
More LessA Gram-stain-positive, aerobic, non-motile, non-spore-forming, coccus-shaped actinobacterium, designated strain 12Sc4-1T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, China. Strain 12Sc4-1T grew at 8‒35 °C (optimum, 28‒30 °C), pH 6.0‒9.0 (optimum, pH 7.0) and in the presence of 0‒3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 12Sc4-1T belonged to the genus Nakamurella and shared the highest 16S rRNA gene sequence similarity to Nakamurella silvestris S20-107T (96.94 %). Strain 12Sc4-1T showed <96.0 % 16S rRNA gene sequence similarities to all other recognized members of the genus Nakamurella . Chemotaxonomic analyses showed that the isolate possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, glucose, mannose and galactose as whole-cell sugars, and MK-8(H4) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, phosphatidylinositol, an unidentified phospholipid, an unidentified phosphoglycolipid and an unidentified glycolipid. The major fatty acids were C16 : 0 and anteiso-C15 : 0. The DNA G+C content was 72.1 mol% (draft genome sequence). On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, strain 12Sc4-1T represents a novel species of the genus Nakamurella , for which the name Nakamurella deserti sp. nov. is proposed. The type strain is 12Sc4-1T (=KCTC 49114T=CGMCC 1.16555T).
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Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill.
More LessA Gram-stain-positive, aerobic, short-rod-shaped, non-spore-forming actinobacterial strain, designated M8JJ-5T, was isolated from a surface-sterilized bark of Neriumindicum Mill. collected from Guizhou, China, and investigated by a polyphasic approach to determine its taxonomic position. Strain M8JJ-5T grew optimally without NaCl at 28 °C and at pH 7.0–8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain M8JJ-5T was most closely related to the type strains of genus Amnibacterium , and shared highest 16S rRNA gene sequence similarity of 97.29 % to Amnibacterium kyonggiense KSL51201-037T. The DNA G+C content of strain M8JJ-5T was 68.6 mol%. The cell-wall peptidoglycan contained l-2,4-diaminobutyric acid and MK-12, MK-11 were the major menaquinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid, while the major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain M8JJ-5T can be characterized to represent a novel species of the genus Amnibacterium , for which the name Amnibacterium flavum sp. nov. is proposed. The type strain is M8JJ-5T (=KCTC 49089T=CGMCC 1.16390T).
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- Bacteroidetes
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Flavobacterium tibetense sp. nov., isolated from a wetland
More LessA novel, Gram-stain-negative, non-motile and rod-shaped bacterium, designated YH5T, was isolated from the YonghuCo wetland on the Tibetan Plateau. The strain was able to grow optimally with 1 % (w/v) NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6–9 (optimum pH 7) and 10–37 °C (optimum 30 °C). Vitamins were not required for growth. The major polar lipid of strain YH5T was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15 : 0, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Genome sequencing revealed a genome size of 2.74 Mbp and a G+C content of 33.3 mol%. Analysis of 16S rRNA gene sequences showed that strain YH5T belonged to the genus Flavobacterium , with the closest neighbours Flavobacterium luticocti xz20T (96.7 % similarity), Flavobacterium jejuense EC11T (96.4 %), Flavobacterium jumunjinense HME7102T (95.9 %) and Flavobacterium dongtanense LW30T (95.6 %). DNA–DNA relatedness between strain YH5T and the closest phylogenetically related strain F. luticocti xz20T was 27.0 %. Strain YH5T was clearly distinguished from the reference type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. Based on its phenotypic and chemotaxonomic characteristics, strain YH5T is classified as a representative of a novel species of the genus Flavobacterium , for which the name Flavobacterium tibetense sp. nov. is proposed. The type strain is YH5T (=CICC 24247T=KCTC 62174T).
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Flavobacterium niveum sp. nov., isolated from a freshwater creek
More LessStrain TAPW14T was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPW14T belonged to the genus Flavobacterium and was most closely related to Flavobacterium akiainvivens IK-1T (96.6 % sequence identity) and Flavobacterium hauense BX12T (96.0 %) and less than 96 % sequence similarity to other members of the genus. Cells of strain TAPW14T were Gram-negative, strictly aerobic, motile by gliding, rod-shaped and formed white colonies. Optimal growth occurred at 20 °C, pH 7 and in the presence of 0.5 % NaCl. Strain TAPW14T contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 46.0 mol%. On the basis of the phylogenetic inference and phenotypic data, strain TAPW14T should be classified as a novel species, for which the name Flavobacteriumniveum sp. nov. is proposed. The type strain is TAPW14T (=BCRC 81055T=LMG 30057T=KCTC 52808T).
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- Firmicutes and Related Organisms
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Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces
More LessTwo isolates of a Gram-positive, non-motile, coccoid or oval-shaped anaerobic bacterium, designated strains N6H1-15T and YH1_16, were isolated from faecal samples obtained from a mature dog. Analysis of 16S rRNA gene sequences indicated that the isolates belonged to the Blautia coccoides rRNA gene group (cluster XIVa) and were closely related to Blautia hansenii KCTC 5951T, Blautia stercoris KCTC 5981T, Blautia producta producta KCTC 3695T and B. coccoides DSM 15327T, with 96.7, 94.4, 94.2 and 93.9 % sequence similarity, respectively. The two isolates contained m-diaminopimelic acid within their peptidoglycans. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the major fatty acids were C16 : 0 (18.5 %), C16 : 0 (18.0 %) and C18 : 1 cis 9 (16.2 %). The predominant metabolic end products of glucose fermentation were acetic and lactic acids, and the G+C content was 44.2 mol%. Thus, the polyphasic data suggest that the two new isolates represent a new species, proposed as Blautia argi sp. nov. The type strain is N6H1-15T (=KCTC 15426=JCM 31394).
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Listeria thailandensis sp. nov.
During a screening of Listeria species in food samples in Thailand, a Listeria -like bacterium was recovered from fried chicken and could not be assigned to any known species. Phylogenetic analysis based on the 16S rRNA gene and on 243 Listeria core genes placed the novel taxon within the Listeria aquatica , Listeria floridensis , Listeria fleishmannii and Listeria costaricensis clade ( Listeria sensu lato), with highest similarity to L. floridensis (98.9 %) and L. costaricensis (98.8 %). Whole-genome sequence analyses based on the average nucleotide blast identity (ANI<86 %), the pairwise amino acid identity (AAI>64 %) and on the percentage of conserved proteins (POCP>77 %) with currently known Listeria species confirmed that the strain constituted a new taxon within the genus Listeria . At the phenotypical level, it differs from other Listeria species by the production of acid from d-tagatose and inositol. The name Listeria thailandensis sp. nov. is proposed for the novel species, and is represented by the type strain CLIP 2015/00305T (=CIP 111635T=DSM 107638T).
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Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding
More LessStrain 82T, a Gram-stain-positive, coagulase-negative staphylococcus was isolated from an air sample obtained from an industrial rabbit holding in Italy. It is phylogenetically closely related to the coagulase-negative species Staphylococcus saprophyticus , Staphylococcus xylosus and Staphylococcus edaphicus . However, it could be distinguished from these species by sequence differences between the 16S rRNA, hsp60, rpoB, dnaJ and gap genes. At the whole genome level, the isolate had an average nucleotide identity of <95 % and an inferred DNA–DNA hybridization of <70 % when compared to these species. Based on the genotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus caeli sp. nov. The type strain is 82BT (=NCTC 14063T=CCUG 71912T).
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Bacillus salidurans sp. nov., isolated from salt-accumulated pepper rhizospheric soil
More LessA Gram-stain-positive, facultatively anaerobic, motile and rod-shaped bacterium, designated KNUC7312T, was isolated from salt-accumulated rhizospheric soil in a pepper greenhouse in Miryang city, Republic of Korea. Cell growth of strain KNUC7312T occurred at 10–45 °C (optimum, 30 °C) and pH 7–12 (optimum, pH 7). In addition, this strain was able to tolerate 0–12 % NaCl (w/v) concentration (optimum, 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain KNUC7312T clustered together with other species of the genus Bacillus and was most closely related to Bacillus humi DSM 16318T (98.0 %). The predominant respiratory quinone was menaquinone-7 (MK-7). The major cellular fatty acids were anteiso C15 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified aminolipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the major diagnostic diamino acid. Strain KNUC7312T showed a low DNA–DNA relatedness value (47.36 %) with B. humi DSM 16318T, which supported that this strain represents a novel Bacillus species. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain KNUC7312T represents a novel species within the genera Bacillus . The name Bacillus salildurans sp. nov. is proposed. The type strain is KNUC7312T (KCTC 33852T=CGMCC 1.13629T).
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Genome-based reclassification of Paenibacillus dauci as a later heterotypic synonym of Paenibacillus shenyangensis
Paenibacillus shenyangensis and Paenibacillus dauci are Gram-stain-positive, rod-shaped and endospore-forming bacteria originally isolated from soil and carrot samples, respectively, in China. Preliminary comparative genomic analysis showed that these bacteria could constitute a single species. Therefore, in this study, their taxonomic statuses were clarified through distinct genomic metrics and phylogenetic analyses. Paenibacillus shenyangensis A9T and P. dauci H9T presented values of average nucleotide identity (ANI) and its derivative metrics (gANI and OrthoANI) ranging from 97.88 to 98.08 %, and digital DNA–DNA hybridization equal to 89.08 %. Furthermore, the identities of 16S rRNA, gyrB, rpoB, recA and recN genes were all equal or higher than 98.7 %. Phylogenies of these marker genes and the concatenated core proteome were congruent in the sense that P. shenyangensis A9T and P. dauci H9T are the closest type-strains of the genus Paenibacillus . A review of their profiles revealed that these strains do not present pronounced differences at the phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, P. dauci should be reclassified as a later heterotypic synonym of P. shenyangensis .
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Paenibacillus flagellatus sp. nov., isolated from selenium mineral soil
More LessStrain DXL2T, a Gram-stain-negative, rod-shaped, endospore-forming, motile, aerobic bacterium, was isolated from selenium mineral soil. DXL2T had the highest 16S rRNA gene sequence similarities with those of Paenibacillus ginsengarvi Gsoil 139T (96.8 %), Paenibacillus hemerocallicola DLE-12T (95.5 %) and Paenibacillus hodogayensis SGT (95.4 %). The genome size of DXL2T was 7.24 Mb, containing 6243 predicted protein-coding genes, with a DNA G+C content of 60.2 mol%. DXL2T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The major quinone was menaquinone 7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, an unidentified aminolipid, phosphatidylmethylethanolamine, an unidentified glycolipid and an unidentified phospholipid. Compared with the other strains, DXL2T had a specific phospholipid and a specific aminolipid, it hydrolyzed Tween 40 and could not assimilate potassium gluconate. On the basis of the phenotypic, chemotaxonomic and phylogenetic results, strain DXL2T represents a novel species within the genus Paenibacillus , for which the name Paenibacillus flagellatus sp. nov. is proposed. The type strain is DXL2T (=KCTC 33976T=CCTCC AB 2018054T).
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Bacillus safensis subsp. osmophilus subsp. nov., isolated from condensed milk, and description of Bacillus safensis subsp. safensis subsp. nov.
A bacterial strain, designated BC09T, was isolated from a contaminated sample of condensed milk. Phylogenetic analyses based on 16S rRNA gene sequences placed strain BC09T into the genus Bacillus with its closest relatives being Bacillus safensis and Bacillus australimaris with 100 and 99.9 % similarity, respectively. Analysis of the gyrB gene confirmed the closeness of strain BC09T with respect to the species B. safensis since it presented 97.8 and 95.2 % similarity values, respectively, to the type strains of B. safensis and B. australimaris. DNA–DNA hybridization confirmed these results showing averages of 67 and 56 %, respectively, between strain BC09T and the type strains of B. safensis and B. australimaris. Average nucleotide identity blast values obtained for BC09T compared to the closest relative type strains were 95.7 and 67.6 %, respectively, and predicted DNA–DNA hybridization values were 93.1 and 51.9 %, respectively. However, strain BC09T differs from the type strains of its closest relatives in several phenotypic characteristics. MK-7 was the only menaquinone detected and iso-C15:0 and anteiso-C15:0 were the major fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, two unidentifed glycolipids, three unidentified lipids and one unidentifed phosphoglycolipid. Meso-diaminopimelic acid was detected in the peptidoglycan. The G+C content was 40.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain BC09T represents a new subspecies of B. safensis, for which the name Bacillus safensis subsp. osmophilus subsp. nov. is proposed. The type strain is BC09T (=LMG 30124T, =CECT 9344T).
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- Other Bacteria
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Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the class Armatimonadia of the phylum Armatimonadetes
More LessAn aerobic bacterial strain designated AX-7T was isolated from the trunk surface of a Japanese beech (Fagus crenata). Cells of strain AX-7T were Gram-stain-negative, non-spore-forming, non-motile rods (1.0–1.2 µm in width and 1.2–3.0 µm in length) with peritrichous fimbriae. Cells were capsulated, and a number of them were surrounded by a thick slime layer. During growth, large aggregates formed, and the culture medium became viscous probably owing to exopolysaccharide release from the slime layer. The temperature range for growth was 10–37 °C, with an optimum at 30 °C. The pH range for growth was 5.0–7.0, with an optimum at pH 6.0. Strain AX-7T used various sugars, including polysaccharides, and yeast extract as growth substrates. Strain AX-7T contained menaquinones MK-9 and MK-10 as the respiratory quinones, and C16 : 1ω5c, C16 : 1ω11c, C16 : 0 and C14 : 0 as the major cellular fatty acids. Four unidentified phospholipids and 11 unidentified polar lipids constituted the polar lipids. The DNA G+C content was 61.0 mol%. The cell-wall peptidoglycan contained ll-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AX-7T belonged to the class Armatimonadia , its closest relative being Armatimonas rosea YO-36T, with sequence similarity of 88.1%. Based on data from this polyphasic study, we propose that strain AX-7T represents a new genus of a novel species within the novel order Capsulimonadales ord. nov. of the class Armatimonadia , for which the name Capsulimonas corticalis gen. nov., sp. nov. is proposed. The type strain of C. corticalis is AX-7T (=DSM 105890T=NBRC 113044T).
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- Proteobacteria
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Shewanella submarina sp. nov., a gammaproteobacterium isolated from marine water
A curved-rod-shaped bacterium was isolated from a marine (100 m depth) water sample collected from Bay of Bengal, Visakhapatnam, India. Strain NIO-S14T, was Gram-stain-negative, motile and pale-yellow. NIO-S14T was able to grow aerobically and anaerobically and could utilize a number of organic substrates. Major fatty acids were C12 : 0, iso-C13 : 0, C14 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3). NIO-S14T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminophospholipids and six unidentified lipids as polar lipids. The DNA G+C content of NIO-S14T was 47.9 mol%. The 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Shewanellaceae within the class Gammaproteobacteria . According to the results of 16S rRNA gene sequence analysis, NIO-S14T was closely related to Shewanella corallii with a pair-wise sequence similarity of 99.26 %. On the basis of the sequence comparison, NIO-S14T clustered with Shewanella corallii and together they clustered with Shewanella mangrovi and seven other species of the genus Shewanella but were distantly related. DNA–DNA hybridization between NIO-S14T and Shewanella corallii DSM 21332Trevealed a relatedness of 35 %. Distinct morphological, physiological and genotypic differences from these previously described taxa supported the classification of NIO-S14T as a representative of a novel species of the genus Shewanella , for which the name Shewanella submarina sp. nov. is proposed. The type strain of Shewanella submarina is NIO-S14T (=MTCC 12524T=KCTC 52277T=LMG 30752T).
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The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov.
More LessSeven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isolated strains comprised distinct and novel species (average nucleotide identity <0.95; in silico DNA–DNA hybridization <70 %; G+C difference >1 %). Multilocus sequence analysis was performed using gyrB, rpoD and 16S rRNA gene sequences from the novel and type strains to determine their phylogenetic positions. The novel strains are facultative anaerobes, mesophilic, facultative alkaliphic and halophilic, test positive for catalase and oxidase activities, for hydrolysis of Tween 20 and phosphate, for production of indole-3-acetic acid, but do not produce H2S. Ubiquinone UQ-9 is present in major amounts in all strains. The major fatty acids include C16 : 0 and the summed feature containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C content ranges from 60.6 to 65.8 mol%. Five strains were confirmed as new species belonging to the genus Salinicola , for which the names Salinicola halimionae sp. nov. (type strain CPA60T=CECT 9338T=LMG 30107T), Salinicola aestuarinus sp. nov. (type strain CPA62T=CECT 9339T=LMG 30108T), Salinicola endophyticus sp. nov. (type strain CPA92T=CECT 9340T=LMG 30109T), Salinicola halophyticus sp. nov. (type strain CR45T=CECT 9341T=LMG 30105T) and Salinicola lusitanus sp. nov. (type strain CR50T=CECT 9342T=LMG 30106T) are proposed.
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Brenneria corticis sp. nov., isolated from symptomatic bark of Populus×euramericana canker
More LessA Gram-stain-negative, facultatively anaerobic, motile bacterial strain, designated gBX10-1-2T, was isolated from symptomatic bark of Populus×euramericana canker in China. Phylogenetic analysis based on its 16S rRNA gene sequence showed that the novel isolate belonged to the genus Brenneria , and shared the highest sequence similarity to Brenneria nigrifluens LMG 2694T (98.3 %). In the phylogenetic trees based on the four housekeeping genes sequences, the novel strain formed a separate branch different from B. nigrifluens LMG 2694T, indicating that the novel strain should be classified as a novel species. The genome sequence-derived average nucleotide identity (ANI) values between the novel isolate and B. nigrifluens LMG 2694T, Brenneria roseae subsp. roseae FRB 222T and Brenneria roseae subsp. americana FRB 223T were less than 85 %, lower than the proposed species boundary ANI cut-off value (95–96 %). The DNA G+C content was 56.2 mol%, and the main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 1ω7c and C17 : 0cyclo. Based on the phenotypic and genotypic characteristics, strain gBX10-1-2T represents a novel species of genus Brenneria , for which the name Brenneria corticis sp. nov. is proposed. The type strain is gBX10-1-2T (=CFCC 11842T=KCTC 42840T).
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Lysobacter silvisoli sp. nov., isolated from forest soil
More LessA yellow-pigmented, Gram-stain-negative, gliding and rod-shaped bacterial strain, designated zong2l5T, was isolated from a forest soil sample at Dinghu Mountain, Guangdong Province, PR China. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain zong2l5T belongs to the genus Lysobacter , and was most closely related to Lysobacter enzymogenes KCTC 12131T (97.7 %) and Lysobacter soli KCTC 22011T (97.6 %). The novel strain showed an average nucleotide identity (ANI) value of 81.5 % and a digital DNA–DNA hybridization (dDDH) value of 25.3 % with L. enzymogenes KCTC 12131T based on draft genome sequences, followed by L. soli KCTC 22011T with ANI and dDDH values of 79.4 % and 22.7 %, respectively. The DNA G+C content of strain zong2l5T based on the whole genome sequence was 69.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). Strain zong2l5T contained Q-8 as the major isoprenoid quinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, three unidentified phospholipids and an unidentified aminolipid. The phenotypic, genotypic and chemotaxonomic anlyses clearly showed that strain zong2l5T represents a novel species of the genus Lysobacter , for which the name Lysobacter silvisoli sp. nov. is proposed. The type strain is zong2l5T (=GDMCC 1.1489T=KCTC 52923T).
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Nitrincola tibetensis sp. nov., isolated from Lake XuguoCo on the Tibetan Plateau
More LessA novel Gram-stain-negative, motile and rod-shaped bacterium, designated xg18T, was isolated from Lake XuguoCo on the Tibetan Plateau. The strain was able to grow optimally at 0–2 % NaCl and tolerate up to 6 % NaCl. Growth occurred at pH 7.0–11.0 (optimum, pH 9.0–10.0) and 15–40 °C (optimum, 37 °C). Vitamins were not required for growth. The major polar lipids of strain xg18T were phosphatidyl ethanolamine and phosphatidylglycerol. The predominant respiratory quinone was Q-8. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The G+C content of genomic DNA was 46.1 mol%. Analysis of 16S rRNA sequences showed that strain xg18T belongs to the genus Nitrincola , with Nitrincola alkalisediminis MEB087T (KC822363, 98.6 %) as its closest neighbour. The DNA–DNA relatedness value of strain xg18T with its closest phylogenetic neighbour, N. alkalisediminis JCM 19317T, was 43.1±3.2 %. Strain xg18T was clearly distinguishable from the type strain of the genus Nitrincola through phylogenetic analysis, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain xg18T could be classified as a representative of a novel species of the genus for which the name Nitrincola tibetensis sp. nov. is proposed. The type strain is xg18T (=CICC 24457T=KCTC 62401T).
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Simplicispira lacusdiani sp. nov., a novel betaproteobacterium isolated from a freshwater reservoir
More LessA Gram-stain-negative, motile, rod-shaped bacterium, designated CPCC 100842T, was isolated from a freshwater reservoir in south-west China. The 16S rRNA gene sequence comparison of strain CPCC 100842T with the available sequences in the GenBank database showed that the isolate was closely related to members of the family Comamonadaceae , with the highest similarities to Simplicispira metamorpha DSM 1837T (98.05 %), Simplicispira limi KCTC 12608T (97.86 %), Simplicispira psychrophila LMG 5408T (97.04 %) and Simplicispira piscis JCM 19291T (97.0 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100842T formed a distinct phylogenetic subclade within the genus Simplicispira . The major cellular fatty acids were as C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1ω6c). Q-8 was detected as the only respiratory quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and glycolipid were found in the polar lipid extraction. The genomic DNA G+C content was 67.4 mol%. The average nucleotide identity value was 80.4 % by comparing the draft genome sequences of strain CPCC 100842T and S. metamorpha DSM 1837T. The DNA–DNA hybridization result between strain CPCC 100842T and S. metamorpha DSM 1837T showed 37±3 % genomic relatedness. On the basis of the genotypic analysis and phenotypic characteristics, we propose that strain CPCC 100842T represents a novel species of the genus Simplicispira in the family Comamonadaceae with the name Simplicispira lacusdiani sp. nov. Strain CPCC 100842T (=KCTC 52093T=DSM 102231T) is the type strain of the species.
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Mesorhizobium carmichaelinearum sp. nov., isolated from Carmichaelineae spp. root nodules
More LessFive strains of Gram-stain-negative, rod-shaped bacteria were isolated from Carmichaelia and Montigena root nodules. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium , and to be most closely related to Mesorhizobium jarvisii ATCC 33669T (100–99.6 % sequence similarity), Mesorhizobium huakuii IAM 14158T (99.9–99.6 %), Mesorhizobium japonicum MAFF303099T (99.8–99.6 %) and Mesorhizobium erdmanii USDA 3471T (99.8–99.5 %). Additionally, the strains formed distinct groups based on housekeeping gene analysis and were most closely related to M. jarvisii ATCC 33669T (89.6–89.5 and 97.6–97.3 % sequence similarity for glnII and recA, respectively), M. erdmanii USDA 3471T (94.3–94.0 and 94.9–94.1 %), M. japonicum MAFF303099T (90.0–89.9 and 96.7–96.2 %) and M. huakuii IAM 14158T (89.9–90.0 and 95.4–94.9 %). Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium and DNA–DNA hybridizations, average nucleotide identity analysis, matrix-assisted laser desorption ionization time-of-flight MS analysis, physiological and biochemical tests differentiated them genotypically and phenotypically from their nearest neighbouring species. Therefore, these strains are considered to represent a novel species, for which the name Mesorhizobium carmichaelinearum sp. nov. is proposed. The type strain is ICMP 18942T (=MonP1N1T=LMG 28414T).
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Arenibacillus arenosus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sea sand
A Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated CAU 1304T, was isolated from sea sand. Strain CAU 1304T grew optimally at pH 8.5 and 30 °C and in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1304T belonged to the family Rhodobacteraceae , and was most closely related to Roseicitreum antarcticum ZS2-28T (96.54 % similarity) and Rhodobacter veldkampii ATCC 35703T (96.46 %). The major fatty acid was C18 : 1ω7c and the respiratory quinone was Q-10. The polar lipids were composed of phosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid. The DNA G+C content was 55.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, it is proposed that strain CAU 1304T represents a novel species of a new genus of the family Rhodobacteraceae , for which the name Arenibacillus arenosus gen. nov., sp. nov. is proposed. The type strain of Arenibacillus arenosus is CAU 1304T (=KCTC 42827T=NBRC 113022T).
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Aliidiomarina celeris sp. nov., isolated from coastal sediment
More LessA Gram-stain-negative, heterotrophic, facultative anaerobic, gliding and motile bacterium, approximately 0.6–0.9 µm wide and 1.5–2.6 µm long, designated F3105T, was isolated from a marine sediment sample collected along the coast of Rongcheng, China . The growth of strain F3105T occurred on media with 1.0–8.0 % (w/v) NaCl (optimum, 2.0–3.0 %) and a pH of 6.5–9.5 (optimum, pH 7.5) at 4–45 °C (optimum, 37 °C). The phylogenetic analysis of the 16S rRNA gene and chemotaxonomic data revealed that the isolate belonged to the genus Aliidiomarina , and is closely related to Aliidiomarina shirensis (95.9 % sequence similarity). The sole isoprenoid quinone was Q-8. The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 1ω9c and iso-C17 : 0, and its polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminolipid, two unidentified lipids and two unidentified aminophospholipids. The DNA G+C content of strain F3105T was 49.5 mol%. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain F3105T is considered to represent a novel species of the genus Aliidiomarina , for which the name Aliidiomarina celeris sp. nov. is proposed. The type strain is F3105T (=MCCC 1H00223T=KCTC 52891T).
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Paraburkholderia phosphatilytica sp. nov., a phosphate-solubilizing bacterium isolated from forest soil
More LessA novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, 7QSK02T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. It grew at 12–37 °C, at pH 4.0–7.5 and in the presence of 0–1.0 % (w/v) NaCl on R2A agar medium, with optimum growth at 28 °C, pH 5.5 and 0 % NaCl. Strain 7QSK02T was closely related to members of the genus Paraburkholderia : P. acidipaludis NBRC 101816T (98.1 % 16S rRNA gene sequence similarity), P. piptadeniae STM 7183T (97.6 %), P. kururiensis JCM 10599T (97.3 %), P. caballeronis TNe-841T (97.3 %) and P. diazotrophica JPY461T (97.1 %). 16S rRNA gene sequence analysis showed that strain 7QSK02T and two closely strains, P. kururiensis JCM 10599T and P. caballeronis TNe-841T, formed a clade within the genus Paraburkholderia , but was clearly separated from the established species. The genomic G+C content of strain 7QSK02T was 64.9 mol% based on total genome calculations. The average nucleotide identity and digital DNA–DNA hybridization value for the complete genomes were 79.2–81.5 and 23.2–24.9 % between strain 7QSK02T and its closely related species listed above. Strain 7QSK02T contained ubiquinone 8 as the major respiratory quinone. Major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, one unidentified aminophospholipid, aminolipid and polar lipid. The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggest that strain 7QSK02T represents a novel species of the genus Paraburkholderia , for which the name Paraburkholderia phosphatilytica sp. nov. is proposed. The type strain is 7QSK02T (=GDMCC 1.1283T=CGMCC 1.15470T=KCTC 62473T).
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Polynucleobacter paneuropaeus sp. nov., characterized by six strains isolated from freshwater lakes located along a 3000 km north–south cross-section across Europe
More LessSix Polynucleobacter ( Burkholderiaceae , Betaproteobacteria ) strains isolated from different freshwater lakes located across Europe were taxonomically investigated. Phylogenetic analyses based on 16S rRNA gene sequences assigns all six strains to the cryptic species complex PnecC within the genus Polynucleobacter . Analyses of partial glutamine synthetase (glnA) genes suggests that all six strains belong to the species-like taxon designated F15 in previous papers. Comparative genome analyses reveal that the six strains form a genomically coherent group characterized by whole-genome average nucleotide identity (gANI) values of >98 % but separated by gANI values of <88 % from the type strains and representatives of the 16 previously described Polynucleobacter species. In phylogenetic analyses based on nucleotide sequences of 319 orthologous genes, the six strains represent a monophyletic cluster that is clearly separated from all other described species. Genome sizes of the six strains range from 1.61 to 1.83 Mbp, which is smaller than genome sizes of the majority of type strains representing previously described Polynucleobacter species. By contrast, the G+C content of the DNA of the strains is well in the range of 44.8–46.6 mol% previously found for other type strains of species affiliated with the subgroup PnecC. Variation among the six strains representing the new species is evident in a number of traits. These include gene content differences, for instance regarding a gene cluster encoding anoxygenic photosynthesis, as well as phenotypic traits. We propose to name the new species represented by the six strains Polynucleobacter paneuropaeus sp. nov. and designate strain MG-25-Pas1-D2T (=DSM 103454T =CIP 111323T) as the type strain.
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Marinobacter maroccanus sp. nov., a moderately halophilic bacterium isolated from a saline soil
During the taxonomic investigation of exopolymer-producing halophilic bacteria, a rod-shaped, motile, Gram-stain-negative, halophilic bacterium, designated strain N4T, was isolated from a saline soil located in northern Morocco. Optimal growth of the isolate was at 30–37 ºC and at pH 7.0–8.0, in the presence of 5–7 % (w/v) NaCl. Useful characteristics for the phenotypic differentiation of strain N4T from other Marinobacter species included α-chymotrypsin and α-glucosidase activities and the carbohydrate assimilation profile. The major fatty acids detected in strain N4T were C16:0 and C18:1ω9c and the predominant respiratory quinone was ubiquinone-9. Sequence analysis of the 16S rRNA gene indicated that strain N4T belonged to the genus Marinobacter and was closely related to the type strains of Marinobacter adhaerens (99.04 % similarity), Marinobacter salsuginis (98.97 %) and Marinobacter flavimaris (98.36 %). Phylogenetic analysis of the rpoD gene sequence also showed that the nearest neighbours of strain N4T were M. salsuginis (91.49 % similarity), M. adhaerens and M. flavimaris (90.63 %). Strain N4T showed 87.98 % average nucleotide identity with M. flavimaris and M. salsuginis, and 87.47 % with M. adhaerens. Regarding in-silico genome-to-genome distance, strain N4T showed DNA–DNA hybridization values of 33.30 % with M. adhaerens, 34.60 % with M. flavimaris and 34.70 % with M. salsuginis. The DNA G+C content of strain N4T was 57.3 mol%. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain N4T represents a novel species of the genus Marinobacter, for which the name Marinobacter maroccanus sp. nov. is proposed. The type strain is N4T (=CECT 9525T=LMG 30466T).
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Kistimonas alittae sp. nov., a gammaproteobacterium isolated from the marine annelid Alitta succinea
A novel Gram-stain-negative, rod-shaped, motile, non-spore-forming, facultatively anaerobic marine bacterium was isolated from the gastrointestinal tract of the sandworm Alitta succinea collected from Grice Cove, South Carolina, USA. The strain was arginine dihydrolase-positive, and oxidase- and catalase-positive. Growth occurred between 10 and 37 °C, with optimal growth occurring between 30 and 32 °C. Comparative 16S rRNA gene sequence analysis showed its nearest neighbours are members of the genus Kistimonas of the family Hahellaceae , which is found in the order Oceanospirillales , class Gammaproteobacteria . The closest related species was Kistimonas asteriae KMD 001T with 16S rRNA gene sequence similarity of 99.0 %. However, DNA–DNA hybridization between these strains revealed less than 70 % DNA–DNA relatedness, supporting the novel species status of the strain. The major fatty acids were C16 : 0, C18 : 0, C18 : 1ω7c and a summed feature that contained C16 : 1ω6c/C16 : 1ω7c. The major respiratory quinone was ubiquinone-9 and the predominant polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 52.5 mol%. Based on the data presented, strain BGP-2T is considered to represent a novel member of the genus Kistimonas , for which the name Kistimonas alittae sp. nov. is proposed. The type strain is BGP-2T (=CCUG 65711T=JCM 30010T).
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Erythrobacter zhengii sp. nov., a bacterium isolated from deep-sea sediment
A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, designated V18T, was isolated from a deep-sea sediment sample collected from the Pacific Ocean and subjected to a polyphasic taxonomic investigation. Cells of strain V18T grew in medium containing 0–10.0 % (w/v) NaCl (optimum 1.0 %), at pH 5.5–9.0 (optimum 6.5–7.0) and at 10–40 °C (optimum 30–37 °C). Aesculin and Tweens 20, 40, 60 and 80 were hydrolysed. The isolate contained carotenoid-like pigments and lacked bacteriochlorophyll a. Strain V18T was closely related to members of the genus Erythrobacter, namely Erythrobacter odishensis JA747T (98.9 % 16S rRNA gene sequence similarity), E. westpacificensis JLT2008T (98.8 %), E. gangjinensis K7-2T (97.7 %), E. aquimixticola JSSK-14T (97.6 %), E. marinus KCTC 23554T (97.4 %), E. atlanticus s21-N3T (97.3 %), E. arachoides RC4-10-4T (97.2 %), E. citreus RE35F/1T (97.1 %) and E. luteus KA37T (97.0 %), and exhibited less than 97.0 % sequence similarity with the type strains of other species with validly published names. Phylogenetic analyses revealed that strain V18T clustered with E. odishensis JA747T and formed an independent lineage. The average nucleotide identity and in silico DNA–DNA hybridization values between strain V18T and the type strains of Erythrobacter species were 70.5–83.4 % and 18.4–26.1 %, respectively. Strain V18T contained ubiquinone 10 (Q-10) as the sole respiratory quinone. The major fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major polar lipids were sphingoglycolipid (SGL), diphosphatidylglycerol (DPG), phosphatidyglycerol (PG), phosphatidylethanolamine (PE) and one unidentified lipid (L1). The DNA G+C content was 62.6 mol%. According to the phenotypic, chemotaxonomic and phylogenetic data, strain V18T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter zhengii is proposed. The type strain is V18T (=KCTC 62389T=MCCC 1K03475T).
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Oceanibium sediminis gen. nov., sp. nov., isolated from marine sediment
More LessA novel Gram-stain-negative, rod-shaped marine bacterium, designated as strain O448T, was isolated from the coastal area of Weihai, China (122° 14′ E, 36° 54′ N). Cells of strain O448T were non-motile, aerobic, approximately 0.4–0.6 µm wide and 1.5–2.0 µm long. Growth occurred at 20–40 °C (optimally between 33–37 °C), pH 6.5–8.0 (optimally at 7.0) and in the presence of 1.0–5.0 % (w/v) NaCl (optimally between 2.0–3.0 %). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain O448T belongs to family Rhodobacteraceae and exhibits 16S rRNA gene sequence similarities of 94.3, 94.1 and 93.8 % to the type strains of Pontivivens insulae , Halovulum dunhuangense and Maritimibacter alkaliphilus , respectively. The major cellular fatty acid was C18 : 1ω7c and the major polar lipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. Strain O448T contained Q-10 as the sole respiratory quinone. The genomic DNA G+C content was 65.6 mol%. It is evident from phenotypic data and phylogenetic inference that strain O448T represents a novel species in a new genus, for which the name Oceanibiumsediminis gen. nov., sp. nov. is proposed. The type strain is O448T (=KCTC 62076T=MCCC 1H00233T).
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Cohaesibacter celericrescens sp. nov., isolated from sea catfish
More LessA novel Gram-stain-negative, rod-shaped, ivory-white, facultatively anaerobic and catalase-positive bacterium, designated H1304T, was isolated from the gut of sea catfish from Coast of Weihai, China. Optimal growth occurred at 30–33 °C (range, 4–37 °C) and pH 7.0–7.5 (range, pH 6.5–9.0) with 2.0–3.0 % (w/v) NaCl (range, 0.5–4.0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that H1304T belonged to the genus Cohaesibacter and was most closely related to Cohaesibactermarisflavi CGMCC 1.9157T (96.7 % 16S rRNA gene sequence similarity), Cohaesibactergelatinilyticus MCCC 1A02698T (96.3 %) and Cohaesibacterhaloalkalitolerans KCTC 32038T (96.0 %). The sole isoprenoid quinone was Q-10, the polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids (>10 %) were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The DNA G+C content of strain H1304T is 50.8 mol%. Based on the combination of phylogenetic analysis, phenotypic data and chemotaxonomic data, strain H1304T is considered to represent a novel species within the genus Cohaesibacter in the family Cohaesibacteraceae , for which the name Cohaesibacter celericrescens sp. nov. is proposed. The type strain of the new species is H1304T (=KCTC 62075T=MCCC 1H00241T).
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Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume
A Gram-stain-negative, strictly aerobic, non-motile strain, SYSUP0003T, was isolated from tubers of Gastrodia elata Blume. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSUP0003T belonged to the genus Paracoccus , with the highest sequence similarity to the type strain of Paracoccus sediminis (97.5 %). Strain SYSUP0003T grew at pH 6.0–8.0 and 4–30 °C with optimum growth at pH 7.0 and 28 °C. Strain SYSUP0003T could tolerate up to 1 % (w/v) NaCl and grew optimally in the absence of NaCl. The isoprenoid quinone of strain SYSUP0003T was Q-10. The major fatty acids were C18 : 0, C16 : 0, C10 : 0 3-OH and summed feature 7. The polar lipids were diphosphatidylglycerol (DPG), aminophospholipids (AL), phosphatidylglycerol (PG), phosphatidylcholine (PC) and four unidentified polar lipids (L). The genome size was 3 204 685 bp, with a DNA G+C content of 69.7 mol%. The average nucleotide identity values between strain SYSUP0003T and P. sediminis DSM 26170T (ANIm 84.2 %, ANIb 75.6 %), Paracoccus solventivorans DSM 6637T (ANIm 84.5 %, ANIb 76.9 %) and Paracoccus alkenifer DSM 11593T (ANIm 84.3 %, ANIb 77.3 %) were below the cut-off level (95–96 %) for species delineation. Based on phenotypic, chemotaxonomic and molecular characterizations, strain SYSUP0003T represents a novel species of the genus Paracoccus , for which the name Paracoccus endophyticus sp. nov. is proposed. The type strain is SYSUP0003T (=KCTC 62180T=CGMCC 1.16545T).
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Martelella caricis sp. nov., isolated from a rhizosphere mudflat
More LessA novel marine bacterium, designated GH2-8T, was isolated from a rhizosphere mudflat of a halophyte (Carexscabrifolia) in Gangwha Island, Republic of Korea and its taxonomic status was investigated by a polyphasic approach. Cells of strain GH2-8T were Gram-stain-negative, strictly aerobic, oxidase-positive, catalase-positive and non-motile rods that showed growth at 10–30 °C, pH 5–10 and 0–11 % (w/v) NaCl. The predominant respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and two unidentified lipids. The major fatty acids were summed feature 8, C16 : 0, C19 : 0cyclo ω8c, C18 : 1 ω7c 11-methyl and summed feature 2. The G+C content of the genomic DNA was 53.4 mol%. Comparative analysis of the 16S rRNA gene sequences revealed that the organism belonged to the order ‘ Rhizobiales ’ and formed a distinct subline at the root of radiation encompassing members of the genus Martelella . The 16S rRNA gene sequence similarities to the phylogenetic neighbours were Martelella mediterranea (97.1 %), Martelella suaedae (96.9 %), Martelella endophytica (96.6 %), Martelella limonii (96.3 %), Martelella mangrovi (96.1 %) and Martelella radicis (95.5 %). Strain GH2-8T showed low 16S rRNA gene sequence similarities (<93.8 %) to other representatives of the order ‘ Rhizobiales ’. On the basis of the results of phenotypic and phylogenetic analyses, strain GH2-8T (=KACC 19402T=KCCM 90275T=KCTC 62126T=NBRC 113213T) is considered to represent a novel species of the genus Martelella for which the name Martelella caricis sp. nov. is proposed.
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Alteromonas alba sp. nov., a marine bacterium isolated from seawater of the West Pacific Ocean
More LessA Gram-stain-negative, strictly aerobic, motile by one polar flagellum, non-spore-forming, rod-shaped bacterium, designated as 190T, was isolated from seawater of the West Pacific Ocean and subjected to a polyphasic taxonomic investigation. Colonies were 1.0–2.0 mm in diameter, smooth, circular, convex and white after growth on marine agar at 30 °C for 24 h. Strain 190T was found to grow at 4–40 °C (optimum, 30 °C), at pH 5.5–10.5 (optimum, pH 6.5) and with 0.5–12.5 % (w/v) NaCl (optimum, 2.0 %). Chemotaxonomic analysis showed the sole respiratory quinone was ubiquinone 8 (Q-8), and the major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), one unidentified aminolipid (AL1) and two unidentified glycolipids (GL1, GL2). The DNA G+C content of strain 190T was 48.7 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that strain 190T was closely related to Alteromonas oceani S35T (99.6 % sequence similarity), A. lipolytica JW12T (98.2 %), A. aestuariivivens JDTF-113T (97.7 %) and A. mediterranea DET (97.5 %); it exhibited 97.0 % or less sequence similarity with the type strains of other species with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain 190T constituted a separate branch with A. oceani , A. confluentis , A. aestuariivivens and A. lipolytica in a clade of the genus Alteromonas . OrthoANI values between strain 190T and A. oceani S35T and A. lipolytica JW12T were 93.5 and 77.9 %, respectively, and in silico DNA–DNA hybridization values were 53.8 and 21.2 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain 190T is clearly distinct from recognized species of the genus Alteromonas . On the basis of these features, we propose that strain 190T (=MCCC 1K03456T=KCTC 62227T) represents a novel species of the genus Alteromonas with the name Alteromonas alba sp. nov.
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Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil
A novel Gram-stain-negative, aerobic, rod-shaped plant growth promoting bacterium, NEAU-SY24T, was isolated from soil in Diaoshuihu, Heilongjiang, China. The isolate grew at temperatures 10–40 °C (optimum, 30 °C), pH 5–8 (optimum, pH 6) and in the presence of up to 1 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-SY24T belonged to the genus Trinickia and was closely related to Trinickia dabaoshanensis NRRL B-59553T (99.16 % similarity) and Trinickia soli DSM 18235T (99.11 %). The average nucleotide identity values between NEAU-SY24T and its most closely related species were 79.30–87.09 %. The in silico DNA–DNA hybridization values between NEAU-SY24T and T. dabaoshanensis NRRL B-59553T and T. soli DSM 18235T were 29.30 and 24.00 %, respectively, again indicating they belong to different taxa. The genomic DNA G+C content was 63.3 mol%. The major cellular fatty acids were C17 : 0cyclo, C18 : 1ω7c, C16 : 0, summed feature 2 (comprising C14 : 0 3-OH and/or C16 : 1iso I) and C16 : 0 3-OH. The predominant respiratory quinone was Q-8 and the whole-cell sugars contained ribose, glucose and galactose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and two unidentified aminolipids. On the basis of morphological, physiological, biochemical and chemotaxonomic analysis, strain NEAU-SY24T was classified as a novel species in the genus Trinickia , for which the name Trinickia diaoshuihuensis sp. nov. is proposed. The type strain is NEAU-SY24T (=DSM 106065T=CCTCC AA 2018003T).
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- Eukaryotic Micro-Organisms
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Moniliella floricola sp. nov., a species of black yeast isolated from flowers
More LessMoniliella yeasts were isolated from flower samples collected in Vietnam using an enrichment medium containing 50 % (w/w) glucose. The yeasts were identified as M. byzovii, M. dehoogii, M. megachiliensis, M. mellis, M. nigrescens and M. spathulata. A group of 20 strains representing a hitherto undescribed species of Moniliella was detected. ITS sequences indicated the presence of four genetic variants differing from each other by 4–14 nt. The strains, however, were identical in the TEF1 sequences and shared 1–2 nt differences in the D1/D2 regions. In the ITS–D1/D2 phylogenetic tree, the strains grouped together and formed a well-supported clade with insect-associated Moniliella species, including M. pollinis, M. megachiliensis and M. oedocephalis. The new group was most closely related to M. pollinis but differed from the latter by 95 nt (58 substitutions, 37 indels) in the ITS, 36 nt (31 substitutions, five indels) in the D1/D2, and 30 nt (30 substitutions) in the TEF1 sequences. Moniliella floricola sp. nov. is proposed to accommodate this group of isolates. The type strain and MycoBank number of M. floricola sp. nov. are TBY 30.1T (=CBS 12758T=NRRL Y-63660T) and MB 825274, respectively.
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Vanrija jinghongensis sp. nov., an asexual basidiomycetous yeast from rotting wood
More LessThree strains of a novel basidiomycetous yeast were isolated from the Xishuangbanna Tropical Rainforest, Yunnan Province, PR China. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions indicated that the novel species represents a member of the genus Vanrija. It differed from the most closely related known species, Vanrija albida CBS 2839T, by 1.5 % sequence divergence (seven substitutions and two gaps out of 597 bp) in the D1/D2 domains and by 7.4 % sequence divergence (17 substitutions and 20 gaps over 495 bp) in the ITS regions, respectively. The three strains of the novel species reproduced asexually, and no mating could be found. In contrast to V. albida, the novel yeast species was able to assimilate d-glucosamine, inulin, erythritol and galactitol and unable to assimilate raffinose. The name Vanrija jinghongensis sp. nov. is proposed to accommodate these strains, with NYNU 17910T (=CICC 33269=CBS 15229) as the type strain.
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Halobasidium xiangyangense gen. nov., sp. nov., a new xylose-utilizing yeast in the family Cystobasidiaceae, isolated from the pickling sauce used to make Datoucai, a high-salt fermented food
More LessIn this study, we describe a new genus and species of yeast with high-salt tolerance. The strain was isolated from the pickling sauce used to make Datoucai, a traditional fermented food made from Brassica juncea in Xiangyang, China. Phylogenetic analysis of sequences from the D1/D2 region of the LSU rRNA gene and from the ITS region demonstrated that the strain, reference HBUAS51001T, was most closely related to members of the genera Occultifur and Cystobasidium. However, the greatest similarities between the D1/D2 and ITS nucleotide sequences of strain HBUAS51001T and the most closely related type strains from Occultifur and Cystobasidium were only 91 and 92 %, respectively. This suggests that strain HBUAS51001T does not belong to any currently described species. Strain HBUAS51001T grew readily on media in which xylose was the sole carbon source. The major ubiquinone was Q9. The genome of strain HBUAS51001T was 42.42 Mb with a G+C content of 53.93 mol%. Three candidate genes associated with xylose metabolism were identified. On the basis of genotypic and phenotypic data, strain HBUAS51001T can be considered as both a new species and a new genus, for which the name Halobasidium xiangyangense gen. nov., sp. nov. is proposed. The type strain is HBUAS51001T (=KCTC27810T=GDMCC 2.231T=CCTCC AY 2018002T).
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