- Volume 67, Issue 9, 2017
Volume 67, Issue 9, 2017
- Notification List
-
- Validation List NO. 177
-
- New taxa
-
-
-
Novosphingobium clariflavum sp. nov., isolated from a household product plant
A Gram-stain-negative, rod-shaped, bright-yellow-pigmented bacterium, designated 164T, was isolated from a used sponge for equipment cleaning at a household product plant in China. The 16S rRNA gene sequence comparisons indicated that strain 164T was most closely related to Novosphingobium panipatense DSM 22890T (98.28 % similarity) and shared sequence similarities of 97.73–98.27 % with other members of the genus Novosphingobium . In DNA–DNA hybridization studies the relatedness between strain 164T and its closest phylogenetic neighbours was <70 %, which indicated that strain 164T represented a novel species of the genus Novosphingobium . The DNA G+C content of strain 164T was 65.9 mol%. The major respiratory quinone was ubiquinone Q-10 (83.5 %) with minor amounts of Q-9 (16.5 %). The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, unidentified aminolipids and unidentified aminophospholipids. Spermidine was the major polyamine. The major fatty acids were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and C14 : 0 2-OH. The results obtained from phylogenetic analysis, DNA–DNA hybridization, and chemotaxonomic and phenotypic analysis support the conclusion that strain 164T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium clariflavum sp. nov. is proposed. The type strain is 164T (=CICC 11035sT=DSM 103351T).
-
-
-
-
Rickettsia gravesii sp. nov.: a novel spotted fever group rickettsia in Western Australian Amblyomma triguttatum triguttatum ticks
A rickettsial organism harboured by Amblyomma triguttatum ticks on Barrow Island, Western Australia, was discovered after reports of possible rickettsiosis among local workers. Subsequent isolation of this rickettsia (strain BWI-1) in cell culture and analysis of its phylogenetic, genotypic and phenotypic relationships with type strains of Rickettsia species with standing in nomenclature suggested that it was sufficiently divergent to warrant its classification as a new species. Multiple gene comparison of strain BWI-1 revealed degrees of sequence similarity with Rickettsia raoultii , its closest relative, of 99.58, 98.89, 97.03, 96.93 and 95.73 % for the 16S rRNA, citrate synthase, ompA, ompB and sca4 genes, respectively. Serotyping in mice also demonstrated that strain BWI-1T was distinct from Rickettsia raoultii . Thus, we propose the naming of a new species, Rickettsia gravesii sp. nov., based on its novel genotypic and phenotypic characteristics. Strain BWI-1T was deposited in the ATCC, CSUR and ARRL collections under reference numbers VR-1664, CSUR R172 and RGBWI-1, respectively.
-
-
-
Desulfovibrio senegalensis sp. nov., a mesophilic sulfate reducer isolated from marine sediment
Several strains of sulfate-reducing bacteria were isolated from marine sediments recovered from Hann Bay (Senegal). All were related to members of the genus Desulfovibrio . A strictly anaerobic, mesophilic and moderately halophilic strain designated BLaC1T was further characterized. Cells of strain BLaC1T stained Gram-negative and were 0.5 µm wide and 2–4 µm long, motile, rod-shaped and non-spore-forming. The four major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. Growth was observed from 15 to 45 °C (optimum 40 °C) and at pH 5.5–8 (optimum pH 7.5). The salinity range for growth was 5–65 g NaCl l−1 (optimum 30 g l−1). Yeast extract was required for growth. Strain BLaC1T was able to grow on lactate and acetate in the presence of sulfate as an electron acceptor. Sulfate, thiosulfate and sulfite could serve as terminal electron acceptors, but not fumarate, nitrate or elemental sulfur. The DNA G+C content was 55.8 mol%. 16S rRNA gene sequence analysis assigned strain BLaC1T to the family Desulfovibrionaceae ; its closest relative was Desulfovibrio oxyclinae DSM 19275T (93.7 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain BLaC1T is proposed as representing a novel species of Desulfovibrio , with the name Desulfovibrio senegalensis sp. nov. The type strain is BLaC1T (=DSM 101509T=JCM 31063T).
-
-
-
Caulobacter hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower)
A Gram-stain-negative, smooth, bright yellow-pigmented, aerobic, catalase- and oxidase-positive and rod-shaped bacterial strain was isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) located in Kyung Hee University, Yongin, Gyeonggi, South Korea. Cells were dimorphic, non-motile or non-stalked, and motile by means of peritrichous flagellum. The strain, named THG-AG3.4T, grew at 15–35 °C, at pH 6.5–9.0 and in the presence of 0–1.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain THG-AG3.4T was most closely related to Caulobacter segnis ATCC 21756T (98.64 % similarity), Caulobacter vibrioides CB51T (98.57 %) and Caulobacter henricii ATCC 15253T (97.41 %). The DNA G+C content of strain THG-AG3.4T was 64.0 mol%. In DNA–DNA hybridization, the DNA–DNA relatedness between strain THG-AG3.4T and its closest phylogenetic neighbour was below 55.0 %. The predominant isoprenoid quinone detected in strain THG-AG3.4T was ubiquinone-10 (Q-10). The major polar lipids were found to be an unidentified lipid, two unidentified phosphoglycolipids, five unidentified glycolipids, eight unidentified aminolipids and phosphatidylglycerol. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Thus, based on the report of the phenotypic, genotypic and phylogenetic characterization of strain THG-AG3.4T, it has been concluded that the isolate represents a novel species of the genus Caulobacter , for which the name Caulobacter hibisci sp. nov. is proposed. The type strain is THG-AG3.4T (=KACC 18849T=CCTCC AB 2016077T).
-
-
-
Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum
A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing Mycobacterium strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus Mycobacterium and was distinguished from the type strains of closely related mycobacterial species, notably from Mycobacterium paraense DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA–DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of Mycobacterium for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).
-
-
-
Pelagibacterium lentulum sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122
A Gram-stain-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain B2T, was isolated from the culture broth of a marine microalga, Picochlorum sp. 122. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain B2T forms a robust cluster with members of the genus Pelagibacterium , and shares the highest sequence similarity of 96.80 % with Pelagibacterium halotolerans CGMCC 1.7692T. Optimal growth of strain B2T was observed at 33 °C, at pH 8 and in the presence of 1 % (w/v) NaCl. The predominant ubiquinone of strain B2T was Q-10, and the G+C content of the genomic DNA was 58.6 mol%. The major fatty acid profile comprised C18 : 1ω7c /ω6c, C19 : 0 cyclo ω8c and C16 : 0. The major polar lipids of strain B2T were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and seven unidentified lipids. Comprehensive analyses based on a polyphasic characterization of strain B2T indicated that it represents a novel species of the genus Pelagibacterium , for which the name Pelagibacterium lentulum sp. nov. is proposed. The type strain is B2T (=MCCC 1K03218T=CGMCC 1.15896T=KCTC 52551T).
-
-
-
Arsenicibacter rosenii gen. nov., sp. nov., an efficient arsenic methylating and volatilizing bacterium isolated from an arsenic-contaminated paddy soil
More LessA novel bacterium with strong arsenic (As) methylation and volatilization abilities, designated strain SM-1T, was isolated from an As-contaminated paddy soil. SM-1T is strictly aerobic, rod-shaped, non-motile, Gram-negative and orange-coloured. Phylogenetic analysis revealed that strain SM-1T showed low 16S rRNA gene sequence similarities (≤88 %) to members of established genera in the family Cytophagaceae . Growth of this strain was observed at 15–45 °C (optimum, 37 °C), pH 6.0–8.0 (optimum, 7.0) and 0–0.5 % (w/v) NaCl. The major cellular fatty acids were C16 : 1ω5c and iso-C15 : 0. The respiratory quinone was MK-7, and the predominant polar lipids were phosphatidylethanolamine, an unidentified lipid (L), and an unidentified aminolipid (AL2). The DNA G+C content was 51.5 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic properties, strain SM-1T represents a novel species in a new genus within the family Cytophagaceae , for which the name Arsenicibacter rosenii gen. nov., sp. nov. is proposed. The type strain of Arsenicibacter rosenii is SM-1T (=CCTCC AB 2017086T=KCTC 52624T).
-
-
-
Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter
Six Gram-negative, non-motile, non-spore-forming, non-pigmented, oxidase- and catalase-positive bacterial strains were deposited in 1972, in the Collection of the Institut Pasteur (CIP), Paris, France. The strains, previously identified as members of the genus Moraxella on the basis of their phenotypic and biochemical characteristics, were placed within the genus Psychrobacter based on the results from comparative 16S rRNA gene sequence studies. Their closest phylogenetic relatives were Psychrobacter sanguinis CIP 110993T, Psychrobacter phenylpyruvicus CIP 82.27T and Psychrobacter lutiphocae CIP 110018T. The DNA G+C contents were between 42.1 and 42.7 mol%. The predominant fatty acids were C18 : 1ω9c, C16 : 0, C12 : 0 3-OH, and C18 : 0. Average nucleotide identity between the six strains and their closest phylogenetic relatives, as well as their phenotypic characteristics, supported the assignment of these strains to two novel species within the genus Psychrobacter . The proposed names for these strains are Psychrobacter pasteurii sp. nov., for which the type strain is A1019T (=CIP 110853T=CECT 9184T), and Psychrobacter piechaudii sp. nov., for which the type strain is 1232T (=CIP110854T=CECT 9185T).
-
-
-
Pigmentiphaga aceris sp. nov., isolated from tree sap
More LessTwo Gram-stain-negative bacterial strains, SAP-32T and SAP-36, were isolated from sap drawn from the Acer pictum from Mount Halla in Jeju, Republic of Korea. The organisms were strictly aerobic, non-sporulating, motile rods and showed growth at 10–30 °C, pH 7–8 and with 0–2 % NaCl. The major isoprenoid quinone was Q-8. The predominant fatty acids were C16 : 0, cyclo-C17 : 0, summed feature 3 and C18 : 0. The polar lipids contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophosphoglycolipid, an unknown glycolipid, an unknown phospholipid and two unknown lipids. The DNA G+C content was 64.4 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that SAP-32T and SAP-36 formed a distinct cluster with members of the genus Pigmentiphaga within the family Alcaligenaceae . Both strains showed 16S rRNA gene sequence similarity of 100 % to each other. The closest relatives of the isolates were Pigmentiphaga daeguensis (97.08 % sequence similarity), Pigmentiphaga kullae (97.01 %) and Pigmentiphaga litoralis (96.73 %). On the basis of data from phenotypic, chemotaxonomic and phylogenetic analyses, SAP-32T (=KCTC 52619T=DSM 104039T) and SAP-36 (=KCTC 52620=DSM 104072) represent members of a novel species of the genus Pigmentiphaga , for which the name Pigmentiphaga aceris sp. nov. is proposed.
-
-
-
Polaribacter pacificus sp. nov., isolated from a deep-sea polymetallic nodule from the Eastern Pacific Ocean
A Gram-staining-negative, yellow-colony-forming, rod-shaped, non-flagellated and facultatively aerobic strain, designed HRA130-1T, was isolated from a deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone (CCFZ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HRA130-1T belonged to the genus Polaribacter (96.3–93.2 % 16S rRNA gene sequence similarity), and exhibited 94 % 16S rRNA gene sequence similarity to Polaribacter filamentus KCTC 23135T (type species) and the highest sequence similarity to Polaribacter huanghezhanensis KCTC 32516T (96.3 %). Optimal growth occurred in the presence of 4 % (w/v) NaCl, at pH 7.0 and 16 °C. The DNA G+C content of strain HRA130-1T was 35.9 mol%. The major fatty acid was iso-C15 : 0. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and an unidentified aminolipid. On the basis of data from the present taxonomic study using a polyphasic approach, strain HRA130-1T represents a novel species of the genus Polaribacter , for which the name Polaribacter pacificus sp. nov. is proposed. The type strain is HRA130-1T (=KCTC 52370T=MCCC 1K03199T=JCM 31460T=CGMCC 1.15763T).
-
-
-
Butyratibacter algicola gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122
A Gram-stain-negative, motile, non-spore-forming, ovoid or rod-shaped bacterium, designated strain B15T, was isolated from the culture broth of a marine microalga, Picochlorum sp. 122. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain B15T forms a stable cluster with Lutibaculum baratangense KCTC 22669T (95.4 % 16S rRNA gene sequence similarity), Tepidamorphus gemmatus CB-27AT (94.9 %) and Microbaculum marinum HSF11T (94.6 %) in the family Rhodobiaceae . Optimal growth of strain B15T was observed at 33 °C, pH 8–9 and in the presence of 3 % (w/v) NaCl. The only detected ubiquinone of strain B15T was Q-10, and the G+C content of the genomic DNA was 66.3 mol%. The major fatty acid profile comprised C19 : 0 cyclo ω8c, C18 : 1ω7c /ω6c and C17 : 1 iso I/anteiso B. The major polar lipids of strain B15T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two unidentified aminolipids, and one unidentified lipid. Comprehensive analyses based on polyphasic characterization of strain B15T indicated that it represents a novel species of a new genusin the family Rhodobiaceae , for which the name Butyratibacter algicola gen. nov., sp. nov. is proposed. The type strain of the type species is B15T (=KCTC 52552T=MCCC 1K03221T).
-
-
-
Conexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter
More LessA Gram-positive, strictly aerobic, non-sporulating, motile, rod-shaped bacterium, designated YC2-25T, was isolated from pieces of stalactites collected from a lava cave in Jeju, Republic of Korea. Colonies were circular, smooth, convex and cream to light yellow in colour. A neighbour-joining tree based on 16S rRNA gene sequences indicated that the organism belonged to the genus Conexibacter with the closest relatives being Conexibacter woesei (99.0 % sequence similarity) and Conexibacter arvalis (98.8 %). Meso-Diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The predominant menaquinone was MK-7(H4). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, two phospholipids and four lipids. The predominant fatty acid was C18 : 1ω9c. The DNA G+C content was 70.3 %. On the basis of distant phenotypic characteristics and DNA–DNA hybridization data, strain YC2-25T (=KCTC 39840T=DSM 103719T) represents a novel species of the genus Conexibacter , for which the name Conexibacter stalactiti sp. nov. is proposed.
-
-
-
Filimonas aquilariae sp. nov., isolated from agarwood chips
More LessA polyphasic approach was used to characterize a Gram-staining negative bacterium (designated strain CC-YHH650T) isolated from agarwood chips. Strain CC-YHH650T was aerobic and rod-shaped, able to grow at 15–37 °C (optimal 30 °С), pH 6.0–8.0 (optimal 7.0) and 0–1 % (w/v) NaCl (optimal 0 %). Phylogenetic analysis based on 16S rRNA genes revealed that strain CC-YHH650T shared highest sequence similarities with Filimonas lacunae (97.5 %), F. zeae (97.4 %), F. endophytica (97.3 %) and F. aurantiibacter (93.0 %), and lower sequence similarity with other genera (less than 93.0 %). The levels of DNA–DNA relatedness between strain CC-YTH209T, F. lacunae , F. endophytica and F. zeae were estimated to be 18.3, 6.1, 24.7 % (the reciprocal values were 9.8, 8.8, 18.3 %). The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1 ω7c/ C16 : 1 ω6c. The polar lipid profile contained phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, three unidentified aminolipids and three unidentified lipids. The DNA G+C content was 46.6 mol% and the predominant quinone was menaquinone-7 (MK-7). The major polyamine was sym-homospermidine. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-YHH650T is considered to represent a novel species of the genus Filimonas , for which the name Filimonas aquilariae sp. nov. is proposed. The type strain is CC-YHH650T (=BCRC 80935T=JCM 31197T).
-
-
-
Paenibacillus aurantiacus sp. nov., isolated from ant nest soil
More LessA Gram-stain-positive, rod-shaped and endospore-forming bacterium, strain RC11T, isolated from ant nest soil collected from Udon Thani Province, Thailand was characterized in a taxonomic study based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain RC11T was affiliated to the genus Paenibacillus and was closely related to Paenibacillus phyllosphaerae LMG 22192T with 98.1 % sequence similarity. Strain RC11T contained meso-diaminopimelic in the cell-wall peptidoglycan. The major menaquinone was MK-7. Anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and C16 : 0 were the predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. The DNA G+C content was 57.9 mol%. In addition, strain RC11T and P. phyllosphaerae LMG 22192T showed a low level of DNA–DNA relatedness (15.6–33.2 %). Therefore, strain RC11T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus aurantiacus sp. nov. is proposed. The type strain is RC11T (=KCTC 33816T=LMG 29659T=TISTR 2452T).
-
-
-
Algoriphagus aquaemixtae sp. nov., isolated from water in an estuary environment
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterium, designated strain KEM-10T, was isolated from water in an estuary environment in the Yellow Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain KEM-10T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain KEM-10T belonged to the genus Algoriphagus , joining the type strain of Algoriphagus litorisediminis showing 97.4 % sequence similarity. Strain KEM-10T exhibited 16S rRNA gene sequence similarity of 92.2–96.1 % to the type strains of the other Algoriphagus species. Strain KEM-10T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids detected in strain KEM-10T were phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain KEM-10T was 40.6 mol%. The mean DNA–DNA relatedness value between strain KEM-10T and the type strain of A. litorisediminis was 12 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain KEM-10T is separated from recognized species of the genus Algoriphagus . On the basis of the data presented, strain KEM-10T is considered to represent a novel species of the genus Algoriphagus , for which the name Algoriphagus aquaemixtae sp. nov. is proposed. The type strain is KEM-10T (=KCTC 52839T=NBRC 112780T).
-
-
-
Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil
More LessThree strains, DHOB09T, DHOC52T and DHON07T, were isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. They were all Gram-stain-negative, aerobic, rod-shaped cells. The ranges (optimum) for the temperature, pH and NaCl concentration for growth of DHOB09T, DHOC52T and DHON07T were 10–42 (25–28) °C, pH 5.5–9.0 (7.0–7.5) and 0–4.0 (0–0.5) % (w/v); 10–42 (28) °C, pH 4.0–7.0 (4.5–6.5) and 0–2.0 (0) % (w/v) and 10–37 (25–28) °C, pH 4.0–7.5 (5.5–6.0) and 0–2.5 (0) % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that DHOB09T, DHOC52T and DHON07T formed a phyletic cluster with seven species of the genus Dyella within the major clade of Dyella with sequence similarities ranged from 96.9 to 98.6 %. This indicated that the three strains may represent three novel species of the genus Dyella . This result was also strongly supported by the concatenated analysis of partial gyrB, lepA and recA gene sequences. DNA–DNA hybridization between strains DHON07T and DHOB09T, as well as DHON07T and Dyella koreensis BB4T was much lower than 70 %. The G+C content of strains DHOB09T, DHOC52T and DHON07T were 59.4, 60.7 and 59.5 %, respectively. The major fatty acids of the three strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 and the predominant respiratory lipoquinone was ubiquinone-8. All of the physiological, phylogenetic and chemotaxonomic data showed that strains DHOB09T, DHOC52T and DHON07T are distinctive from each other and from all species of the genus Dyella with validly published names. Therefore, we suggest that they represent three novel species of the genus, for which the names Dyella caseinilytica sp. nov. (type strain DHOB09T=CGMCC 1.15434T=LMG 29202T), Dyella flava sp. nov. (type strain DHOC52T=NBRC 111979T=KCTC 52128T) and Dyella mobilis sp. nov. (type strain DHON07T=CGMCC 1.15400T=NBRC 111475T) are proposed.
-
-
-
Saonia flava gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal seawater
More LessA Gram-stain-negative, aerobic, yellow-pigmented, straight rod-shaped bacterium, strain MOLA117T, was isolated from a coastal water sample from the north-western Mediterranean Sea, near Banyuls-sur-Mer, France. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, strain MOLA117T was placed within the family Flavobacteriaceae , but showed less than 93 % 16S rRNA gene sequence similarity to other recognized species within the family. The most closely related genera included Arenibacter , Cellulophaga , Maribacter and Zobellia . The only isoprenoid quinone was menaquinone MK-6 and the predominant fatty acid was iso-C17 : 0 3-OH, representing over 33 % of the total fatty acids. The DNA G+C content was 36.9 mol%. Strain MOLA117T required NaCl for growth, and did not exhibit gliding motility or produce flexirubin. Based on the phenotypic and phylogenetic data, strain MOLA117T should be considered to represent a novel species of a new genus, for which the name Saonia flava gen. nov., sp. nov. is proposed. The type strain of Saonia flava is MOLA117T (=CIP 110873T=DSM 29762T).
-
-
-
Gracilimonas halophila sp. nov., isolated from a marine solar saltern
More LessA Gram-stain-negative and facultatively anaerobic bacterium, designated WDS2C40T, was isolated from a marine solar saltern in Weihai, China. Cells of strain WDS2C40T were 0.4–0.5 µm wide and 4.0–9.0 µm long, catalase-positive and oxidase-negative. Strain WDS2C40T was tolerant to moderate salt concentrations. Growth occurred at 20–42 °C (optimum, 37–40 °C), at pH 7.0–8.5 (optimum, 7.5–8.0) and with 2–16 % (w/v) NaCl (optimum, 6–8 %). A phylogenetic analysis of the 16S rRNA gene indicated that strain WDS2C40T was a member of the genus Gracilimonas within the family Balneolaceae . The most closely related neighbour was Gracilimonas rosea JCM 18898T (95.92 % similarity). The major respiratory quinone of strain WDS2C40T was menaquinone MK-7, and the dominant fatty acids were iso-C13 : 0, iso-C15 : 0 and summed feature 3. The major polar lipids were diphosphatidylglycerol, one kind of glycolipid and two unidentified phospholipids. The genomic DNA G+C content was 41.7 mol%. Based on this polyphasic taxonomic study, strain WDS2C40T is considered to represent a novel species in the genus Gracilimonas , for which the name Gracilimonas halophila sp. nov. is proposed. The type strain is WDS2C40T (=KCTC 52042T=MCCC 1H00135T).
-
-
-
Brumimicrobium aurantiacum sp. nov., isolated from coastal sediment
More LessA Gram-negative, facultatively anaerobic, non-motile, rod-shaped and orange-coloured bacterium, designated N62T, was isolated from marine sediment of the coast of Weihai, PR China. Strain N62T was found to grow optimally at 28–30 °C, pH 7.0–7.5 and with 2.0–3.0 % (w/v) NaCl. The dominant cellular fatty acids of strain N62T were iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and iso-C17 : 1 3-OH. The major respiratory quinone was MK-6, and the DNA G+C content was 35.3 mol%. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that N62T was a member of the family Crocinitomicaceae and had a 16S rRNA gene sequence similarity of 95.8–97.2 % with recognized Brumimicrobium species. On the basis of the phylogenetic and phenotypic evidences, strain N62T represents a novel species of the genus Brumimicrobium , for which the name Brumimicrobium aurantiacum sp. nov. is proposed. The type strain is N62T (=KCTC 42589T=MCCC 1H00117T).
-
-
-
Polynucleobacter sphagniphilus sp. nov. a planktonic freshwater bacterium isolated from an acidic and humic freshwater habitat
More LessStrain MWH-Weng1-1T, isolated from an acidic freshwater habitat located in the Wenger Moor, Austria, was characterized by investigating its phenotypic, chemotaxonomic and genomic traits. Phylogenetic analyses based on 16S rRNA gene sequencing placed the strain in the cryptic species complex PnecC within the genus Polynucleobacter . The strain had a genome of 2.04 Mbp with a G+C content of 45.6 mol%. The major fatty acids of the strain were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. In order to resolve the systematic position of the strain within the species complex PnecC, concatenated partial sequences of eight housekeeping genes were used for phylogenetic analyses. The obtained trees did not place strain MWH-Weng1-1T close to any of the six previously described species within this cryptic species complex. Pairwise whole genome average nucleotide identity comparisons with genome sequences of strains representing the six previously described species of the subcluster resulted throughout in values <78 %, which clearly suggested that strain MWH-Weng1-1T (DSM 24018T=CIP 111099T) represents a novel species. We propose the name Polynucleobacter sphagniphilus sp. nov. and strain MWH-Weng1-1T as the type strain for this new species.
-
-
-
Tenacibaculum haliotis sp. nov., isolated from the gut of an abalone Haliotis discus hannai
More LessA Gram-stain-negative, non-flagellated, gliding, non-spore-forming bacterial strain, designated RA3-2T, was isolated from the gut of an abalone (Haliotis discus hannai) collected from the sea around Jeju island, South Korea, and subjected to a polyphasic taxonomic study. RA3-2T grew optimally at 20 °C and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences indicated that RA3-2T fell within the clade comprising the type strains of species of the genus Tenacibaculum , clustering with the type strains of Tenacibaculum soleae , Tenacibaculum ovolyticum and Tenacibaculum dicentrarchi ; showing 16S rRNA gene sequence similarity values of 96.2–96.8 %. The novel strain exhibited 16S rRNA gene sequence similarity values of 93.5–96.9 % to the type strains of the other species of the genus Tenacibaculum . RA3-2T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids of RA3-2T were phosphatidylethanolamine, two unidentified lipids, one unidentified aminophospholipid and one unidentified glycolipid. The DNA G+C content of RA3-2T was 31.7 mol%. The differential phenotypic properties, together with the phylogenetic data, revealed that RA3-2T is separated from other species of the genus Tenacibaculum with validly published names. On the basis of the data presented, RA3-2T is considered to represent a novel species of the genus Tenacibaculum , for which the name Tenacibaculum haliotis sp. nov. is proposed. The type strain is RA3-2T (=KCTC 52419T=NBRC 112382T).
-
-
-
Silanimonas algicola sp. nov., isolated from laboratory culture of a bloom-forming cyanobacterium, Microcystis
More LessA Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated M23T, was isolated from a laboratory culture of a bloom-forming cyanobacterium, Microcystis , which was isolated from a eutrophic lake in Korea. The strain grew optimally without NaCl and at 25–30 °C on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the genus Silanimonas , with the highest similarity to Silanimonas lenta DSM 16282T (98.5 %). DNA–DNA relatedness between strain M23T and the closely related species in the genus Silanimonas was <30 %. Strain M23T contained iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C16 : 0 as major fatty acids and ubiquinone-8 (Q-8) as the major quinone. Strain M23T contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethylethanolamine as major polar lipids. The DNA G+C content of strain M23T was 69.6 mol%. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain M23T represents a novel species in the genus Silanimonas , for which the name Silanimonas algicola sp. nov. is proposed. The type strain is M23T (=KCTC 52219T=JCM 31889T)
-
-
-
Mycobacterium aquaticum sp. nov., a rapidly growing species isolated from haemodialysis water
The characterization of five Iranian isolates, four from hospital haemodialysis water and one from the sputum of a patient, led to the detection of a novel mycobacterium species. The strains were characterized by mucoid colonies developing in 3–5 days at temperatures ranging from 25 to 37 °C. The biochemical test pattern was unremarkable while the HPLC profile of mycolic acids resembled that of Mycobacterium fortuitum . The sequences of three major housekeeping genes (16S rRNA, hsp65 and rpoB) were unique and differed from those of any other mycobacterium. Mycobacterium brisbanense , which is the species that shared the highest 16S rRNA gene sequence similarity (99.03 %), was distinct, as shown by the average nucleotide identity and by the genome to genome distance values (91.05 and 43.10 %, respectively). The strains are thus considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium aquaticum sp. nov. is proposed. The type strain is RW6T (=DSM 104277T=CIP111198T).
-
-
-
Angustibacter speluncae sp. nov., isolated from a lava cave stalactite
More LessGram-reaction-positive, strictly aerobic, motile coccoid- to rod-shaped actinobacteria, designated strains YC2-20T and YC2-19 were isolated from pieces of stalactites collected at the Yongcheon Cave in Jeju, Republic of Korea. The cells of orange-coloured colonies grew at 20–37 °C, pH 6–10 and in the absence of NaCl. In the neighbour-joining tree based on 16S rRNA gene sequences, the novel isolates formed a distant sublineage at the base of the radiation of the genus Angustibacter. The novel isolates shared identical 16S rRNA gene sequences to each other and revealed a 16S rRNA gene sequence similarity of 95.6 % to the closest relative, Angustibacter aerolatus and <95 % to other members of the family Kineosporiaceae. Albeit with a low similarity of 16S rRNA gene sequences and a distinct phylogenetic position, most of the chemotaxonomic characteristics were in agreement with those of the genus Angustibacter: meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall; MK-9(H4) as the major menaquinone; polar lipids including diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside; and a DNA G+C content of 73.1 mol%. On the basis of the phenotypic and phylogenetic distinctiveness, the novel isolates are considered to represent members of a novel species of the genus Angustibacter, for which the name Angustibacter speluncae sp. nov. is proposed, with type strain YC2-20T (=KCTC 39842T=DSM 103769T).
-
-
-
Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.
More LessThree strains (JA826T, JA912T and JA913), which were yellowish brown colour, rod to oval shaped, Gram-stain-negative, motile, phototrophic bacteria with a vesicular architecture of intracytoplasmic membranes, were isolated from different pond samples. The DNA G+C content of the three strains was between 64.6 and 65.5 mol%. The highest 16S rRNA gene sequence similarity of all three strains was with the type strains of the genus Rhodobacter sensu stricto in the family Rhodobacteraceae . Strain JA826T had highest sequence similarity with Rhodobacter maris JA276T (98.5 %), Rhodobacter viridis JA737T (97.5 %) and other members of the genus Rhodobacter (<97 %). Strain JA912T had highest sequence similarity with Rhodobacter viridis JA737T (99.6 %), Rhodobacter sediminis N1T (99.3 %), Rhodobacter capsulatus ATCC 11166T (98.8 %) and less than 97 % similarity with other members of the genus Rhodobacter . The 16S rRNA gene sequence similarity between strains JA826T and JA912T was 96.9 %. DNA–DNA hybridization showed that strains JA826T and JA912T (values among themselves and between the type strains of nearest members <44 %) did not belong to any of the nearest species of the genus Rhodobacter . However, strains JA912T and JA913 were closely related (DNA–DNA hybridization value >90 %). The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics in order to propose strains JA826T (=KCTC 15478T=LMG 28758T) and JA912T (=KCTC 15475T=LMG 28748T) as new species in the genus Rhodobacter sensu stricto with the names Rhodobacter lacus and Rhodobacter azollae, respectively.
-
-
-
Phreatobacter stygius sp. nov., isolated from pieces of wood in a lava cave and emended description of the genus Phreatobacter
More LessAn aerobic, Gram-negative, catalase-positive, oxidase-positive bacterium, designated strain YC6-17T, was isolated from pieces of wood collected at the bottom of Youngcheon Cave in Jeju, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YC6-17T formed a tight cluster with Phreatobacter oligotrophus DSM 25521T (98.1 % sequence similarity) and was distinctly separate from other taxa of the order Rhizobiales . Cells were motile rods and showed growth at 10–30 °C, pH 6–8 and 2 % NaCl. Colonies were smooth, circular, convex and pale yellow in colour. The predominant ubiquinone was Q-10. The predominant fatty acids were C18 : 1ω7c, 11-methyl-C18 : 1ω7c, summed feature 3 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two glycolipids and a lipid. The DNA G+C content was 64.4 mol%. DNA–DNA relatedness between strain YC6-17T and the closest relative was 15.6±7.9 %. Based on combined data from phenotypic characterization and DNA–DNA hybridization as well as phylogenetic analysis, it was suggested that the isolate represents a novel species of the genus Phreatobacter , for which the name Phreatobacter stygius sp. nov. is proposed. The type strain is strain YC6-17T (=KCTC 52518T=DSM 103734T).
-
-
-
Kryptousia macronema gen. nov., sp. nov. and Kryptousia microlepis sp. nov., nostocalean cyanobacteria isolated from phyllospheres
Tropical ecosystems worldwide host very diverse microbial communities, but are increasingly threatened by deforestation and climate change. Thus, characterization of biodiversity in these environments, and especially of microbial communities that show unique adaptations to their habitats, is a very urgent matter. Information about representatives of the phylum Cyanobacteria in tropical environments is scarce, even though they are fundamental primary producers that help other microbes to thrive in nutrient-depleted habitats, including phyllospheres. In order to increase our knowledge of cyanobacterial diversity, a study was conducted to characterize isolates from Avicennia schaueriana and Merostachys neesii leaves collected at a mangrove and an Atlantic forest reserve located at the littoral of São Paulo state, south-east Brazil. The morphological, ultrastructural, phylogenetic, molecular and ecological features of the strains led to the recognition of the new genus Kryptousia, comprising two new species, Kryptousia macronema gen. nov., sp. nov. and Kryptousia microlepis sp. nov., described here according to the International Code of Nomenclature for algae, fungi and plants. The new genus and species were classified in the nostocalean family Tolypotrichaceae. This finding advances knowledge on the microbial diversity of South American ecosystems and sheds further light on the systematics of cyanobacteria.
-
-
-
Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK
The novel Gram-negative, aerobic, non-motile, non-spore-forming, short-rod bacterium, strain C7T, was isolated from a seawater sample from Menai Straits (Wales, UK) and characterized. Phylogenetic analysis of 16S rRNA gene sequences showed that this strain represented a distinct lineage within the Roseobacter clade of family Rhodobacteracea within Alphaproteobacteria . The members of the genera Pontivivens ( Pontivivens insulae GYSW-23T), Celeribacter ( Celeribacter manganoxidans DY2-5T), Donghicola ( Donghicola eburneus SW-277T), Roseovarius ( Roseovarius halotolerans HJ50T and Roseovarius pacificus 81-2T), Cribrihabitans ( Cribrihabitans marinus CZ-AM5T) and Aestuariihabitans ( Aestuariihabitans beolgyonensis BB-MW15T) were the closest relatives with 16S rRNA gene sequence identities between 93.4 and 95.6 %. Strain C7T could utilize a restricted number of complex substrates with a preference for yeast extract and tryptone, which is consistent with earlier observations that peptides may serve as an important energy and carbon source for bacteria from the Roseobacter clade. Growth occurred in the absence of sodium ions. The isolate C7T is a mesophilic bacterium that optimally grows at 20 °C. The strain can grow under microaerophilic conditions. The major fatty acid was C18 : 1 cis d11. The only detected ubiquinone was Q10. The polar lipids of strain C7T were phosphatidylglycerol, two unknown aminolipids and three unknown lipids. The DNA G+C content of the strain was 60.0 mol%. Based on the results of the morphological, physiological and phylogenetic analyses, the new genus, Monaibacterium gen. nov., to include the new species Monaibacterium marinum sp. nov., is proposed. Strain C7T (=DSM 100241T, =LMG 28800T) is the type and only strain of M. marinum.
-
-
-
Arenivirga flava gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a mangrove tidal flat
More LessA novel Gram-stain-positive actinobacterium, designated HIs16-32T, was isolated from a sand sample collected from a mangrove tidal flat in Japan and its taxonomic position was investigated by a polyphasic approach. The cells of strain HIs16-32T were Gram-stain-positive, rod-shaped, non-motile and non-endospore-forming. Strain HIs16-32T contained glutamic acid, glycine and lysine in the peptidoglycan; however, alanine was absent. Galactose and mannose were detected as cell-wall sugars. The isoprenoid quinones were identified as MK-11, MK-12 and MK-10, and the major fatty acids as anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was determined to be 72.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIs16-32T was related to members of the family Microbacteriaceae but did not form a reliable cluster with any known members of the family. The highest 16S rRNA gene sequence similarity values were obtained with species of the genera Herbiconiux (96.1–96.8 %), Plantibacter (96.5–96.7 %) and Schumannella (96.7 %). However, strain HIs16-32T was distinguishable from the phylogenetically related genera in terms of chemotaxonomic characteristics and phylogenetic relationship. Therefore, strain HIs16-32T is concluded to represent a novel genus and species of the family Microbacteriaceae , for which the name Arenivirga flava gen. nov., sp. nov. is proposed. The type strain of A. flava is HIs16-32T (=NBRC 112289T=TBRC 7038T).
-
-
-
Polycladomyces subterraneus sp. nov., isolated from soil in Thailand
A thermophilic poly(L-lactide)-degrading Gram-stain-positive filamentous bacterial strain that develops single spores on the aerial mycelium was isolated from forest soil at Srinagarind Dam, Kanchanaburi Province, Thailand. The results of a polyphasic taxonomic study showed that our isolate had characteristics typical of members of the genus Polycladomyces . The isolate grew aerobically at an optimum temperature of 50–55 °C and optimal pH 6–7. Meso-diaminopimelic acid was present as the diagnostic diamino acid in the peptidoglycan but no characteristic sugars are detected. The predominant menaquinone was MK–7. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylmethylethanolamine diphosphatidylglycerol, phosphatidylglycerol and phosphatidylserine. The predominant cellular fatty acid was iso–C15 : 0. The DNA G+C content of strain KSR 13T was 53.4 mol%. The 16S rRNA gene sequence analysis also indicated that strain KSR 13T belonged to the genus Polycladomyces , being most closely related to Polycladomyces abyssicola JIR-001T (99.2 %). The DNA–DNA relatedness values that distinguished KSR 13T from P. abyssicola JIR-001T were 17.8–32.1 %, which were significantly below the 70 % cutoff value recommended for species delineation. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, the new isolate is proposed as a novel species and named Polycladomyces subterraneus sp. nov. The type strain is KSR 13T (=BCC 50740T=NBRC 109332T).
-
-
-
Phylogenetically distant clade of Nostoc-like taxa with the description of Aliinostoc gen. nov. and Aliinostoc morphoplasticum sp. nov.
More LessNostoc is a complex and tough genus to differentiate, and its morphological plasticity makes it taxonomically complicated. Its cryptic diversity and almost no distinguishable morphological characteristics make this genus incredibly heterogeneous to evaluate on taxonomic scales. The strain NOS, isolated from a eutrophic water body, is being described as a new genus Aliinostoc with the strain showing motile hormogonia with gas vesicles as an atypical feature, which is currently considered as the diacritical feature of the genus but should be subjected to critical evaluation in the near future. The phylogenetic placement of Aliinostoc along with some other related sequences of Nostoc clearly separated this clade from Nostoc sensu stricto with high bootstrap support and robust topology in all the methods tested, thus providing strong proof of the taxa being representative of a new genus which morphologically appears to be Nostoc -like. Subsequent phylogenetic assessment using the rbcL, psbA, rpoC1 and tufA genes was done with the aim of facilitating future multi-locus studies on the proposed genus for better taxonomic clarity and resolution. Folding of the 16S–23S internal transcribed spacer region and subsequent comparisons with members of the genera Nostoc , Anabaena , Aulosira, Cylindrospermum , Sphaerospermopsis, Raphidiopsis, Desmonostoc and Mojavia gave entirely new secondary structures for the D1-D1′ and box-B helix. Clear and separate clustering from Nostoc sensu stricto supports the establishment of Aliinostoc gen. nov. with the type species being Aliinostoc morphoplasticum sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants.
-
-
-
Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake
A novel halophilic archaeon, designated strain WIIAL99T, was isolated from Lake Meyghan, a hypersaline lake in Iran. Cells of strain WIIAL99T were non-motile, catalase-positive and oxidase-negative. Strain WIIAL99T required at least 2.5 M NaCl and 0.05 M MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 37–40 °C; it was able to grow at pH 6.0–8.5 and 20–55 °C. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of strain WIIAL99T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether and one unidentified glycolipid. The DNA G+C content of strain WIIAL99T was 66.7 mol%. The closest relative was Natronoarchaeum rubrum JCM 17119T with 98.2 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB′ gene sequences indicated that strain WIIAL99T is a member of the genus Natronoarchaeum in the family Halobacteriaceae and forms a distinct cluster. It was concluded that strain WIIAL99T (=IBRC-M 11062T=LMG 29814T) represents a novel species of the genus Natronoarchaeum , for which the name Natronoarchaeum persicum sp. nov. is proposed.
-
-
-
Flavobacterium gossypii sp. nov. isolated from the root tissue of field-grown cotton
More LessA yellow-pigmented bacterial strain, JM-222T, isolated from the root tissue of field-grown cotton (Gossypium hirsutum) in Auburn, Alabama, USA, was studied for its taxonomic allocation. Cells of the isolate were rod-shaped and Gram-stain-negative. A blast analysis using the EzTaxon database showed that strain JM-222T shared highest 16S rRNA gene sequence similarity with the type strain of Flavobacterium endophyticum (98.9 %) followed by Flavobacterium qiangtangense (96.7 %). 16S rRNA gene sequence similarities to all other Flavobacterium species were below 95 %. The fatty acid profile of strain JM-222T consisted of the major fatty acids C15 : 0, iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids. The quinone system consisted predominantly of menaquinone MK-6. The polyamine pattern consisted of the major compound sym-homospermidine and only minor amounts of other polyamines. These data and the differential biochemical and chemotaxonomic properties showed that the isolate JM-222T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium gossypii sp. nov. is proposed. The type strain is JM-222T (LMG 28821T=CCM 8610T).
-
-
-
Echinicola sediminis sp. nov., a marine bacterium isolated from coastal sediment
A novel Gram-stain-negative, rod-shaped, gliding bacterium, designated strain 001-Na2T, was isolated from coastal sediment of the Yellow Sea in Sindu-ri, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. Colonies were dark salmon-coloured, circular, and pulvinate with entire margins. 16S rRNA gene sequence analysis revealed that strain 001-Na2T belonged to the genus Echinicola and these species formed a distinct lineage within the family Cyclobacteriaceae . The closest phylogenetic neighbours were ‘ Echinicola shivajiensis ’ AK12T (98.1 % 16S rRNA gene sequence similarity), Echinicola vietnamensis LMG 23754T (96.4 %), Echinicola jeungdonensis HMD 3054T (96.0 %), Echinicola pacifica KMM 6172T (96.0 %) and Echinicola rosea JL 3085T (95.8 %). The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and three unidentified lipids. The DNA G+C content was 44.6 mol%. DNA–DNA relatedness between strain 001-Na2T and ‘ E. shivajiensis ’ JCM 17847T was 20.8–21.1 %. On the basis of the phenotypic features, and phylogenetic and DNA–DNA hybridization analyses presented, strain 001-Na2T (=KCTC 52495T=JCM 31786T=DSM 103729T) is the type strain of a novel species of the genus Echinicola , for which the name Echinicola sediminis sp. nov. is proposed.
-
-
-
Kodamaea neixiangensis f.a., sp. nov. and Kodamaea jinghongensis f.a., sp. nov., two yeast species isolated from rotting wood
More LessSeven strains representing two novel yeast species were isolated from rotting wood in Henan and Yunnan Provinces, PR China. The results of phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) rRNA gene revealed that these two species are members of the genus Kodamaea, although the formation of ascospores was not observed. Kodamaea neixiangensis f.a., sp. nov. (type strain NYNU 167139T=CICC 33170T=CBS 14699T) formed a clade with Candida kaohsiungensis and Candida hsintzibuensis, from which it differed by 10–16 substitutions in the D1/D2 domain. The ITS sequences of K. neixiangensis sp. nov. differed by 27 substitutions from those of the type strain of C. kaohsiungensis. The most closely related species with a validly published name to Kodamaea jinghongensis f.a., sp. nov. (type strain NYNU 167162T=CICC 33171T=CBS 14700T) was Candida fukazawae, but this differed by 14 substitutions in the D1/D2 domain and by 15 substitutions in the ITS region.
-
-
-
Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae)
More LessTwo strains (pika_113T and pika_114) of a previously undescribed Actinomyces -like bacterium were recovered from the intestinal contents of plateau pika (Ochotona curzoniae) on the Tibet-Qinghai Plateau, China. Results from biochemical characterization indicated that the two strains were phenotypically homogeneous and distinct from other previously described species of the genus Actinomyces . Based on the comparison of 16S rRNA gene sequences and genome analysis, the bacteria were determined to be a hitherto unknown subline within the genus Actinomyces , being most closely related to type strains of Actinomyces denticolens and Actinomyces timonensis with a respective 97.2 and 97.1 % similarity in their 16S rRNA gene sequences. Phylogenetic analyses confirmed that pika_113T was well separated from any other recognized species of the genus Actinomyces and within the cluster with A. denticolens and A. timonensis. The genome of strain pika_113T displayed less than 42 % relatedness in DNA–DNA hybridization with all the available genomes of existing species of the genus Actinomyces in the NCBI database. Collectively, based on the phenotypic characteristics and phylogenetic analyses results, we propose the novel isolates as representatives of Actinomyces gaoshouyii sp. nov. The type strain of Actinomyces gaoshouyii is pika_113T (=CGMCC 4.7372T=DSM 104049T), with a genomic DNA G+C content of 71 mol%.
-
-
-
Rhodopseudomonas telluris sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil
More LessA strain of anoxygenic phototrophic bacteria isolated from paddy soil (designated strain TUT3615T) was studied taxonomically in comparison with Rhodopseudomonas strain ATCC 17005 as its nearest phylogenetic relative. Strains TUT3615T and ATCC 17005 had budding rod-shaped cells and showed in vivo absorption maxima at 804 and 860 nm in the near infrared region, indicating the presence of bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3615T and ATCC 17005 had a 99.7 % level of similarity to one another and were closest to Rhodopseudomonas palustris ATCC 17001T (98.6 % similarity) among the established species of the genus Rhodopseudomonas . Genomic DNA–DNA hybridization studies revealed that strains TUT3615T and ATCC 17005 had an average similarity level of 65 % to one another and of less than 40 % to the available type strains of Rhodopseudomonas species. Results of phenotypic studies showed that strains TUT3615T and ATCC 17005 could be differentiated from one another and from any previously described species of Rhodopseudomonas . The G+C contents of the genomic DNA of strain TUT3615T and ATCC 17005 were 66.3 and 66.5 mol%, respectively. Based on these data, we propose the name Rhodopseudomonas telluris sp. nov. for strain TUT3615T. The type strain is TUT3615T (=KCTC 23279T=NBRC 107609T). We suspend a proposal to reclassify strain ATCC 17005 as a novel species or subspecies until a genome-wide analysis provides more definite information on its taxonomic position.
-
-
-
Mabikibacter ruber gen. nov., sp. nov., a bacterium isolated from marine sediment, and proposal of Mabikibacteraceae fam. nov. in the class Alphaproteobacteria
More LessBacterial strain YP382-1-AT was isolated from marine sediment at Gimnyeong Beach, Jeju Island, Republic of Korea. This strain was found to be aerobic and Gram-stain-negative, with red to purple pigmentation. Cells of strain YP382-1-AT were motile, had a single polar flagellum and were short rod-shaped. The predominant quinone in strain YP382-1-AT was Q-10. The major fatty acid was C18 : 1ω7c and the DNA G+C content was 60.3 mol%. Phylogenetic analysis based on comparisons of 16S rRNA gene sequences showed that strain YP382-1-AT belonged to the order Rhizobiales in the class Alphaproteobacteria . This strain exhibited very low 16S rRNA gene sequence similarity (no higher than 94.5 %) to the type strains of recognized bacterial species of the order Rhizobiales . Strain YP382-1-AT appeared as a distinct branch within Rhizobiales in the phylogenetic tree generated. On the basis of the data presented, strain YP382-1-AT is considered to represent a novel species of a new genus, classified within a new family. The name Mabikibacter ruber gen. nov., sp. nov., of the new family Mabikibacteraceae fam. nov. is proposed. The type strain of Mabikibacter ruber is YP382-1-AT (=JCM 31727T=KCCM 90265T).
-
-
-
Prauserella oleivorans sp. nov., a halophilic and thermotolerant crude-oil-degrading actinobacterium isolated from an oil-contaminated mud pit
A crude-oil-degrading, Gram-stain-positive actinobacterial strain, RIPIT, was isolated from a soil sample collected from an oil-contaminated mud pit in Khangiran oil and gas field, in the north-east of Iran. RIPIT was strictly aerobic, catalase- and oxidase-positive. The strain grew with 0–12.5 % (w/v) NaCl (optimum 3–5 %), at 25–55 °C (optimum 45 °C) and at pH 6.0–9.5 (optimum pH 7.0). The results of 16S rRNA gene sequence comparative analysis indicated that RIPIT represents a member of the genus Prauserella , with high phylogenetic similarity to Prauserella coralliicola SCSIO 11529T (97.5 %), Prauserella endophytica SP28S-3T (97.5 %) and Prauserella marina MS498T (97.2 %). DNA–DNA relatedness values between the novel strain and P. coralliicola DSM 45821T, P. endophytica DSM 46655T and P. marina DSM 45268T were 28 , 19 and 23 %, respectively. The cell wall peptidoglycan of RIPIT contained meso-diaminopimelic acid as the diamino acid and the whole-cell sugars are galactose and arabinose. The polar lipids pattern contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. Its cellular fatty acids pattern consisted of C17 : 1ω6c, iso-C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 69 mol%. On the basis of polyphasic taxonomic data we propose that RIPIT represents a novel species of the genus Prauserella , for which the name Prauserella oleivorans sp. nov. is proposed. The type strain of Prauserella oleivorans is RIPIT (=IBRC-M 10906T=LMG 28389T).
-
-
-
Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil
Little is known on members of the genus Amycolatopsis inhabiting acidic habitats. In this study, a moderately acidophilic Amycolatopsis strain, designated 2-5T, was isolated from coal mine soil, and subjected to a polyphasic taxonomic characterization. Analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the type strain of Amycolatopsis bartoniae , sharing 99.30 % similarity, while similarity to all other Amycolatopsis species was less than 97 %. The DNA–DNA relatedness between the new isolate and the type strain of A. bartoniae was 56.5±0.7 %. The optimal pH range of the isolate for growth was 5.5–6.0, but growth also occurred at pH 4.5 and 7.5. The isolate tolerated up to 6 % (w/v) NaCl (optimum, 0 %), and the temperature range for growth was 15–40 °C (optimum, 30 °C). The isolate was able to utilize most substrates tested for sole carbon sources, showing its metabolic versatility. The isolate exhibited antimicrobial activity against Serratia marcescens and weak antifungal activity against Fusarium proliferatum. The chemotaxonomic profiles of strain 2-5T included polar lipids containing phosphatidylethanolamine, phsphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol dimannosides, fatty acids containing C17 : 1ω6c and iso-C16 : 0 as the major components, MK-9(H4) as the predominant menaquinone, and meso-diaminopimelic acid and arabinose, galactose, glucose and ribose as the diagnostic diamino acid and sugars in the cell wall. The combined phenotypic, chemotaxonomic and genotypic analyses clearly indicated that the isolate merits recognition as represnting a novel species of Amycolatopsis , for which the name Amycolatopsis acidiphila sp. nov. is proposed. The type strain is 2-5T (=KCTC 39523T=JCM 30562T).
-
-
-
Lysinimicrobium sediminis sp. nov., an actinobacterium isolated from estuary sediment
More LessA novel Gram-stain-positive actinobacterium, designated HT7-17T, was isolated from a sediment sample collected from the estuary of the Tama River, Japan, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HT7-17T was closely related to members of the genus Lysinimicrobium , with a similarity range of 97.1–98.2 %. The peptidoglycan type of strain HT7-17T was A4α, the predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content was 69.9 mol%. These chemotaxonomic features corresponded to those of the genus Lysinimicrobium . Meanwhile, the differences in some phenotypic characteristics, along with the result of DNA–DNA hybridization, indicated that strain HT7-17T should be distinguished from the recognized species of the genus Lysinimicrobium . Therefore, strain HT7-17T represents a novel species of the genus Lysinimicrobium , for which the name Lysinimicrobium sediminis sp. nov. is proposed. The type strain is HT7-17T (=NBRC 112286T=TBRC 7037T).
-
-
-
Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula
A novel coccus-shaped, Gram-stain-positive, non-motile and facultative aerobic bacterium, designated strain D7T301T, was isolated from the small intestine of a marten, Martes flavigula, which was killed on the road in Pocheon-si, Gyeonggi-do, Republic of Korea. Grown on a tryptic soy yeast agar plate, colonies had a creamy colour and irregular form. The new isolate formed a monophyletic clade with Vagococcus penaei CD276T on a phylogenetic consensus tree based on the 16S rRNA gene sequence. The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5 % (w/v) NaCl. The isolate was catalase- and oxidase-negative. The cell-wall peptidoglycan was type A4α l-Lys-d-Asp. The major cellular fatty acids were C16 : 0, C14 : 0, and C16 : 1 ω9c. The predominant respiratory quinone was menaquinone MK-7 (85.1 %). The DNA G+C content based on genome sequencing was 33.8 mol%. The average nucleotide identity value obtained from comparative genomic analysis between strain D7T301T and V. penaei CIP 109914T was 72.6 %. On the basis of the phenotypic, phylogenetic, biochemical, chemotaxonomic, and genotypic analyses, Vagococcus martis is proposed as a novel species of the genus Vagococcus . The type strain is D7T301T (=KCTC 21069T=JCM 31178T).
-
-
-
Description of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligately anaerobic bacterium isolated from coastal marine sediments, and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov.
More LessAn obligately anaerobic spirochaete (strain SY2T) was isolated from coastal marine sediments of Tongyeong-Si, South Korea. Strain SY2T was helical-shaped and Gram-stain-negative. Strain SY2T was able to grow at 10–40 °C (optima, 25–30 °C), pH 6.3–8.8 (optima, pH 7.0–8.0) and with 1–7 % (optimum, 2–3 %) NaCl concentration. Strain SY2T was negative for catalase and oxidase activity. The major end-products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. C14 : 0, C16 : 0, iso-C15 : 0, iso-C14 : 0 3-OH, iso-C15 : 1 H/C13 : 0 3-OH and iso-C17 : 1ω9c were predominant fatty acids (>5 %) with minor amounts (<5 %) of C18 : 0, iso-C13 : 0, iso-C17 : 0, iso-C17 : 1/anteiso-C17 : 1 B and C16 : 1ω6c/C16 : 1ω7c. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were major polar lipids. The genomic DNA G+C content was 53.5 mol%. 16S rRNA gene sequence comparisons indicated that strain SY2T represents a member of the family Spirochaetaceae in the phylum Spirochaetes . Strain SY2T has a sequence similarity of 95.1 % with Spirochaeta litoralis R1T and <90.1 % with other members of the genus Spirochaeta . Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain SY2T as a representative of a novel genus and species in the family Spirochaetaceae , for which the name Oceanispirochaeta sediminicola gen. nov., sp. nov. is proposed. The type strain is SY2T (=KEMB 3001-381T=DSM 104770T=KCTC 15593T). Reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov. is also proposed based on polyphasic taxonomic analyses.
-
-
-
Altererythrobacter aquiaggeris sp. nov., isolated from water of an estuary bank
More LessA Gram-stain-negative, oval- or short-rod-shaped and non-motile bacterial strain, designated KEM-3T, was isolated from water of Geumgang Estuary Bank, South Korea, and was subjected to a polyphasic taxonomic study. Strain KEM-3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3% (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain KEM-3T fell within the clade comprising Altererythrobacter species, clustering with Altererythrobacter confluentis KEM-4T and Altererythrobacter gangjinensis KJ7T, with which it exhibited 97.3 and 96.0 % sequence similarity, respectively. The 16S rRNA gene sequence similarity values between strain KEM-3T and the type strains of other Altererythrobacter species were 92.9–95.2 %. The DNA G+C content of strain KEM-3T was determined to be 59.0 mol% and its mean DNA–DNA relatedness with A. confluentis KEM-4T was 8.6±3.1 %. Strain KEM-3T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18:1ω7c and/or C18:1ω6c), C17:1ω6c and summed feature 3 (C16:1ω6c and/or C16:1ω7c) as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, a sphingoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain KEM-3T is distinguishable from other Altererythrobacter species. On the basis of the data presented, strain KEM-3T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter aquiaggeris sp. nov. is proposed. The type strain is KEM-3T (=KCTC 52471T=NBRC 112425T).
-
-
-
Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs
Sixteen isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from Sphagnum bogs in West Virginia and Maine, USA. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genome sequencing of two isolates, IIBBL 14B-1T and IIBBL 37-2 (from West Virginia and Maine, respectively), revealed highly similar genomic sequences. The average nucleotide identity (gANI) calculated for these two isolates was found to be in excess of 99 %, but did not exceed 88 % when comparing either isolate with genomic sequences of Chromobacterium violaceum ATCC 12472T, C. haemolyticum DSM 19808T, C. piscinae ND17, C. subtsugae PRAA4-1T, C. vaccinii MWU205T or C. amazonense CBMAI 310T. Collectively, gANI and 16S rRNA gene sequence comparisons suggested that isolates IIBBL 14B-1T and IIBBL 37-2 were most closely related to C. subtsugae , but represented a distinct species. We propose the name Chromobacterium sphagni sp. nov. for this taxon; the type strain is IIBBL 14B-1T (=NRRL B-67130T=JCM 31882T).
-
-
-
Marinicauda algicola sp. nov., isolated from a marine red alga Rhodosorus marinus
More LessAn aerobic Gram-stain-negative prosthecate bacterium, designated RMAR8-3T, was isolated from a marine red alga Rhodosorus marinus in the Republic of Korea. Cells were dimorphic rods with a single polar prostheca (non-motile) or flagellum (motile) showing catalase- and oxidase-positive reactions. Growth of strain RMAR8-3T was observed at 15–45 °C (optimum, 40 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–10 % (w/v) NaCl (optimum, 2 %). Ubiquinone-10 was detected as the sole isoprenoid quinone and C18 : 0, summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1ω6c), C17 : 0, C12 : 0 3-OH and C16 : 0 were identified as the major cellular fatty acids. The major polar lipids were sulfo-quinovosyldiacylglycerol, glucuronopyranosyldiglyceride and monoglycosyldiglyceride. The G+C content of the genomic DNA was 66.3 mol%. Strain RMAR8-3T was most closely related to Marinicauda pacifica P-1 km-3T with a 97.6 % 16S rRNA gene sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain RMAR8-3T formed a tight phylogenic lineage with M. pacifica P-1 km-3T within the family Hyphomonadaceae . On the basis of phenotypic, chemotaxonomic and molecular features, strain RMAR8-3T clearly represents a novel species of the genus Marinicauda , for which the name Marinicauda algicola sp. nov. is proposed. The type strain is RMAR8-3T (=KACC 18990T=JCM 31718T).
-
-
-
Oceanospirillum sanctuarii sp. nov., isolated from a sediment sample
More LessA novel Gram-staining-negative, spiral-shaped, pale-yellow, non-sporulating, motile, aerobic bacterium, designated strain AK56T, was isolated from a sediment sample collected at the Coringa Wildlife Sanctuary, India. Colonies on marine agar were circular, pale yellow, shiny, translucent, 1–2 mm in diameter, convex and had an entire margin. The major fatty acids included C16 : 1, C16 : 1 ω7 c/C16 : 1ω6c and C18 : 1ω7c. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and five unidentified lipids. DNA–DNA hybridization between strain AK56T and Oceanospirillum linum LMG 5214T and ‘ Oceanospirillum nioense ’ NIO-S6 showed relatedness values of 39.91 and 23.62 %, respectively. The DNA G+C content of strain AK56T was found to be 50.3 mol%. A sequence similarity search for the 16S rRNA gene sequence revealed that O. linum and O. nioense were the nearest phylogenetic neighbours, with a pair-wise sequence similarity of 98.9 and 98.2 %, respectively. Phylogenetic analysis also showed the formation of a cluster including strain AK56T with close relative O. linum and O. nioense . Based on the observed phenotypic, chemotaxonomic characteristics and phylogenetic analysis, strain AK56T is described in this study as a novel species in the genus Oceanospirillum , for which the name Oceanospirillum sanctuarii sp. nov. is proposed. The type strain of Oceanospirillum sanctuarii is AK56T (=MTCC 12005T=JCM 19193T=KCTC 52973T).
-
-
-
Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant
An aerobic, Gram-stain-negative, non-spore-forming, non-flagellated, rod-shaped or filamentous bacterial strain, T16R-86T, was isolated from rhizosphere of a tomato plant collected from a farm on Buyeo-gun, Chungcheongnam-do, South Korea. It grew at the temperature range 10–37 °C (optimum, 28 °C) and pH range 6.0–9.0 (optimum, pH 7.0), and tolerated up to 2 % (w/v) NaCl. According to 16S rRNA gene sequence analysis, strain T16R-86T shared the highest similarity with Chitinophaga barathri YLT18T (96.8 %) and C. pinensis DSM 2588T (96.7 %), forming a subcluster with C. barathri YLT18T, C. cymbidii R156-2T and C. niabensis JS13-10T in the phylogenetic tree. The major fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone MK-7. Polar lipids were phosphatidylethanolamine, five unknown aminolipids, an unknown aminophospholipid, one unknown phospholipid and two unknown lipids. The DNA G+C content was 53.6 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain T16R-86T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga rhizosphaerae sp. nov. is proposed. The type strain is T16R-86T (=KACC 18790T=JCM 31600T).
-
-
-
Swionibacillus sediminis gen. nov., sp. nov., a member of the family Bacillaceae isolated from ocean sediment
More LessA Gram-stain-negative, non-motile, strictly aerobic bacterium designated BW11-2T was isolated from marine sediment of the south-west Indian Ocean. Cells of BW11-2T were rod-shaped, endospore-forming, 0.3–0.5 µm wide, 1.8–2.0 µm long, catalase-positive and oxidase-negative. The isolate was capable of growing at 15–45 °C (optimum 30 °C), pH 5–9 (optimum 7) and with 0.5–10 % (w/v) NaCl (optimum 3 %). Based on 16S rRNA gene sequence similarities, BW11-2T was shown to belong to the family Bacillaceae within the phylum Firmicutes and formed a distinct lineage, showing the highest sequence similarities to closely related genera: Bacillus (93.9–94.7 %), Graci libacillus (93.3–93.7 %), Amphibacillus (93.5 %), Virgibacillu s (92.9–93.1 %) and Anaerobacillus (92.6–93.0 %). BW11-2T shared the highest 16S rRNA gene sequence similarity with the species Bacillus oleronius (94.7 %). The predominant fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The major quinone was menaquinone-7 (MK-7). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified aminolipid. The genomic DNA G+C content of strain BW11-2T was 43.3 mol%. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, strain BW11-2T represents a novel genus and species in the family Bacillaceae , for which the name Swionibacillus sediminis gen. nov., sp. nov. is proposed. Strain BW11-2T (=CICC 24196T=JCM 31924T) is the type strain.
-
-
-
Altererythrobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated JSSK-8T, was isolated from the place where the ocean and a freshwater spring meet at Jeju Island, South Korea. Strain JSSK-8T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2.0 % (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain JSSK-8T fell within the clade comprising the type strains of species of the genus Altererythrobacter . Strain JSSK-8T exhibited 16S rRNA gene sequence similarity values of 97.7 and 97.2 % to the type strains of Altererythrobacter aestiaquae and Altererythrobacter luteolus , respectively, and of 93.5–96.2 % to the type strains of the other species of the genus Altererythrobacter . Strain JSSK-8T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c, C16 : 0 and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids detected in strain JSSK-8T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain JSSK-8T was 59.0 mol%, and its mean DNA–DNA relatedness values with the type strains of A . aestiaquae and A . luteolus were 13 and 16 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain JSSK-8T is separated from recognized species of the genus Altererythrobacter . On the basis of the data presented, strain JSSK-8T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter aquaemixtae sp. nov. is proposed. The type strain is JSSK-8T (=KCTC 52763T=NBRC 112764T).
-
-
-
Lactobacillus cerevisiae sp. nov., isolated from a spoiled brewery sample
More LessA Gram-stain-positive, non-motile, rod-shaped bacterium, designated TUM BP 140423000-2250T (=DSM 100836T=LMG 29073T), was isolated from spoiled beer. This bacterium did not form spores, and was catalase-negative and facultatively anaerobic. Its taxonomic position was determined in a polyphasic study. The 16S rRNA gene sequence similarity data showed that the strain belonged to the Lactobacillus genus with the nearest neighbours being Lactobacillus koreensis DCY50T (sequence similarity 99.5 %), Lactobacillus yonginensis THK-V8T (99.2 %) and Lactobacillus parabrevis LMG 11984T (98.7 %). Sequence comparisons of additional phylogenetic markers, pheS and rpoA, confirmed the 16S rRNA gene sequence tree topology. The maximum rpoA sequence similarity was 92.3 % with L. yonginensis THK-V8T. The DNA G+C content of the isolate was 50.0 mol%. The DNA–DNA relatedness showed that strain TUM BP 140423000-2250T could be clearly distinguished from L. koreensis DCY 50T (30.8±0.4 %) and L. yonginensis THK-V8T (23.6±5.9 %). The major fatty acids were C18 : 1ω9c, summed feature 7 (comprised of C19 : 0 cyclo ω10c/C19 : 1ω6c) and C16 : 0. Based on phenotypic and genotypic studies, the authors propose classifying the new isolate as a representative of a novel species of the genus Lactobacillus , Lactobacillus cerevisiae sp. nov. The type strain is deposited at the Research Centre Weihenstephan for Brewing and Food Quality as TUM BP 140423000-2250T (=DSM 100836T=LMG 29073T).
-
-
-
Sulfurivermis fontis gen. nov., sp. nov., a sulfur-oxidizing autotroph, and proposal of Thioprofundaceae fam. nov.
More LessA novel Gram-stain-negative, chemolithoautotrophic sulfur oxidizer, strain JG42T, was isolated from a hot spring microbial mat. As an electron donor for autotrophic growth, strain JG42T utilized sulfide, thiosulfate, tetrathionate and elemental sulfur. Cells of strain JG42T were oxidase-positive and catalase-negative. The G+C content of the genomic DNA was 65 mol%. The predominant cellular fatty acid was C16 : 0. Phylogenetic analysis of the 16S rRNA gene indicated that strain JG42T belonged to the order Chromatiales , but sequence similarities to the known species were less than 94 %. On the basis of its properties, strain JG42T (=DSM 104776T=NBRC 112696T) is proposed as the type strain of a novel species of a new genus, Sulfurivermis fontis gen. nov., sp. nov., which belongs to the family Thioalkalispiraceae. A new family, Thioprofundaceae fam. nov., is also proposed to accommodate the genus Thioprofundum , transferred from the family Thioalkalispiraceae .
-
-
-
Amylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi
Dandan Wang, Yuxi Wei, Qiu Cui and Wenli LiA Gram-stain-negative, non-motile, aerobic and rod-shaped bacterial strain, designated H-12T, was isolated from a sea squirt (Ciona savignyi) collected from Tsingtao Port, Jiaozhou Bay, China, and its taxonomic position was investigated. Strain H-12T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of 3.0–4.0 % (w/v) NaCl. The 16S rRNA gene sequence of strain H-12T exhibited the highest similarity to that of the type strain of Amylibacter marinus (95.3 %). A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain H-12T clustered with the type strain of A. marinus . The predominant ubiquinone in strain H-12T was identified as Q-10. The major fatty acids of strain H-12T were C18 : 1ω7c and C18 : 1ω7c 11-methyl. The major polar lipids detected in strain H-12T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The DNA G+C content of strain H-12T was 52.7 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic properties, strain H-12T is considered to represent a novel species within the genus Amylibacter , for which the name Amylibacter cionae sp. nov. is proposed. The type strain is H-12T (=KCTC 52581T=CGMCC 1.15880T).
-
-
-
Nocardia heshunensis sp. nov., an actinomycete isolated from soil
A novel Gram-stain-positive, aerobic, non-motile and acid-fast actinomycete strain, designated CFH S0067T, was isolated from a soil sample collected from Heshun old town in Tengchong, Yunnan province, in south-west PR China. The taxonomic position of strain CFH S0067T was studied in detail using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain CFH S0067T belongs to the genus Nocardia and is closely related to Nocardia concava JCM 12351T (99.3 % similarity), forming a separated branch with this type strain. However, the strain shared 96.0 % gyrB gene sequence similarity with N. concava JCM 12351T. Furthermore, DNA–DNA hybridization showed 56.5±0.6 % DNA relatedness between the novel strain and N. concava JCM 12351T. The whole-cell hydrolysates contained meso-diaminopimelic acid (type IV) and arabinose, galactose, fructose and mannose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. Strain CFH S0067T contained MK-8 (H4ω-cycl) as the predominant menaquinone. C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω9c and C18 : 0 10-methyl (TBSA) were the major cellular fatty acids. Mycolic acids were also detected. The G+C content of the genomic DNA was determined to be 66.9 mol%. A combination of the low DNA–DNA hybridization values and phenotypic properties demonstrated that strain CFH S0067Tis clearly distinguishable from its most closely related strain, N. concava JCM 12351T. On the basis of this polyphasic study, it is concluded that strain CFH S0067T should be considered to represent a novel species of the genus Nocardia , for which the name Nocardia heshunensis sp. nov. is proposed. The type strain is CFH S0067T (=DSM 46764T=JCM 30085T).
-
-
-
Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a thermophilic, chemolithoautotrophic bacterium capable of respiratory ammonification of nitrate with elemental sulfur
An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain ST65T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the south-western Pacific Ocean, at a depth of 1870 m. Cells of strain ST65T were non-motile straight or slightly curved short rods, 0.5–0.6 µm in diameter and 0.8–1.5 µm in length. The temperature range for growth was 47–75 °C, with an optimum at 65 °C. The pH range for growth was 5.5–7.5, with an optimum at pH 6.5. Growth of strain ST65T was observed at NaCl concentrations ranging from 1.5 to 4.5 % (w/v), with an optimum at 2.0–2.5 %. Strain ST65T grew anaerobically with inorganic carbon as a carbon source and with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. It was also able to grow by disproportionation of elemental sulfur, thiosulfate and sulfite. Sulfate was not utilized as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to a deep lineage in the phylum Thermodesulfobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents a novel species of a new genus, Thermosulfuriphilus ammonigenes gen. nov., sp. nov. ST65T (=DSM 102941T=VKM B-2855T) is the type strain of the type species.
-
-
-
Puniceibacterium confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Puniceibacterium
More LessA Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated JSSK-17T, was isolated from the place where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain JSSK-17T 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, showed that strain JSSK-17T clustered with the type strains of Puniceibacterium antarcticum and Puniceibacterium sediminis , exhibiting sequence similarities of 98.1–98.2 %. Strain JSSK-17T and the type strains of P. antarcticum and P. sediminis contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The predominant polar lipids detected in strain JSSK-17T and the type strains of P. antarcticum and P. sediminis were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid and one unidentified phospholipid. The DNA G+C content of strain JSSK-17T was 64.4 mol% and its DNA–DNA relatedness values with the type strains of P. antarcticum and P. sediminis were 24 and 15 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain JSSK-17T is separated from the two reference species of the genus Puniceibacterium with validly published names . On the basis of the data presented, strain JSSK-17T is considered to represent a novel species of the genus Puniceibacterium , for which the name Puniceibacterium confluentis sp. nov. is proposed. The type strain is JSSK-17T (=KCTC 52765T=NBRC 112766T).
-
-
-
Chitinophaga sedimenti sp. nov., isolated from sediment
Na Li, Tao Chen, Dan Cheng, Xun-Jun Xu and Jian HeA bacterial strain designated TFL-3T was isolated from sediment of the Yangtze River in Nanjing, Jiangsu province, China. Strain TFL-3T was Gram-staining-negative, non-spore-forming, rod-shaped and non-motile. Growth occurred at 10–40 °C (optimum 30 °C). Strain TFL-3T grew at pH 6.0–9.0 (optimum pH 7.0) and NaCl concentrations of 0–2.5 % (optimum 0.5 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain TFL-3T belonged to the genus Chitinophaga and showed the highest sequence similarity to Chitinophaga barathri YLT18T (94.9 %). The DNA G+C content of strain TFL-3T was determined as 50.5±1.0 mol%. The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1 ω5c and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant respiratory ubiquinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids and seven unidentified lipids. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain TFL-3T represents a novel species in the genus Chitinophaga , for which the name Chitinophaga sedimenti sp. nov. is proposed. The type strain is TFL-3T (=ACCC 19966T=KCTC 52590T).
-
-
-
Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil
An alkaliphilic and moderately halophilic strain characterized by optimal growth at pH 9.0–10.0 and 7 % (w/v) NaCl, and designated B16-24T, was isolated from the rhizosphere soil of the bayonet grass Bolboschoenus maritimus at a soda pond in the Kiskunság National Park, Hungary. Cells of the strain were Gram-staining-positive, non-motile, straight rods, and formed central, ellipsoidal endospores with slightly swollen sporangia. The isolate was facultative anaerobic, catalase positive, oxidase negative, and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 the major cellular fatty acid. The DNA G+C content of strain B16-24T was 36.6 mol%. The 16S rRNA gene-based phylogenetic analysis revealed that the novel isolate had the greatest similarities to the type strains of Bacillus okhensis Kh10-101T (97.8 %), B. akibai 1139T (97.4 %), B. alkalisediminis K1-25T (97.3 %) and B. wakoensis N-1T (97.1 %). The DNA–DNA relatedness of strain B16-24T and the closely related Bacillus species ranged between 24±6 % and 35±3 %. The distinctive phenotypic and genetic results of this study confirmed that strain B16-24T represents a novel species within the genus Bacillus , for which the name Bacillus kiskunsagensis sp. nov. is proposed. The type strain is B16-24T (=DSM 29791T=NCAIM B.02610T).
-
-
-
Reyranella aquatilis sp. nov., an alphaproteobacterium isolated from a eutrophic lake
A novel Gram-stain-negative, rod-shaped and non-motile bacterial strain, designated strain Seoho-37T, was isolated from a eutrophic lake in South Korea. Polyphasic studies were performed to investigate the taxonomic position of the new isolate. The isolate grew aerobically with 0–1.0 % (w/v) NaCl (optimum 0 %), at pH 6.0–10.0 (optimum pH 7.0–9.0) and at temperatures of 15–36 °C (optimum 25–30 °C) on R2A medium. In the phylogenetic analysis of 16S rRNA gene sequences, strain Seoho-37T formed a clear cluster with the strains of Reyranella graminifolii , Reyranella massiliensis and Reyranella soli with a bootstrap resampling value of 100 %. DNA–DNA relatedness between strain Seoho-37T and the type strains of each species in the genus Reyranella was <20 %. The genomic DNA G+C content of strain Seoho-37T was 66.5 mol%. Ubiquinone-10 (Q-10) and ubiquinone-9 (Q-9) were found as the respiratory quinones. The cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylmethylethanolamine. The major fatty acid components included C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C18 : 1 2-OH. Based on the above evidence from a polyphasic study, strain Seaho-37T represents a novel species of the genus Reyranella , for which the name Reyranella aquatilis sp. nov. is proposed. The type strain is Seoho-37T (=KCTC 52223T=JCM 31892T).
-
-
-
Planktotalea arctica sp. nov., isolated from Arctic seawater
More LessA Gram-staining-negative, non-motile, non-pigmented, rod-shaped bacterium was isolated from an Arctic coastal seawater sample and was designated strain IMCC9565T. Analysis of the 16S rRNA gene sequence of strain IMCC9565T revealed that the closest phylogenetic neighbours of the strain were members of the genus Planktotalea . Furthermore, the strain formed a robust clade with Planktotalea frisia SH6-1T, with which it shared 97.9 % 16S rRNA gene sequence similarity. Determination of genomic relatedness based on average nucleotide identity and genome-to-genome distance showed that strain IMCC9565T was distantly related to P. frisia , meaning the Arctic strain represents a novel species. Optimum growth of strain IMCC9565T was observed at 20 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and the major polar lipids consisted of phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified lipids. The principal fatty acids were C18 : 1ω7c and/or C18 : 1ω6c, C18 : 1ω7c 11-methyl and C16 : 0, and the DNA G+C content was 57.1 mol%. Based on these data, Planktotalea arctica sp. nov. is proposed to accommodate the bacterial isolate and the type strain is IMCC9565T (=KACC 18009T=NBRC 110393T).
-
-
-
Vibrio palustris sp. nov. and Vibrio spartinae sp. nov., two novel members of the Gazogenes clade, isolated from salt-marsh plants (Arthrocnemum macrostachyum and Spartina maritima)
Two bacterial strains, EAod9T and SMJ21T, isolated from salt-marsh plants, were determined to be related to species of the genus Vibrio from from 16S rRNA sequence comparisons. Their closest phylogenetic relatives are members of the Gazogenes clade, Vibrio mangrovi and Vibrio rhizosphaerae , which show the greatest similarity to the SMJ21TrRNA sequence (97.3 and 97.1 %, respectively), while EAod9T had less than 97.0 % similarity to any other species of the genus Vibrio . Both strains share the basic characteristics of the genus Vibrio , as they are Gram-stain negative, motile, slightly halophilic, facultatively anaerobic bacteria. In addition, they are oxidase-negative and unable to grow on TCBS Agar; they grow between 15 to 26 °C, pH 6 to 8 and in up to 10 % (w/v) total salinity. They produce indol, are positive in the Voges-Proskauer test and are negative for arginine dihydrolase, lysine and ornithine decarboxylases. Strain SMJ21T is aerogenic and red-pigmented, due to prodigiosin production, while strain EAod9T ferments glucose without gas and is not pigmented. The major cellular fatty acids of both novel strains were C16 : 1ω7c/C16 : 1ω6c and C16 : 0. WGSobtained for both strains, along with the other five members of the clade, allowed the determination of ANI indexes and in silico estimations of DDH values, which confirmed that the two strains represent two novel species of the genus Vibrio: Vibrio palustris sp. nov. (with EAod9T=CECT 9027T=LMG 29724T as the proposed type strain) and Vibrio spartinae sp. nov. (with SMJ21T=CECT 9026T=LMG 29723T as the proposed type strain).
-
-
-
Citrobacter portucalensis sp. nov., isolated from an aquatic sample
A Gram-stain-negative strain, A60T, isolated from a water well sample in Portugal, was characterized phenotypically, genotypically and phylogenetically. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A60T belonged to the genus Citrobacter , and recN gene phylogeny revealed one strongly supported clade encompassing strain A60T and 13 other strains from public databases, distinct from currently recognized species of the genus Citrobacter . Furthermore, multilocus sequence analysis (MLSA) based on concatenated partial fusA, leuS, pyrG and rpoB sequences confirmed the classification obtained with the recN sequence. In silico genomic comparisons, including average nucleotide identity (ANI) and the genome-to-genome distance calculator (GGDC), showed 94.6 % and 58.4 % identity to the closest relative Citrobacter freundii ATCC 8090T, respectively. The ability to metabolize different compounds further discriminated strain A60T from other species of the genus Citrobacter . The G+C content of strain A60T is 52.0 %. The results obtained support the description of a novel species within the genus Citrobacter , for which the name Citrobacter portucalensis sp. nov. is proposed, with the type strain A60T (=DSM 104542T=CECT 9236T).
-
-
-
Psychromarinibacter halotolerans gen. nov., sp. nov., isolated from seawater of the Yellow Sea
More LessA Gram-stain-negative, strictly aerobic, motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain YBW34T, was isolated from seawater from the bottom of the Yellow Sea at station H12 (−73m in depth). Growth occurred at 10–45 °C (optimum 28 °C), in the presence of 1–12 % NaCl (w/v, optimum 4 %) and at pH 6.0–8.0 (optimum pH 7.0). The major fatty acids (>10 %) were C18 : 1 ω7c and C16 : 0. The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain YBW34T was 64.2 mol%. The most closely related species was Tropicimonas isoalkanivorans JCM 14837T with 95.8 % sequence similarity in Alphaproteobacteria. It showed 16S rRNA gene sequence similarities of 93.03–95.49, 93.03–95.49 and 95.31–95.32 % to species of genera Rhodovulum , Lutimaribacter and Oceanicola , respectively. Nevertheless, strain YBW34T formed a distinct lineage in the trees which did not join the genera mentioned above in the phylogenetic dendrogram based on 16S rRNA gene sequences. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain YBW34T represents a novel genus and species, for which the name Psychromarinibacter halotolerans gen. nov., sp. nov. is proposed. The type strain is YBW34T (=JCM 31462T=KCTC 52366T=MCCC 1K03203T).
-
-
-
Microvirga indica sp. nov., an arsenite-oxidizing Alphaproteobacterium, isolated from metal industry waste soil
A novel Gram-stain-negative bacterium, strain S-MI1bT, belonging to the genus Microvirga was isolated from a metal industry waste soil sample in Pirangut village, Pune District, Maharashtra, India. Cells were non-spore-forming, small rod-shapes, motile and strictly aerobic with light-pink colonies. The strain grew in 0–7.0 % (w/v) NaCl and at 25–45 °C, with optimal growth at 40 °C. The predominant fatty acids detected were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C19 : 0 cyclo ω8c. The predominant isoprenoid quinone was Q-10. The G+C content was 67.2 mol% and DNA–DNA relatedness values between strain S-MI1bTand Microvirga subterranea DSM 14364T and Microvirga aerophila 5420S-12T were 53.9 and 54.8 %, respectively. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain S-MI1bT is a member of the genus Microvirga , with greatest sequence similarities of 97.7 and 97.4 % with M. subterranea DSM 14364T and M. aerophila 5420S-12T, respectively. Phylogenetic analysis showed that strain S-MI1bT forms a clade with the type strain of M. subterranea DSM 14364T, and was readily distinguishable from it due to various phenotypic characteristics. The combination of genotypic and phenotypic data suggests that the isolate represents a novel species of the genus Microvirga , for which the name Microvirga indica sp. nov. is proposed. The type strain is S-MI1bT (=NCIM-5595T=KACC 18792T=BCRC 80972T).
-
-
-
Pleomorphobacterium xiamenense Yin et al. 2013 is a later heterotypic synonym of Oceanicella actignis Albuquerque et al. 2012
More LessPleomorphobacterium xiamenense CLWT was compared with Oceanicella actignis PRQ-67T to examine the taxonomic relationship between the two organisms. The 16S rRNA gene sequence comparison showed that the two strains had 99.9 % sequence similarity. Phylogenetic analysis showed the two strains formed an independent tight cluster, distinctly branching from the closely related species in the family Rhodobacteraceae . Whole genomic comparison between the two strains revealed a digital DNA–DNA hybridization estimate of 88.4 % and average nucleotide identity of 98.8 %, strongly supporting that the two strains represented a single species. In addition, neither strain displayed any striking difference in biochemical characteristics, fatty acid composition, and polar lipid profile. According to priority, Pleomorphobacterium xiamenense is reclassified as a later heterotypic synonym of Oceanicella actignis based on the phylogenetic relationship, whole genomic comparison, fatty acid composition and polar lipid profile, and other phenotypic and biochemical properties.
-
-
-
Nocardioides taihuensis sp. nov., isolated from fresh water lake sediment
More LessA novel actinobacterial strain, designated X17T, was isolated from the sediment of Taihu Lake in China and its taxonomic position was investigated by using a polyphasic approach. The isolate formed milky-white colonies comprising aerobic, Gram-stain-positive, rod-shaped cells. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the organism belonged to the genus Nocardioides and consistently formed a distinct cluster with Nocardioides agariphilus JCM 16020T and Nocardioides islandensis MSL 26T, sharing 95.5 and 94.8 % 16S rRNA gene sequence similarities, respectively. The genomic DNA G+C content was 69.9 mol%. Chemotaxonomically, the isolate contained ll-diaminopimelic acid in the cell-wall peptidoglycan, MK-8 (H4) as the predominant menaquinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids found in the cell wall. The major fatty acids were 18 : 1 ω9c (38.6 %), 16 : 0 iso (20.3 %), 15 : 0 iso (6.8 %) and 18 : 0 (5.8 %). Based on its physiological, biochemical and chemotaxonomic characteristics, the strain represents a novel species of the genus Nocardioides , for which the name Nocardioides taihuensis sp. nov. (type strain X17T=CGMCC 4.7318T=NBRC 112321T) is proposed.
-
-
-
Winogradskyella flava sp. nov., isolated from the brown alga, Sargassum fulvellum
More LessAn aerobic, gliding and yellow-pigmented bacterium, designated strain SFD31T, was isolated from brown alga collected from the South Sea, Republic of Korea. Cells were Gram-stain-negative, and catalase- and oxidase-positive. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SFD31T forms an independent lineage within the genus Winogradskyella . Strain SFD31T was related distantly to Winogradskyella echinorum KMM 6211T (97.9 %, 16S rRNA gene sequence similarity), Winogradskyella litoriviva KMM 6491T (97.4 %), Winogradskyella pulchriflava EM106T (97.2 %) and Winogradskyella eckloniae EC29T (96.9 %). The major fatty acids of strain SFD31T were iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and unknown 13.565. The only isoprenoid quinone of the isolate was menaquinone 6. The major polar lipids were phosphatidylethanolamine, four unidentified aminolipids and two unidentified lipids. The DNA G+C content of strain SFD31T was 36.0 mol%. Phenotypic characteristics distinguished strain SFD31T from the related species of the genus Winogradskyella . On the basis of the evidence presented in this study, a novel species, Winogradskyella flava sp. nov., is proposed for strain SFD31T (=KCTC 52348T=JCM 31798T).
-
-
-
Bacillus iocasae sp. nov., isolated from Pacmanus hydrothermal field, Manus Basin
More LessA novel bacterial strain S36T was isolated from the deep-sea sediment collected from Pacmanus hydrothermal field, Manus Basin. The strain was Gram-stain-positive, aerobic, rod-shaped, endospore-forming, and motile. It was able to grow at 16–50 °C, pH 6.0–10.0, and in the presence of 0–11 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain S36T was a member of genus Bacillus and shares the highest sequence identity with Bacillus herbersteinensis D-1,5aT (97.0 %). The value of DNA–DNA hybridization between strain S36T and B. herbersteinensis D-1,5aT was 22.8 %. The cell wall diagnostic diamino acid of strain S36T was meso-diaminopimelic acid and the polar lipid profile of strain S36T contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The predominant respiratory quinine was MK-7. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of strain S36T was 43.0 mol%. On the basis of phylogenetic analysis, DNA–DNA hybridization, and phenotypic characteristics, it was concluded that strain S36T represents a novel species of the genus Bacillus , for which the name Bacillus iocasae sp. nov. was proposed. The type strain is S36T (=KCTC 33864T=DSM 104297T=CGMCC 1.16030T).
-
-
-
Streptomyces solisilvae sp. nov., isolated from tropical forest soil
More LessA novel streptomycete (strain HNM0141T) was isolated from tropical forest soil collected from Bawangling mountain of Hainan island, PR China and its taxonomic position was established in a polyphasic study. The organism had chemical and morphological properties consistent with its classification as a member of the Streptomyces violaceusniger clade. On the basis of the results of 16S rRNA gene sequence analysis, HNM0141T showed highest similarity to Streptomyces malaysiensis CGMCC4.1900T (99.4 %), Streptomyces samsunensis DSM 42010T (98.9 %), Streptomyces yatensis NBRC 101000T (98.3 %), Streptomyces rhizosphaericus NBRC 100778T (98.0 %) and Streptomyces sporoclivatus NBRC 100767T (97.9 %). The strain formed a well-delineated subclade with S. malaysiensis CGMCC4.1900T and S. samsunensis DSM 42010T. The levels of DNA–DNA relatedness between HNM0141T and S. malaysiensis CGMCC4.1900T and S. samsunensis DSM 42010T were 62 and 44 %, respectively. On the basis of phenotypic and genotypic characteristics, HNM0141T represents a novel species in the S. violaceusniger clade for which the name Streptomyces solisilvae sp. nov. is proposed. The type strain is HNM0141 T (=CCTCC AA 2016045T=KCTC 39905T).
-
-
-
Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree
More LessA new strain of the genus Promicromonospora , CAP94T, was isolated from the surface sterilized root of Callitrispreissii (Australian native pine tree). This strain was a Gram-stain-positive, aerobic actinobacterium with hyphae breaking up into fragments which were non-motile, rod-like, coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of the family Promicromonospora ceae , and most closely to Promicromonospora sukumoe NBRC 14650T (99.4 %), Promicromonospora kroppenstedtii DSM 19349T (99.2 %) and Promicromonosporaaerolata V54AT (99.1 %). Chemotaxonomic data including cell-wall components, major menaquinone and major fatty acids confirmed the affiliation of strain CAP94T to the genus Promicromonospora . The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain CAP94T and the closest species with validly published names. The name proposed for the new species is Promicromonospora callitridis sp. nov. The type strain is CAP94T (=DSM 103339T=TBRC 6025T).
-
-
-
Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.)
A Gram-stain-positive, aerobic, non-motile, short-rod shaped actinobacterium, designated THG-T2.14T, was isolated from soil sampled from the rhizosphere of mugunghwa. Growth occurred at 10–40 °C (optimum 30 °C), at pH 5.0–10.0 (optimum 7.0) and at 0–7.0 % NaCl (optimum 3.0 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T2.14T were identified as Microbacterium yannicii DSM 23203T (98.8 %), Microbacterium trichothecenolyticum DSM 8608T (98.8 %), Microbacterium arthrosphaerae DSM 22421T (98.7 %) and Microbacterium jejuense KACC 17124T (98.4 %). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified lipid, two unidentified phospholipids and two unidentified phosphoglycolipids. The menaquinones were MK-12, and MK-13. The major polyamine was spermidine. The peptidoglycan contained ornithine, alanine, glycine, homoserine and glutamic acid. The diagnostic diamino acid was ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose, ribose, galactose, arabinose, xylose and glucose. The DNA G+C content of strain THG-T2.14T was 71.2 mol%. The DNA–DNA relatedness between strain THG-T2.14T and its closest reference strains were significantly lower than the threshold value of 70 %. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-T2.14T represents a novel species of the genus Microbacterium , for which the name Microbacterium hibisci sp. nov. is proposed. The type strain is THG-T2.14T (=KACC 18931T=CCTCC AB 2016180T).
-
-
-
Molecular characterization and phylogeny of four new species of the genus Trichonympha (Parabasalia, Trichonymphea) from lower termite hindguts
Members of the genus Trichonympha are among the most well-known, recognizable and widely distributed parabasalian symbionts of lower termites and the wood-eating cockroach species of the genus Cryptocercus. Nevertheless, the species diversity of this genus is largely unknown. Molecular data have shown that the superficial morphological similarities traditionally used to identify species are inadequate, and have challenged the view that the same species of the genus Trichonympha can occur in many different host species. Ambiguities in the literature, uncertainty in identification of both symbiont and host, and incomplete samplings are limiting our understanding of the systematics, ecology and evolution of this taxon. Here we describe four closely related novel species of the genus Trichonympha collected from South American and Australian lower termites: Trichonympha hueyi sp. nov. from Rugitermes laticollis, Trichonympha deweyi sp. nov. from Glyptotermes brevicornis, Trichonympha louiei sp. nov. from Calcaritermes temnocephalus and Trichonympha webbyae sp. nov. from Rugitermes bicolor. We provide molecular barcodes to identify both the symbionts and their hosts, and infer the phylogeny of the genus Trichonympha based on small subunit rRNA gene sequences. The analysis confirms the considerable divergence of symbionts of members of the genus Cryptocercus, and shows that the two clades of the genus Trichonympha harboured by termites reflect only in part the phylogeny of their hosts.
-
-
-
Kushneria konosiri sp. nov., isolated from the Korean salt-fermented seafood Daemi-jeot
More LessA halophilic bacterial strain, X49T, was isolated from the Korean traditional salt-fermented seafood Daemi-jeot. X49T was an obligately aerobic, Gram-stain-negative, motile, oval or rod-shaped (0.5–1.0×1.2–3.2 µm) bacterium. After 2 days of growth, colonies on Marine agar medium were orange and circular with entire margins. X49T growth was detected at 10–37 °C and pH 4.5–8.5 in the presence of 0–26 % (w/v) NaCl. The 16S rRNA gene sequence of strain X49T was most similar to that of the type strain of Kushneria marisflavi SW32T and shared a sequence similarity of 94.7–98.6 % with type strains of species of the genus Kushneria . The predominant fatty acids were C16 : 0, C18 : 1ω7c and C12 : 0 3OH. The major isoprenoid quinone was Q9 (93 %), and minor quinones were Q8 (4 %) and Q10 (3 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylserine, two unidentified aminolipids, two unidentified phospholipids and two unidentified lipids. The genomic DNA G+C content was 59.1 mol%. The level of the ANI value between strain X49T and K. marisflavi SW32T, the most closely related species of the genus Kushneria , was 89.32 %. Based on the low ANI value, strain X49T and its reference strains represent genotypically distinct species. Based on this polyphasic taxonomic analysis, strain X49T represents a novel species of the genus Kushneria . The name Kushneria konosiri sp. nov. is proposed and the type strain is X49T (=KACC 14623T=JCM 16805T).
-
-
-
Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils
Two strains of aerobic, budding, pink-pigmented bacteria, P12T and P515, were isolated from a lichen-dominated peatland and a forested tundra soil of north-western Siberia, respectively. Cells of these isolates were represented by non-motile spheres that occurred singly or were arranged in short chains and aggregates. While growing on solid media, cells of strains P12T and P515 attached to the surface by means of holdfast-like appendages. These isolates were mildly acidophilic (optimum growth at pH 5.5–6.0), psychrotolerant bacteria, which displayed tolerance of low temperatures (4–15 °C), grew optimally at 15–22 °C and did not grow at temperatures above 28 °C. The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C18 : 1ω9c, C16 : 0 and C14 : 0. Trimethylornithine lipid was the major polar lipid. The only quinone was MK-6, and the G+C content of the DNA was 61.2–62.2 mol%. Strains P12T and P515 possessed identical 16S rRNA gene sequences, which affiliated them with the family Isosphaeraceae , order Planctomycetales , and these displayed the highest similarity (93–94 %) to 16S rRNA gene sequences from members of the genus Singulisphaera . However, the signature fatty acid of species of the genus Singulisphaera , i.e. C18 : 2 ω6c,12c, was absent in cells of strains P12T and P515. They also differed from members of the genus Singulisphaera by substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Tundrisphaera lichenicola gen. nov., sp. nov, is proposed. The type strain is P12T (=LMG 29571T=VKM B-3044T).
-
-
-
Novosphingobium ipomoeae sp. nov., isolated from a water convolvulus field
More LessA bacterial strain designated Tese-5T was isolated from a water convolvulus field in Taiwan and characterized using the polyphasic taxonomic approach. Strain Tese-5T was an aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium and formed bright yellow coloured colonies. Strain Tese-5T grew at 15–35 °C (optimum, 30 °C), with 0–1.0 % NaCl (optimum, 0–0.5 %) and at pH 5.5–7 (optimum, pH 6). The major fatty acids (>10 %) of strain Tese-5T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and sphingoglycolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Tese-5T belonged to the genus Novosphingobium and showed the highest levels of sequence similarity to Novosphingobium chloroacetimidivorans BUT-14T and Novosphingobium mathurense SM117T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the closest-related species of the genus Novosphingobium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Tese-5T represents a novel species in the genus Novosphingobium , for which the name Novosphingobium ipomoeaesp. nov. is proposed. The type strain is Tese-5T (=BCRC 80904T=LMG 28838T=KCTC 42656T).
-
-
-
Rubrobacter spartanus sp. nov., a moderately thermophilic oligotrophic bacterium isolated from volcanic soil
More LessBacterial strain HPK2-2T was isolated from soil adjacent to the caldera of Kilauea Volcano in Hawaii Volcanoes National Park. HPK2-2T is a chemoorganoheterotroph that shows optimal growth at 50 °C (range 45–55 °C) and pH 8.0 (range 5.0–10.0). Sequence analysis of the 16S subunit of the rRNA gene showed that HPK2-2T is most closely related to the type strain of Rubrobactertaiwanensis (ATCC BAA-406T), with which it shared 94.5 % sequence identity. The major fatty acids detected in HPK2-2T were C18 : 0 14-methyl and C16 : 0 12-methyl; internally branched fatty acids such as these are characteristic of the genus Rubrobacter . The only respiratory quinone detected was MK-8, which is the major respiratory quinone for all members of the family Rubrobacteraceae examined thus far. We propose that HPK2-2T represents a novel species of the genus Rubrobacter , for which we propose the name Rubrobacter spartanus (type strain HPK2-2T; DSM 102139T; LMG 29988T).
-
-
-
Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments
More LessTwo Gram-staining-negative, rod-shaped, aerobic, marine bacteria, designated HME9321T and HME9359T, were isolated from seawater and lagoon water samples in the Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains revealed that they belonged to the genus Lewinella within the family Saprospiraceae . The 16S rRNA gene sequence similarity of strain HME9321T showed highest similarities with Lewinella aquimaris HDW-36T (95.2 %), Lewinella marina MKG-38T (94.7 %) and Lewinella xylanilytica 13–9-B8T (94.0 %). Strain HME9359T had highest sequence similarities with Lewinella agarilytica SST-19T (94.7 %), Lewinella persica T-3T (94.1 %) and Lewinella antarctica IMCC3223T (93.3 %). The predominant fatty acids of strain HME9321T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and summed feature 9 (comprising iso-C16 : 0 10-methyl and/or C17 : 1 ω9c) while those of strain HME9359T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0. The major isoprenoid quinone of both strains was MK-7. Strain HME9321T contained the polar lipids, phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and nine unidentified polar lipids, while strain HME9359T contained phosphatidylethanolamine, one unidentified phospholipid and nine unidentified polar lipids. The DNA G+C contents of strains HME9321T and HME9359T were 58.7 and 62.0 mol%, respectively. Based on the results of the phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Lewinella maritima sp. nov. and Lewinella lacunae sp. nov. are proposed. The type strains are HME9321T (=KACC 17619T=CECT 8419T) and HME9359T (=KCTC 42187T=CECT 8679T), respectively.
-
-
-
Cryptotrichosporon argae sp. nov., Cryptotrichosporon brontae sp. nov. and Cryptotrichosporon steropae sp. nov., isolated from forest soils
More LessYeast strains belonging to the basidiomycetous genus Cryptotrichosporon were isolated from forest soils in Serra da Arrábida Natural Park in Portugal. Similar to the already-known representatives of this genus, the new isolates formed pigmented colonies of a distinctive pale orange colour. Phylogenetic analyses employing concatenated sequences of the D1/D2 domains of the 26S (large subunit) rRNA gene and the internal transcribed spacer (ITS) region supported the recognition of three novel species: Cryptotrichosporon argae sp. nov. (type strain CM 19T=CBS 14376T=PYCC 7010T=DSM 104550T; MycoBank accession number MB 817168), Cryptotrichosporon brontae sp. nov. (type strain CM 1562T=CBS 14303T=PYCC 7011T=DSM 104551T; MycoBank accession number MB 817077) and Cryptotrichosporon steropae sp. nov. (type strain OR 395T=CBS 14302T=PYCC 7012T=DSM 104552T; MycoBank accession number MB 817078).
-
-
-
Cellvibrio zantedeschiae sp. nov., isolated from the roots of Zantedeschia aethiopica
More LessA bacterial strain, designated TPY-10T, was isolated from calla lily roots in Taiwan and characterized by using a polyphasic taxonomy approach. Cells of strain TPY-10T were Gram-stain-negative, strictly aerobic, motile and creamy white rods. Growth occurred at 15–35 °C (optimum, 25–30 °C), at pH 6–7 (optimum, pH 6) and with 0–1 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TPY-10T belonged to the genus Cellvibrio and was most closely related to Cellvibriomixtus ACM 2601T with sequence similarity of 97.8 %. Strain TPY-10T contained C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the predominant fatty acids. The only isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of the genomic DNA was 49.8 mol%. The DNA–DNA hybridization value for strain TPY-10T with Cellvibriomixtus ACM 2601T was less than 21 %. On the basis of the phylogenetic inference and phenotypic data, strain TPY-10T should be classified as a novel species, for which the name Cellvibrio zantedeschiae sp. nov. is proposed. The type strain is TPY-10T (=BCRC 80525T=LMG 27291T=KCTC 32239T).
-
-
-
Salinirussus salinus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA halophilic archaeal strain, YGH44T, was isolated from the Yinggehai marine solar saltern in Hainan Province of China. Cells were rod-shaped, stained Gram-negative and formed red-pigmented colonies on agar plates. Optimal growth was obtained with 3.4 M NaCl (range: 2.6–4.8 M), 0.5 M MgCl2 (range: 0.005–1.0 M), at 37 °C (range: 25–55 °C) and at pH 7.0 (range: pH 5.0–9.0). The cells lysed in distilled water, and the minimal NaCl concentration to prevent cell lysis was 1.7 M. Phylogenetic tree reconstructions based on 16S rRNA genes and rpoB′ genes revealed that strain YGH44T was distinct from the related genera, Halovenus , Halapricum , Halorientalis , Halorhabdus and Halosimplex of the order Halobacteriales . The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three unidentified glycolipids. The DNA G+C content of strain YGH44Twas 69.0 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YGH44T (=CGMCC 1.12234T=JCM 18646T) represents a novel species of a new genus within the order Halobacteriales , for which the name Salinirussus salinus gen. nov., sp. nov. is proposed.
-
-
-
Pacificibacter aestuarii sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, strictly aerobic bacterium, designated KJ21T, was isolated from a tidal flat in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain KJ21T was observed at 10–35 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 7.0) and in the presence of 1–5 % (w/v) NaCl (optimum, 2 %). Strain KJ21T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, 10-methyl C19 : 0 and C10 : 0 3-OH as the major fatty acids and ubiquinone-10 as the major isoprenoid quinone. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. The G+C content of the genomic DNA was 53.9 mol%. Phylogenic analysis based on 16S rRNA gene sequences showed that strain KJ21T formed a tight phylogenetic lineage with the members of the genus Pacificibacter with a 100 % bootstrap value. Strain KJ21T was most closely related to Pacificibacter maritimus KMM 9031T (98.7 %) and Pacificibacter marinus HDW-9T (98.4 %), and the DNA–DNA relatedness values between strain KJ21T and the type strains of P. maritimus and P. marinus were 46.9±4.2 % and 39.8±5.7, respectively. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain KJ21T represents a novel species of the genus Pacificibacter , for which the name Pacificibacter aestuarii sp. nov. is proposed. The type strain is KJ21T (=KACC 19098T=JCM 31805T).
-
-
-
Brenneria populi subsp. brevivirga subsp. nov. isolated from symptomatic bark of Populus × euramericana canker, and description of Brenneria populi subsp. populi subsp. nov.
More LessTwo Gram-stain-negative, facultatively anaerobic, motile bacterial strains isolated from symptomatic bark of Populus × euramericana canker in China were investigated using a polyphasic approach, including 16S rRNA gene sequencing, multilocus sequence analysis, and biochemical and physiological assays. 16S rRNA gene sequencing indicated that these strains belonged to the genus Brenneria , family Pectobacteriaceae , and had the highest sequence similarity with Brenneria populi CFCC 11963T (98 %). DNA–DNA hybridization experiments revealed DNA–DNA relatedness values of 72.1–78.2 % between the new isolates and strains of B. populi , revealing that these strains belonged to the same species. The 16S rRNA gene sequencing and multilocus sequence analysis suggested that the two novel strains and those of B. populi are phylogenetically closely related but form two clearly separated subgroups. Based on the data, the two novel isolates represent a subspecies of B. populi for which the name B. populi subsp. brevivirga subsp. nov. is proposed with D8-10-4-5T (=CFCC 11935T=KCTC 42841T) as the type strain, with the automatic creation of B. populi subsp. populi subsp. nov. (type strain D9-5T=CFCC 11963T=KCTC 42088T).
-
-
-
Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage
Three Gram-stain positive, non-motile, non-spore-forming, catalase-negative and rod-shaped bacterial strains (IWT5T, IWT25T and IWT140), isolated from silage, were investigated by using a polyphasic taxonomic approach. Strains IWT5T and IWT25T grew at 10–37 °C and 30–37 °C, and at pH 4.0–7.5 and 4.0–7.0, respectively. The G+C contents of genomic DNA of strains IWT5T and IWT25T were 43.2 and 44.4 mol%, respectively. Strains IWT5T and IWT25T contained C16 : 0, C18 : 1 ω9c and summed feature 7 (unknown 18.846/C19 : 1 ω6c/C19 : 0cyclo ω10c) as the major fatty acids. Strain IWT5T was most closely related to the type strains of Lactobacillus mixtipabuli (99.9 % 16S rRNA gene sequence similarity) and Lactobacillus silagei (99.5 %). For IWT25T, the 16S rRNA gene sequence similarities with the closely related neighbour type strains L. mixtipabuli and L. silagei were 99.5 and 99.5 %, respectively. The 16S rRNA gene sequence similarities among the three novel isolates were 99.5–99.9 %. The average nucleotide identities of strains IWT5T and IWT25T to other neighbours of the genus Lactobacillus were less than 82 % and the genomes of IWT25T and IWT140 shared 97.3 % average nucleotide identity, demonstrating that the three strains were allocated to two different novel species of the genus Lactobacillus . Together with multilocus sequence analysis, phenotypic and chemotaxonomic characteristics, strains IWT5T (=JCM 31144T=DSM 102973T) and IWT25T (=JCM 31145T=DSM 102974T) are proposed as the type strains of novel species of the genus Lactobacillus , with the names Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., respectively.
-
-
-
Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida
More LessWe describe two new species of the genus Xanthomonas , represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonas cassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonas vesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
-
-
-
Altererythrobacter xixiisoli sp. nov., isolated from wetland soil
More LessA Gram-stain-negative, coccoid, yellow, non-motile, aerobic bacterium, designated strain S36T, was isolated from soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain S36T could represent a novel species of genus Altererythrobacter showing highest similarity to Altererythrobacter atlanticus 26DY36T (96.31 % 16S rRNA gene sequence similarity). The temperature, pH and NaCl concentration ranges for growth were 10–37 °C (optimum 32 °C), pH 5.0–10.0 (optimum pH 7.0) and 0.5–3 % (optimum 1 %, w/v), respectively. The predominant respiratory quinone of strain S36T was Q-10. The major fatty acids were C16 : 0, C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 62.7 mol%. These data all support the affiliation of strain S36T to the genus Altererythrobacter . The polar lipids profile of strain S36T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and two unidentified glycolipids. The results of physiological and biochemical tests allowed differentiation of strain S36T from other members of the genus Altererythrobacter . Therefore, strain S36T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter xixiisoli sp. nov. is proposed; the type strain is S36T (=CGMCC 1.12804T=NBRC 110413T).
-
-
-
Defining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov.
To clarify the taxonomic classification of Streptococcus suis serotype 33, we performed biochemical and molecular genetic analyses using isolates (GUT-183, GUT-184, GUT-185, GUT-186, GUT-187T, GUT-188, GUT-189, GUT-190, GUT-191, GUT-192 and GUT-193) from bovine endocarditis. A comparative sequence analysis showed 99.2–100 % sequence similarity among the reference strain of S. suis serotype 33 and our isolates for the 16S rRNA gene. These similarities were higher than those between the isolate GUT-187T and S. suis and other streptococci. Comparison of sodA genes also showed high degrees of similarities among the reference strain of S. suis serotype 33 and our isolates (99.7–100 %), which were higher than those between the GUT-187T and S. suis and other streptococci. DNA–DNA relatedness among three isolates (GUT-186, GUT-187T, the reference strain of S. suis serotype 33) was over 76.7 %. In contrast, the relatedness between GUT-187T and the other streptococcal species ( S. suis , Streptococcus parasuis , Streptococcus acidominimus and Streptococcus porci ) was 8.4–24.9 %. Phylogenetic analyses showed that the isolates did not affiliate closely to any known species of the genus Streptococcus . Moreover, GUT-187T could be distinguished from S. suis and other closely related species of genus Streptococcus using biochemical tests. On the basis of the phenotypic and molecular genetic data, we propose that the isolates of S. suis serotype 33 should be classified into the genus Streptococcus , Streptococcus ruminantium sp. nov. with the type strain GUT-187T (=DSM 104980T=JCM 31869T).
-
-
-
Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China
More LessA new species of the genus Phytophthora was isolated from stream water in the subtropical forests of China during a survey of forest Phytophthora from 2011 to 2013. This new species is formally described here and named Phytophthora pseudopolonica sp. nov. This new homothallic species is distinct from other known Phytophthora species in morphology and produces nonpapillate and noncaducous sporangia with internal proliferation. Spherical hyphal swellings and thin-walled chlamydospores are abundant when the species is kept in sterile water. The P. pseudopolonica sp. nov. forms smooth oogonia with paragynous and sometimes amphigynous antheridia. The optimum growth temperature of the species is 30 °C in V8-juice agar with β-sitosterol, yet it barely grows at 5 °C and 35 °C. Based on sequences of the internal transcribed spacer and the combined β-tubulin and elongation factor 1α gene sequence data, isolates of the new species cluster together into a single branch and are close to Phytophthora polonicabelonging to clade 9.
-
-
-
Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a freshwater reservoir
More LessA phosphate-solubilizing bacterium, designated CPCC 100624T, was isolated from a freshwater reservoir in south-west China. The 16S rRNA gene sequence comparison of strain CPCC 100624T with the available sequences in the GenBank database showed that the isolate was closely related to members of the genus Spirosoma . In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100624T formed a stable phylogenetic subclade with Spirosoma soli MIMBbqt12T within the genus Spirosoma , which indicated that strain CPCC 100624T could be identified as a member of the genus Spirosoma . The strain grew at 10–40 °C (optimum 30 °C), at pH 6.5–8.0 (optimum pH 7.0–7.5) and in the presence of 0–5 % (w/v) NaCl (optimum 0–1 %). MK-7 was detected as the main menaquinone, with a minor amount of MK-7(H6) in its menaquinone system. Cells contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c and iso-C15 : 0 as the major fatty acids. The polar lipids of strain CPCC 100624T contained phosphatidylethanolamine, one unidentified aminolipid, two aminophospholipids and three unidentified lipids. The genomic DNA G+C content was 49.3 mol%. On the basis of the above taxonomic data and differences in physiological characteristics from the closely related type strains, strain CPCC 100624T represents a novel species of the genus Spirosoma , for which the name Spirosoma lacussanchae sp. nov. is proposed. The type strain is CPCC 100624T (=NBRC 111852T=DSM 101771T).
-
- Research Article
-
-
-
Molecules illuminate morphology: phylogenomics confirms convergent evolution among ‘oligotrichous’ ciliates
More Less‘Oligotrichous’ ciliates have been traditionally placed in a presumed monophyletic taxon called the Oligotrichia. However, gene sequences of the small subunit rRNA gene, and several other genes, suggest that the taxon is not monophyletic: although statistical support for this is not strong, the oligotrich Halteria grandinella is associated with the hypotrich ciliates and not with other oligotrich genera, such as Strombidium and Strombidinopsis. This has convinced some taxonomists to emphasize that morphological features strongly support the monophyly of the oligotrichs. To further test this hypothesis of monophyly, we have undertaken a phylogenomic analysis using the transcriptome of H. grandinella cells amplified by a single-cell technique. One hundred and twenty-six of 159 single-gene trees placed H. grandinella as sister to hypotrich species, and phylogenomic analyses based on a subset of 124 genes robustly rejected the monophyly of the Oligotrichia and placed the genus Halteria as sister to the hypotrich genera Stylonychia and Oxytricha. We use these phylogenomic analyses to assess the convergent nature of morphological features of oligotrichous ciliates. A particularly ‘strong’ morphological feature supporting monophyly of the oligotrichs is enantiotropic cell division, which our results suggest is nevertheless a convergent feature, arising through the need for dividing ciliates to undertake rotokinesis to complete cell division.
-
-
- Taxonomic Note
-
-
-
Proposal to modify Rule 10a and to delete Recommendation 10a(3) from the International Code of Nomenclature of Prokaryotes
More LessPrinciple 2 of the Prokaryotic Code, as modified by the ICSP in 1999, reads: ‘The nomenclature of prokaryotes is not independent of botanical and zoological nomenclature. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi and plants’. But in the current version of the Prokaryotic Code no Rule implements this version of Principle 2. I therefore propose adding the following sentence to Rule 10a: ‘As from January 2001, newly proposed generic names must not be later homonyms of names in use in botany or zoology’. Recommendation 10a(3) of the Code states: ‘Avoid introducing into bacteriology as generic names such names as are in use in botany or zoology, in particular well-known names’. This Recommendation contravenes the current version of Principle 2 and the proposed new version of Rule 10a. Therefore I propose to delete Recommendation 10a(3) from the Prokaryotic Code.
-
-
- ICSP Matters
-
-
-
Proposal to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus. Request for an Opinion
More LessMethylothermus thermalis , the designated type species of the genus Methylothermus , is not available from culture collections and its nomenclatural type is a patent strain. According to Rule 20a of the International Code of Nomenclature of Prokaryotes, only species whose names are legitimate may serve as types of genera. Therefore, the name Methylothermus and the names of the species Methylothermus thermalis and Methylothermus subterraneus are not validly published and are illegitimate. We therefore submit a Request for an Opinion to the Judicial Commission of the ICSP to consider the later-named Methylothermus subterraneus as the new type species of the genus Methylothermus based on Rule 20e(2).
-
-
-
-
Proposal to correct the generic name Flaviaesturariibacter Kang, Chun, Seo, Kim and Jahng 2015, 2212 to Flavaestuariibacter. Request for an Opinion
More LessThe generic name Flaviaesturariibacter Kang, Chun, Seo, Kim and Jahng 2015, 2212 is malformed: being derived from the Latin noun aestuarium, …aestuarii… instead of …aesturarii… is required. Moreover, according to Appendix 9 of the Prokaryotic Code, a connecting vowel must be dropped when the following word element starts with a vowel. I therefore propose to correct the name Flaviaesturariibacter to Flavaestuariibacter.
-
-
-
Proposal to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as the nomenclatural type of the class Actinobacteria. Request for an Opinion
More LessThe name of the class Actinobacteria is illegitimate according to Rules 15, 22 and 27(3) because it was proposed without the designation of a nomenclatural type. I therefore propose to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as its nomenclatural type, based on Rule 22 of the International Code of Nomenclature of Prokaryotes.
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)