- Volume 66, Issue 2, 2016
Volume 66, Issue 2, 2016
- Notification List
-
-
-
Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 11, of the IJSEM
More LessThis listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
-
-
- NEW TAXA
-
- Archaea
-
-
Halosiccatus urmianus gen. nov., sp. nov., a haloarchaeon from a salt lake
A novel, orange-pigmented, halophilic archaeon, strain DC8T, was isolated from Urmia salt lake in north-west Iran. The cells of strain DC8T were non-motile and pleomorphic, from small rods to triangular or disc shaped. The novel strain needed at least 2.5 M NaCl and 0.02 M MgCl2 for growth. Optimal growth was achieved at 4.0 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 45 °C, respectively, and it was able to grow over a pH range of 7.0 to 8.5 and a temperature range of 25 to 55 °C. Analysis of the 16S rRNA gene sequence showed that strain DC8T was a member of the family Halobacteriaceae; however, its similarity was as low as 90.1 %, 89.3 % and 89.1 % to the most closely related haloarchaeal taxa, including type species of members of the genera Halosimplex, Halobaculum and Halomicrobium, respectively. The G+C content of its DNA was 68.1 mol%. Polar lipid analyses revealed that strain DC8T contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and phosphatidic acid. One unknown phospholipid, two major glycolipids and one minor glycolipid were also detected. The only quinone present was MK-8 (II-H2). The physiological, biochemical and phylogenetic differences between strain DC8T and other extremely halophilic archaeal genera with validly published names supported that this strain represents a novel species of a new genus within the family Halobacteriaceae, for which the name Halosiccatus urmianus gen. nov., sp. nov. is proposed. The type strain is strain DC8T ( = IBRC-M 10911T = CECT 8793T).
-
- Actinobacteria
-
-
Egicoccus halophilus gen. nov., sp. nov., a halophilic, alkalitolerant actinobacterium and proposal of Egicoccaceae fam. nov. and Egicoccales ord. nov.
A novel Gram-stain-positive, non-motile, moderately halophilic and alkalitolerant actinobacterium, designated EGI 80432T, was isolated from a saline–alkaline soil of Xinjiang province, north-west China. Cells were non-endospore-forming cocci with a diameter of 0.5–0.8 μm. Strain EGI 80432T grew in the presence of 0–9 % (w/v) NaCl (optimum at 3–5 %), and also grew within the pH range 6.0–10.0 (optimum at pH 8.0–9.0) on marine 2216E medium. The peptidoglycan type was A1γ. The whole-cell hydrolysates contained glucose, galactose, mannose and three unknown sugars as major sugars. The predominant menaquinone was MK-9(H4). The major fatty acids were C17 : 1ω8c, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C18 : 1ω9c and iso-C15 : 0 The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, three unknown phospholipids and four unknown polar lipids. The genomic DNA G+C content was 75.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EGI 80432T clustered within the radius of the class Nitriliruptoria. Levels of sequence similarity between strain EGI 80432T and its phylogenetic neighbours Nitriliruptor alkaliphilus ANL-iso2T and Euzebya tangerina F10T were 94.1 and 88.1 %, respectively. Based on morphological, physiological and chemotaxonomic characteristics and phylogenetic analysis, a novel species of a new genus, Egicoccus halophilus gen. nov., sp. nov., is proposed, within the new family and new order Egicoccaceae fam. nov. and Egicoccales ord. nov. in the class Nitriliruptoria. The type strain of Egicoccus halophilus is EGI 80432T ( = CGMCC 1.14988T = KCTC 33612T).
-
-
-
Monashia flava gen. nov., sp. nov., an actinobacterium of the family Intrasporangiaceae
A novel actinobacterial strain, MUSC 78T, was isolated from a mangrove soil collected from Peninsular Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 78T represented a novel lineage within the class Actinobacteria. Strain MUSC 78T formed a distinct clade in the family Intrasporangiaceae and was related most closely to members of the genera Terrabacter (98.3–96.8 % 16S rRNA gene sequence similarity), Intrasporangium (98.2–96.8 %), Humibacillus (97.2 %), Janibacter (97.0–95.3 %), Terracoccus (96.8 %), Kribbia (96.6 %), Phycicoccus (96.2–94.7 %), Knoellia (96.1–94.8 %), Tetrasphaera (96.0–94.9 %) and Lapillicoccus (95.9 %). Cells were irregular rod-shaped or cocci and stained Gram-positive. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid as the diagnostic diamino acid. The main cell-wall sugar was mannose and lower amounts of galactose and rhamnose were present. The predominant menaquinone was MK-8(H4). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, diphosphatidylglycerol and phosphoglycolipid. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 73.1 mol%. Based on this polyphasic study, MUSC 78T exhibited phylogenetic and phenotypic differences from members of the genera of the family Intrasporangiaceae, and therefore a novel species of a new genus, Monashia flava gen. nov., sp. nov., is proposed. The type strain of Monashia flava is MUSC 78T ( = DSM 29621T = MCCC 1K00454T = NBRC 110749T).
-
-
-
Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families
More LessTwo Gram-type-positive, non-spore-forming bacteria, strains D16/0/H6T and A22/0/F9_1T, were isolated from Namibian semiarid savannah soils. 16S rRNA gene sequence analysis revealed 96.6 % identity between the two strains and placed them within the order Solirubrobacterales of the class Thermoleophilia. The closest phylogenetic relatives with validly published names were several strains of the genus Solirubrobacter and the species Conexibacter arvalis, with pairwise sequence similarities of ≤ 94.0 %. Cells of strain D16/0/H6T were ovoid to rod-shaped, whereas strain A22/0/F9_1T formed regular rods. Cells of both strains were motile and divided by binary fission. Colonies were pink and white to pale yellowish/brownish, respectively. Strains D16/0/H6T and A22/0/F9_1T were aerobic, chemoheterotrophic mesophiles with broad temperature (13–43 and 17–43 °C, respectively) and pH (pH 4.5–8.5 and 5.0–9.5) ranges for growth. Complex proteinaceous substrates and glucose were the preferred carbon and energy sources. Strain A22/0/F9_1T also grew on various carboxylic acids. For both strains, the peptidoglycan diamino acid was meso-2,6-diaminopimelic acid. The major quinone was MK-8. As a minor compound, MK-7 occurred in strain D16/0/H6T; strain A22/0F9_1T also contained MK-7, MK-7(H2) and MK-8(H2). Major fatty acids of strain D16/0/H6T were 10-methyl C17 : 0, iso-C16 : 0 and C18 : 1ω9c. Strain A22/0F9_1T contained C18 : 1ω9c, C17 : 1ω8c, C17 : 1ω6c and iso-C16 : 0 as major components. The DNA G+C contents of strains D16/0/H6T and A22/0/F9_1T were 72.8 and 74.0 mol%, respectively. Based on these characteristics, the two isolates are assigned to novel species of the new genus Parviterribacter gen. nov., the type species Parviterribacter kavangonensis sp. nov. (type strain D16/0/H6T = DSM 25205T = LMG 26950T) and a second species Parviterribacter multiflagellatus sp. nov. (type strain A22/0/F9_1T = DSM 25204T = LMG 26949T). As the novel genus and species cannot be clearly assigned to an established family within the order Solirubrobacterales, the novel family Parviterribacteraceae fam. nov. is proposed. Emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families are also provided.
-
-
-
Cnuibacter physcomitrellae gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from the moss of Physcomitrella patens
More LessA Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated strain XAT, was isolated from the moss, Physcomitrella patens, and characterized by using a polyphasic taxonomic approach. The novel strain was non-spore-forming, non-motile, catalase-positive and oxidase-negative. Its optimal temperature for growth occurred at 28–30 °C and the optimum pH for growth was 7.0–7.5. The major fatty acids comprised anteiso-C15 : 0, iso-C16 : 0, ω-cyclohexyl-C17 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, seven unidentified glycolipids, one unidentified phospholipid and one unidentified lipid. The major menaquinone was MK-11, followed by MK-10 and MK-12. The peptidoglycan type was B2γ and contained the amino acids 2,4-diaminobutyric acid, alanine, glycine, 3-hydroxy-glutamic acid and small amounts of glutamic acid. The genomic DNA G+C content of strain XAT was 68.2 mol%. Strain XAT exhibited highest 16S rRNA gene sequence similarity with Leifsonia lichenia 2SbT (96.3 %) and Humibacter antri D7-27T (96.2 %). However, phylogenetic analyses showed that strain XAT did not cluster with any species of the genera Leifsonia, Humibacter or other genera of the family Microbacteriaceae and the phylum Actinobacteria. Based on 16S rRNA gene sequence analyses, and the phenotypic and chemotaxonomic data, strain XAT is considered to represent a novel species of a novel genus, for which the name Cnuibacter physcomitrellae gen. nov., sp. nov. is proposed. The type strain is XAT ( = CGMCC 1.15041T = DSM 29843T).
-
-
-
Streptomyces spongiicola sp. nov., an actinomycete derived from marine sponge
More LessA novel actinomycete (strain HNM0071T) was isolated from an unidentified marine sponge collected from the coast of Sanya City, PR China and its taxonomic position was investigated. The major menaquinones were MK-9 (H6) (65.6 %), MK-9 (H4) (23.8 %) and MK-9 (H8) (10.6 %). The predominant fatty acids were anteiso-C15 : 0 (25.5 %), iso-C16 : 0 (19.5 %) and iso-C15 : 0 (15.4 %). The predominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, four unidentified phospholipids were found. The G+C content of the genomic DNA was 69.8 mol%. Based on 16S rRNA gene sequence analysis, strain HNM0071T was most closely related to Streptomyces wuyuanensis FX61T (97.3 %). The 16S rRNA gene sequence similarity to all other species of the genus Streptomyces was less than 97.0 %. DNA–DNA hybridization between strain HNM0071T and its closest phylogenetic relative, Streptomyces wuyuanensis FX61T, showed 25.0 % relatedness. Based on phenotypic and genotypic characteristics, strain HNM0071T represents a novel species of the genus Streptomyces whose name is proposed as Streptomyes spongiicola sp. nov. The type strain is HNM0071T ( = CCTCCAA2015018T = KCTC 39604T).
-
-
-
Micromonospora ovatispora sp. nov. isolated from mangrove soil
More LessAn oval spore-forming actinomycete, designated 2701SIM06T, was isolated from mangrove soil in Sanya, Hainan province, China. The 16S rRNA gene sequence of strain 2701SIM06T showed highest similarity to Micromonospora pattaloongensis TJ2-2T (98.6 %), Micromonospora polyrhachis NEAU-ycm2T (98.6 %) and Micromonospora sonneratiae 274745T (98.5 %). Phylogenetic analysis based on both the 16S rRNA gene and the gyrB gene supported this relationship. The chemotaxonomic results confirmed the isolate as a member of the genus Micromonospora, but morphological, physiological and biochemical properties differentiated it from its closest relatives. Based on these observations, strain 2701SIM06T represents a novel species, for which the name Micromonospora ovatispora sp. nov. is proposed. The type strain is 2701SIM06T ( = CCTCC AA 2012009T = DSM 45759T).
-
-
-
Nonomuraea thermotolerans sp. nov., a thermotolerant actinomycete isolated from mushroom compost
More LessA novel thermotolerant actinomycete, designated strain 3-33-9BT, was isolated from mushroom compost in Nanning, Guangxi province, China. The strain grew at 25–60 °C, pH 7.0–11.0 and with 0–2.0 % (w/v) NaCl. Strain 3-33-9BT formed extensively branched aerial mycelia and substrate mycelia. Spiral spore chains with one to three turns were composed of about 3–15 non-motile spores with a wrinkled surface. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell hydrolysates contained madurose, galactose, glucose and ribose. The cellular fatty acid profile mainly consisted of iso-C16 : 0 and C17 : 0. The quinone system was predominantly composed of MK-9(H4). The DNA G+C content of strain 3-33-9BT was 72.5 mol%. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Nonomuraea. Moreover, 16S rRNA gene sequence analysis also showed that the organism belonged to the genus Nonomuraea; in the 16S rRNA gene tree of the genus Nonomuraea, strain 3-33-9BT formed a distinct phyletic line and was most closely related to Nonomuraea fastidiosa NBRC 14680T (97.3 % 16S rRNA gene sequence similarity). However, phenotypic characteristics of strain 3-33-9BT were significantly different from N. fastidiosa NBRC 14680T, and DNA–DNA hybridization showed little relatedness (31.6–35.2 %) between the two strains. Based on the phenotypic and phylogenetic data, strain 3-33-9BT represents a novel species of the genus Nonomuraea, for which the name Nonomuraea thermotolerans sp. nov. is proposed. The type strain is 3-33-9BT ( = ATCC BAA-2629T = CGMCC 4.7161T).
-
-
-
Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov.
Strain ATCC 39727, which produces the antibiotic A40926 (the natural precursor of the antibiotic dalbavancin), was isolated from a soil sample collected in India, and it was originally classified as a member of the genus Actinomadura on the base of morphology and cell-wall composition. A phylogenetic analysis based on 16S rRNA gene sequences indicates that the strain forms a distinct clade within the genus Nonomuraea, and it is most closely related to Nonomuraea angiospora DSM 43173T (98.72 % similarity) and Nonomuraea jabiensis A4036T (98.69 %). The strain forms an extensively branched substrate mycelium and aerial hyphae that form spiral chains of spores with ridged surfaces. The cell wall contains meso-diaminopimelic acid and the whole-cell sugars are glucose, ribose, galactose, mannose and madurose (madurose as the diagnostic sugar). The N-acyl type of muramic acid is acetyl. The predominant menaquinone is MK-9(H4), with minor amounts of MK-9(H2), MK-9(H6) and MK-9(H0). The polar-lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylmethylethanolamine, phosphatidylinositol and a series of uncharacterized phospholipids, glycolipids and phosphoglycolipids. The major cellular fatty acids are iso-C16 : 0 and 10-methyl C17 : 0. The genomic DNA G+C content is 71.2 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, together with DNA–DNA relatedness between strain ATCC 39727 and closely related type strains, clearly demonstrated that strain ATCC 39727 represents a novel species of the genus Nonomuraea, for which the name Nonomuraea gerenzanensis sp. nov. is proposed. The type strain is ATCC 39727T ( = DSM 100948T).
-
-
-
Tessaracoccus rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis
More LessA novel Gram-stain-positive, non-spore-forming, irregular rod-shaped, non-motile and facultatively anaerobic actinobacterium, designated strain YIM 101269T, was isolated from the faeces of Rhinoceros unicornis living in Yunnan Wild Animal Park, Yunnan province, south-west China. The isolate grew at 10–35 °C, at pH 6–12 and with 0–9 % (w/v) NaCl. The cell-wall peptidoglycan of the organism contained ll-diaminopimelic acid as the diagnostic diamino acid. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, three unidentified polar lipids, one unidentified aminophospholipid and three unknown glycolipids. The major cellar fatty acid was anteiso-C15 : 0.MK-10(H4) was the predominant menaquinone. The DNA G+C content was 69.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 101269T belonged to the genus Tessaracoccus, closely related to Tessaracoccus flavescens DSM 18582T (97.4 % similarity). Based on the evidence from the present study, strain YIM 101269T is considered to represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus rhinocerotis sp. nov. is proposed. The type strain is YIM 101269T ( = DSM 27579T = CCTCC AB 2013217T).
-
-
-
Actinorectispora indica gen. nov., sp. nov. isolated from soil, a member of the family Pseudonocardiaceae
The taxonomic positions of three Gram-stain-positive, aerobic strains, designated YIM 75722, 75726 and 75728T, and isolated from a soil sample collected from Kurnool of Andhra Pradesh province, India, were assessed using a polyphasic approach. Growth was observed at pH 7.0–10.0 (optimum pH 7.0), 15–28 °C (optimum 28 °C) and 0–8 % (w/v) NaCl (grew without NaCl). Strains showed cylindrical spores with straight-chain morphology on aerial mycelium, but did not reveal sporangium-like structures or fragmentation of the substrate mycelium. Whole-cell hydrolysates of all strains contained galactose and ribose as the diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4); MK-9 (H6) and MK-10 (H4) were present in smaller amounts. The phospholipid pattern consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were i-C15 : 0, ai-C15 : 0, i-C17 : 0 and ai-C17 : 0. The genomic DNA G+C content was 68.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain YIM 75728T should be placed within the family Pseudonocardiaceae, in which the strain formed a distinct lineage. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data support the conclusion that strain YIM 75728T represents a novel species of a novel genus of the family Pseudonocardiaceae for which the name Actinorectispora indica gen. nov., sp. nov., is proposed. Strain YIM 75728T ( = DSM 45410T = CCTCC AA 209065T) is the type strain of Actinorectispora indica. Strain YIM 75728T was considered as the type strain over the other two strains based on the highest sequence read length of the strain.
-
-
-
Saccharothrix stipae sp. nov., an actinomycete isolated from the rhizosphere of Stipa grandis
More LessAn actinomycete, strain D34T, was isolated from a soil sample collected from the rhizosphere of Stipa grandis at Yunwu Mountain in Ningxia, north-west China. Strain D34T showed highest 16S rRNA gene sequence similarity to Saccharothrix espanaensis DSM 44229T (99.0 %), Saccharothrix texasensis NRRL B-16107T (98.7 %) and Saccharothrix variisporea NRRL B-16296T (98.6 %). The strain contained meso-diaminopimelic acid, alanine, glycine and glutamic acid as major cell-wall amino acids. Mannose, rhamnose and galactose were the characteristic whole-cell sugars. The fatty acid profile consisted predominantly of iso-C15 : 0, iso-C16 : 0, iso-C16 : 1, C17 : 1ω6c, anteiso-C17 : 0 and anteiso-C15 : 0. The phospholipid profile included phosphatidylethanolamine (typical of phospholipid pattern type II). Furthermore, a combination of some physiological and biochemical properties and low DNA–DNA relatedness values indicated that strain D34T was differentiated from members of closely related species. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain D34T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix stipae sp. nov. is proposed. The type strain is D34T ( = JCM 30560T = ACCC19714T).
-
-
-
Kocuria arsenatis sp. nov., an arsenic-resistant endophytic actinobacterium associated with Prosopis laegivata grown on high-arsenic-polluted mine tailing
A Gram-stain-positive, aerobic, non-motile, coccoid, arsenic-resistant actinobacterial strain, designated CM1E1T, was isolated from the lateral root tissue of Prosopis laegivata grown on a mine tailing in San Luis Potosi, Mexico. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CM1E1T was clustered closely with species of the genus Kocuria, and showed the highest sequence similarity of 98.7 % to Kocuria rhizophila TA68T. The DNA G+C content of strain CM1E1T was 74.5 mol% (T m ). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The peptidoglycan of the cell wall contained lysine and alanine. The major respiratory quinones were MK-7(H2) and MK-8(H2). On the basis of the phenotypic characterization, phylogenetic relationships and chemotaxonomic analyses, strain CM1E1T represents a novel species of the genus Kocuria, for which the name Kocuria arsenatis sp. nov. is proposed. The type strain is CM1E1T ( = CCBAU 101092T = HAMBI 3625T = LMG 28671T).
-
-
-
Streptosporangium algeriense sp. nov., an actinobacterium isolated from desert soil
The taxonomic position of a novel actinobacterium, strain 169T, isolated from a sample of Algerian Saharan soil, was determined using a polyphasic taxonomic approach. The aerial mycelium produced non-motile, round- to oval-shaped spores, with a smooth surface, which were sessile or carried by short sporophores. Chemotaxonomically, isolate 169T showed the same results as members of the genus Streptosporangium, but madurose, the so far diagnostic sugar of the genus, was not detected in the whole-cell hydrolysate. Despite the absence of sporangia, the 16S rRNA gene sequence analysis confirmed that strain 169T was a member of the genus Streptosporangium. Strain 169T was most closely related to Streptosporangium jomthongense NBRC 110047T (99.3 % 16S rRNA gene sequence similarity), which is the only non-sporangia-forming species reported among the genus. However, DNA–DNA hybridization studies with this species showed 60 % relatedness. Based upon genotypic and phenotypic data, a novel species, Streptosporangium algeriense sp. nov., is proposed, with 169T ( = DSM 45455T = MTCC 11561T = CCUG 62974T) as the type strain.
-
- Firmicutes and related organisms
-
-
Brevibacillus sediminis sp. nov., isolated from a hot spring
Strain YIM 78300T, a novel Gram-stain-positive, moderately thermophilic, endospore-forming, rod-shaped, motile bacterium, was recovered from the sediment of a hot spring in the Tagejia Geothermal Field, Angren, Tibet province, western China. Optimum growth was observed at 50–55 °C, at pH 7.0 and with 0–1.5 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence of strain YIM 78300T indicated that it belongs to the genus Brevibacillus. Similarity levels between the 16S rRNA gene sequences of the new isolate and those of the type strains of Brevibacillus members were 96.9–96.3 %; highest sequence similarity was with Brevibacillus thermoruber DSM 7064T. The predominant menaquinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 and iso-C17 : 0. The major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified phospholipids, an unidentified aminophospholipid and two unidentified polar lipids. The G+C content of the genomic DNA of strain YIM 78300T was 57.9 mol%. Based on phylogenetic analyses, and physiological and biochemical characteristics, strain YIM 78300T is considered to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus sediminis sp. nov. is proposed. The type strain is YIM 78300T ( = DSM 29928T = CPCC 100738T).
-
-
-
Paenibacillus cavernae sp. nov., isolated from soil of a natural cave
More LessA Gram-reaction-variable, strictly aerobic, motile, rod-shaped bacterium, designated strain C4-5T, was isolated from soil of a natural cave. Cells were oxidase- and catalase-positive and formed endospores in sporangia. The 16S rRNA gene sequence comparison showed that the organism formed a distinct clade within the genus Paenibacillus and was most closely related to Paenibacillus contaminans CKOBP-6T ( = KCTC 13623T) (96.85 % 16S rRNA gene sequence similarity) followed by Paenibacillus doosanensis CAU 1005T ( = KCTC 33036T) (94.82 %). The following chemotaxonomic features of strain C4-5T are typical for the genus Paenibacillus: meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, the major fatty acids of anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 and the DNA G+C content of 54.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminophospholipids. The phenotypic and phylogenetic data presented support that strain C4-5T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus cavernae sp. nov. is proposed. The type strain is C4-5T ( = KCTC 33652T = DSM 100100T).
-
-
-
Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments
More LessA halotolerant, Gram-positive bacterium (strain NE-14T), which was isolated from sediment samples of the South China Sea, was subjected to a taxonomic study. Strain NE-14T grew well at wide temperature and pH ranges, 10.0–45.0 °C and pH 6–10, with an optimum at 30 °C and pH 8.0, respectively. Growth of strain NE-14T was observed at total salt concentrations of 0–10 % (w/v) with optimum at 2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that the isolate belongs to the genus Bacillus. Strain NE-14T was related most closely to Bacillus shackletonii LMG 18435T, Bacillus bataviensis LMG 21833T, Bacillus idriensis SMC 4352-2T and Bacillus drentensis LMG 21831T with 16S rRNA gene sequence similarities of 96.2, 95.9, 95.8 and 95.7 %, respectively. DNA–DNA hybridization between strain NE-14T and B. shackletonii LMG 18435T, B. bataviensis LMG 21833T, B. idriensis SMC 4352-2T and B. drentensis LMG 21831T gave reassociation values of about 27.4, 22.4, 16.4 and 15.9 %, respectively. The DNA G+C content of strain NE-14T was 39.2 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain NE-14T were iso-C15 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain NE-14T be classified as representing a novel species of the genus Bacillus, for which the name Bacillus ectoiniformans sp. nov. is proposed. The type strain is NE-14T ( = DSM 28970T = JCM 30397T).
-
-
-
Saccharibacillus deserti sp. nov., isolated from desert soil
More LessA Gram-stain-positive, facultatively anaerobic bacterial strain, designated WLJ055T, with polar and subpolar flagella was isolated from the top layer of desert soil from Erdos, Inner Mongolia, northern China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain WLJ055T was a member of the genus Saccharibacillus, and shared 97.17–97.24 % 16S rRNA gene sequence similarities with Saccharibacillus sacchari GR21T and Saccharibacillus kuerlensis HR1T. The major polar lipids of strain WLJ055T were diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone, while anteiso-C15 : 0, C16 : 0, iso-C16 : 0, and anteiso-C17 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 55.5 mol%. DNA–DNA hybridization revealed that strain WLJ055T showed 45 ± 5 % and 40 ± 5 % genomic DNA relatedness with its two closest relatives, S. sacchari GR21T and S. kuerlensis HR1T, respectively. The results of physiological and biochemical tests allowed the discrimination of strain WLJ055T from its phylogenetic relatives. Saccharibacillus deserti sp. nov. is therefore proposed to be a novel species of the genus Saccharibacillus, with strain WLJ055T ( = CGMCC 1.15276T = KCTC 33693T) as the type strain.
-
-
-
Haloimpatiens lingqiaonensis gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater
An anaerobic bacterium, strain ZC-CMC3T, was isolated from a wastewater sample in Zhejiang, China. Cells were Gram-stain-positive, peritrichous, non-spore-forming, rod-shaped (0.6–1.2 × 2.9–5.1 μm) and catalase- and oxidase-negative. Strain ZC-CMC3T was able to grow at 25–48 °C (optimum 43 °C) and pH 5.5–8.0 (optimum pH 7.0). The NaCl concentration range for growth was 0–3 % (w/v) (optimum 0 %). The major polar lipids of the isolate were diphosphatidylglycerol, phosphatidylglycerol, several phospholipids and glycolipids. Main fermentation products from PYG medium were formate, acetate, lactate and ethanol. Substrates which could be utilized were peptone, tryptone, yeast extract and beef extract. No respiratory quinone was detected. The main fatty acids were C14 : 0, C16 : 0, C16 : 1 cis 7 and C16 : 1 cis 9. The DNA G+C content was 30.0 mol%. 16S rRNA gene sequence analysis revealed that the isolate belonged to the family Clostridiaceae. Phylogenetically, the most closely related species were Oceanirhabdus sediminicola NH-JN4T (92.8 % 16S rRNA gene sequence similarity) and Clostridium tepidiprofundi SG 508T (92.6 %). On the basis of phylogenetic, chemotaxonomic and phenotypic characteristics, strain ZC-CMC3T represents a novel species of a new genus in the family Clostridiaceae, for which the name Haloimpatiens lingqiaonensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZC-CMC3T ( = KCTC 15321T = JCM 19210T = CCTCC AB 2013104T).
-
-
-
Brevibacillus gelatini sp. nov., isolated from a hot spring
More LessTwo Gram-stain-positive, moderately thermophilic, endospore-forming, rod-shaped, motile bacteria designated PDF4T and PDF10, were isolated from Camkoy hot spring in the provinces of Aydın, Turkey and were characterized in order to determine their phylogenetic position. 16S rRNA gene sequence analysis revealed that the two strains belonged to the genus Brevibacillus. Strain PDF4T showed highest 16S rRNA gene sequence similarity to strain PDF10 (99.5 %), Brevibacillus brevis DSM 30T (98.9 %), Brevibacillus parabrevis DSM 8376T (98.6 %) and Brevibacillus formosus DSM 9885T (98.5 %); similarities to other species of the genus Brevibacillus were less than 98.5 %. The predominant fatty acids of strain PDF4T were anteiso-C15 : 0 (60.0 %) and iso-C15 : 0 (22.3 %). The polar lipids of strain PDF4T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unknown phospholipid, two unknown lipid, an unknown aminophospholipid and two unknown aminolipids. MK-7 was detected as a sole respiratory quinone, and the cell wall of strain PDF4T contained meso-diaminopimelic acid. The DNA G+C content of strain PDF4T was 51.7 mol%. DNA–DNA hybridization showed less than 60 % relatedness between strain PDF4T and type strains of the most closely related species given above. Based on these data, the two strains are considered to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus gelatini sp. nov. is proposed. The type strain is PDF4T ( = NCCB 100559T = DSM 100115T).
-
-
-
Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor
More LessStrain BEY10T was isolated from an old fermentation pit, which had been used for the production of Chinese strong-flavoured liquor for over 20 years. The strain was strictly anaerobic, Gram-stain positive, rod-shaped, non-motile and spore-forming. Strain BEY10T grew at temperatures of 22–47 °C (optimum 37 °C), at pH 5.5–9.0 (optimum pH 7.5–8.5) and with NaCl concentrations of 0–4 % (w/v) (optimum 0 %). The isolate was able to utilize glucose, mannitol, lactose, xylose, maltose, glycerol, cellobiose and trehalose as carbon sources for growth. The major end-products from glucose fermentation were ethanol and butyric acid. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phospholipids, a glycolipid and an aminolipid. The predominant fatty acids (>10 %) were C20 : 0, C18 : 0, C16 : 0, C12 : 0 and C14 : 0. The DNA G+C content was 34.4 mol%. Sequence analysis of the 16S rRNA gene indicated that strain BEY10T belongs to the genus Clostridium in the family Clostridiaceae. The closest phylogenetic neighbour is Clostridium lundense DSM 17049T, showing 97.6 % 16S rRNA gene sequence similarity with strain BEY10T. DNA–DNA relatedness values of strain BEY10T with Clostridium lundense DSM 17049T, Clostridium tetanomorphum DSM 4474T and Clostridium pascui DSM 10365T were 58.8 %, 57.9 % and 42.2 %, respectively. This characterization based on phylogenetic, phenotypic and chemotaxonomic evidence demonstrated that strain BEY10T represents a novel species of the genus Clostridium, for which the name Clostridium liquoris sp. nov. is proposed. The type strain is BEY10T ( = ACCC 00785T = DSM 100320T).
-
-
-
Paenibacillus marchantiophytorum sp. nov., isolated from the liverwort Herbertus sendtneri
More LessA Gram-stain-positive, aerobic, motile, rod-shaped, endospore-forming bacterium, designated strain R55T, was isolated from the liverwort Herbertus sendtneri growing at Gawalong glacier, Tibet, and characterized by using a polyphasic taxonomic approach. The major fatty acids of strain R55T were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the predominant polar lipids and occurred along with two unidentified aminophospholipids, one unidentified phospholipid and one unidentified aminolipid. Strain R55T contained MK-7 as the dominant menaquinone and meso-diaminopimelic acid as the major diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R55T was affiliated to species of the genus Paenibacillus, and was related most closely to Paenibacillus ferrarius CY1T (97.1 % similarity). However, the DNA–DNA relatedness between this strain and strain R55T was only 44.1 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain R55T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus marchantiophytorum sp. nov. is proposed. The type strain is R55T ( = CGMCC 1.15043T = DSM 29850T).
-
-
-
Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp. nov.
More LessA genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of ‘Desulfotomaculum reducens’ strain MI-1. Phenotypically, ‘Desulfotomaculum reducens’ strain MI-1 can be distinguished from the other described Desulfotomaculum species of subgroup 1a by its ability to grow with propionate and butyrate. In addition, the strain is able to use a variety of metals as electron acceptors. Metal reduction has not been tested in the other species, but seems likely based on our genome analysis. Phylogenetic 16S rRNA gene sequence analysis and the average nucleotide identity between the genomes of the species of subgroup 1a show that strain MI-1 represents a novel species within the Desulfotomaculum 1a subgroup, Desulfotomaculum reducens sp. nov. The type strain is MI-1T.
-
-
-
Reclassification of Eubacterium rectale (Hauduroy et al. 1937) Prévot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows
Three strains of a butyrate-producing bacterium were isolated from the rumen contents of grazing sheep and cows. The strains were anaerobic, with Gram-positive cell walls, straight-to-slightly-curved, rod-shaped, non-spore-forming and single flagellate. C14 : 1, C14 : 0, C16 : 0 and C16 : 1 were the predominant fatty acids. The cell-wall peptidoglycan type was A1γ. The DNA G+C content varied from 41.4 to 42.2 mol%. 16S rRNA gene sequence similarities between the isolates and Eubacterium rectale, Roseburia hominis and Roseburia intestinalis were found to be 96, 95 and 95 %, respectively. The phylogenetic tree showed that the strains constituted a different taxon, separate from other taxa with validly published names and forming a cluster with strains of Eubacterium rectale. On the basis of phenotypic, chemotaxonomic and phylogenetic results (16S RNA, dnaK, groEL, atpA genes), the isolates are considered to represent a novel species of a new genus of the family Lachnospiraceae, for which the name Agathobacter ruminis gen. nov., sp. nov. is proposed (type strain JK623T = DSM 29029T = LMG 28559T). We also propose the transfer of Eubacterium rectale to the new genus as Agathobacter rectalis gen. nov., comb nov. This new genus represents saccharoclastic, chemo-organotrophic and obligatory anaerobic, non-spore-forming rods with Gram-positive membrane. The main fermentation products on peptone yeast glucose (PYG) medium were butyrate, acetate, hydrogen and lactate. The type species of the genus is Agathobacter rectalis gen. nov., comb nov. ( Prévot, 1938 ) with type strain ATCC 33656T ( = JCM 17463T).
-
-
-
Lachnotalea glycerini gen. nov., sp. nov., an anaerobe isolated from a nanofiltration unit treating anoxic groundwater
A strictly anaerobic bacterium, strain DLD10T, was isolated from a biofilm that developed on a nanofiltration membrane treating anoxic groundwater using glycerol as substrate. Cells were straight to slightly curved rods 0.2–0.5 μm in diameter and 1–3 μm in length, non-motile and non-spore-forming. The optimum temperature and pH for growth were 30 °C and pH 7.0. Strain DLD10T was able to grow in the presence of 0.03–4.5 % (w/v) NaCl. Substrates utilized by strain DLD10T included glycerol and various carbohydrates (glucose, sucrose, fructose, mannose, arabinose, pectin, starch, xylan), which were mainly converted to ethanol, acetate, H2 and formate. Thiosulphate, sulphur and Fe(III) were used as electron acceptors, but sulphate, fumarate and nitrate were not. The predominant membrane fatty acids were C16 : 0, iso-C17 : 1 and C17 : 1ω8c. The DNA G+C content was 36.4 mol%. Strain DLD10T belongs to the family Lachnospiraceae and is distantly related to Clostridium populeti DSM 5832T, Hespellia porcina DSM 15481T and Robinsoniella peoriensis CCUG 48729T (93 % 16S rRNA gene sequence similarity). Physiological characteristics and phylogenetic analysis indicated that strain DLD10T is a representative of a novel species of a new genus, for which the name Lachnotalea glycerini gen. nov., sp. nov. is proposed. The type strain of Lachnotalea glycerini is DLD10T ( = DSM 28816T = JCM 30818T).
-
-
-
Bacillus oceani sp. nov., isolated from seawater
More LessTwo Gram-staining-positive, endospore-forming, rod-shaped bacterial strains, designated strain SW109T and strain W006, were isolated from a seawater sample collected from the Indian Ocean. The strains were strictly aerobic, catalase- and oxidase-positive and motile by peritrichous flagella. The predominant cellular fatty acids (>10 %) were anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0. The major menaquinone was menaquinone-7 (MK-7) and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content of strain SW109T and strain W006 was 46.3 and 46.1 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains represented a novel member of the genus Bacillus, showing the highest similarity with Bacillus halodurans LMG 7121T and Bacillus okuhidensis DSM 13666T (96.4 and 96.2 % sequence similarity, respectively). On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that the two strains represent a novel species of the genus Bacillus, for which the name Bacillus oceani sp. nov. is proposed. The type strain is SW109T ( = CGMCC 1.12347T = DSM 100579T).
-
-
-
Paenibacillus etheri sp. nov., able to grow on media supplemented with methyl tert-butyl ether (MTBE) and isolated from hydrocarbon-contaminated soil
More LessA bacterial strain, designated SH7T, was isolated from the hydrocarbon-contaminated soil of a pilot plant (Granada, Spain). The strain was selected for its capacity to grow in media supplemented with methyl tert-butyl ether (MTBE) as sole energy and carbon source. Strain SH7T was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. Phylogenetic analysis using 16S rRNA gene sequences showed that strain SH7T belongs to a cluster comprising species of the genus Paenibacillus and was closely related to Paenibacillus borealis KK19T (97 % 16S rRNA gene sequence similarity) and Paenibacillus odorifer TOD45T (98 %). DNA–DNA hybridization tests showed low relatedness of strain SH7T with the type strains of Paenibacillus borealis (16.9 ± 1.5 %) and Paenibacillus odorifer (16.6 ± 2.1 %). The cell wall of strain SH7T contained meso-diaminopimelic acid. The predominant respiratory quinone was MK-7, and anteiso-C15 : 0 (32.9 %) and C16 : 0 (29.0 %) were the predominant cellular fatty acids. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and three unknown aminophospholipids were the major phospholipids. The DNA G+C content was 44.3 mol%. Data obtained in this study indicate that strain SH7T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus etheri sp. nov. is proposed. The type strain is SH7T ( = CECT 8558T = DSM 29760T).
-
-
-
Paenibacillus nasutitermitis sp. nov., isolated from a termite gut
More LessA Gram-stain-positive, non-motile, aerobic and terminal-endospore-forming rod-shaped bacterium, strain P5-1T, was isolated from the hindgut of a wood-feeding higher termite, Nasutitermes sp. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain was closely related to Paenibacillus sepulcri CCM 7311T (97.5 % similarity). Growth was observed at 10–40 °C (optimum, 30 °C) and at pH 5.5–9.0 (optimum, pH 7.5). The DNA G+C content of strain P5-1T was 48.9 mol%. Cells contained menaquinone 7 (MK-7) as the sole respiratory quinone and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid and one unidentified aminophospholipid. The diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained within this study, strain P5-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus nasutitermitis sp. nov. is proposed. The type strain is P5-1T ( = CGMCC 1.15178T = NBRC 111536T).
-
-
-
Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples
More LessA novel aerobic bacterium, designated strain LAM0050T, was isolated from a biogas slurry sample, which had been enriched with diesel oil for 30 days. Cells of strain LAM0050T were gram-stain-negative, non-motile, non-spore-forming and coccoid-shaped. The optimal temperature and pH for growth were 30–35 °C and 8.5, respectively. The strain did not require NaCl for growth, but tolerated up to 5.3 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain LAM0050T was a member of the genus Advenella, and was most closely related to Advenella faeciporci KCTC 23732T, Advenella incenata CCUG 45225T, Advenella kashmirensis DSM 17095T and Advenella mimigardefordensis DSM 17166T, with 98.1, 96.6, 96.6 and 96.3 % sequence similarity, respectively. The DNA–DNA hybridization relatedness between strain LAM0050T and A. faeciporci KCTC 23732T was 41.7 ± 2.4 %. The genomic DNA G+C content was 51.2 mol%, as determined by the T m method. The major fatty acids of strain LAM0050T were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant ubiquinone was Q-8. The main polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and four unidentified phospholipids. Based on the phenotypic and genotypic properties, strain LAM0050T is suggested to represent a novel species of the genus Advenella, for which the name Advenella alkanexedens sp. nov., is proposed, the type strain is LAM0050T ( = ACCC 06485T = JCM 30465T).
-
-
-
Sellimonas intestinalis gen. nov., sp. nov., isolated from human faeces
More LessA Gram-stain-positive and obligately anaerobic bacterial strain, BR72T, forming ivory yellow colonies was isolated from a faecal sample of a healthy Korean woman. 16S rRNA gene sequence analysis indicated that strain BR72T belongs to Clostridium cluster XIVa and represents a distinct phyletic line within the family Lachnospiraceae. The most closely related strains were Clostridium nexile DSM 1787T (94.1 % 16S rRNA gene sequence similarity), Coprococcus comes ATCC 27758T (93.5 %), Ruminococcus torques ATCC 27756T (93.5 %), Ruminococcus lactaris ATCC 29176T (93.5 %), Clostridium aerotolerans DSM 5434T (93.1 %) and Eubacterium fissicatena DSM 3598T (92.9 %). The DNA G+C content of strain BR72T based on its genome sequence was 45.3 mol%. The major cellular fatty acids were C16 : 0, C14 : 0, and iso-C17 : 1 I and/or anteiso-C17 : 1 B. Acetic acid was produced from glucose fermentation. Other physiological and biochemical comparisons allowed the phenotypic differentiation of strain BR72T from the members of the family Lachnospiraceae. Based on the phylogenetic and phenotypic findings, this strain is considered to represent a novel species of a new genus belonging to the family Lachnospiraceae and the name Sellimonas intestinalis gen. nov., sp. nov. is proposed. The type strain of Sellimonas intestinalis is BR72T ( = KCTC 15479T = JCM 30749T).
-
-
-
Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus
Qing-Lei Sun and Li SunIn this study, we report a novel Gram-stain-positive bacterium, designated strain S6T, isolated from deep-sea sediment in Okinawa Trough. Growth of strain S6T occurred at 10–45 °C (optimum, 35 °C), at pH 6.0–11.0 (optimum, 8.0) and with 0–8 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain S6T belonged to the genus Domibacillus. The closest phylogenetic neighbours of strain S6T were Domibacillus robiginosus WS 4628T ( = DSM 25058T) (98.6 %16S rRNA gene sequence similarity), D. indicus SD111T ( = DSM 28032T) (97.6 %), D. enclensis NIO-1016T ( = DSM 25145T) (97.6 %), and ‘D. tundrae’ PAMC 80007 ( = DSM 29572) (97.6 %). Levels of similarity between strain S6T and other close relatives were below 96 %. The levels of DNA–DNA relatedness between strain S6T and its closest relatives in the genus Domibacillus were well below 70 %. The genomic DNA G+C content of strain S6T was 44.4 mol%. The major menaquinone was MK-6. The polar lipids of strain S6T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylethanolamine and three unknown phospholipids. Strain S6T harboured meso-diaminopimelic acid as the diagnostic diamino acid and an A1γ type of peptidoglycan. The major cell-wall sugars of strain S6T were xylose and glucose. Phylogenetic, physiological, biochemical and morphological analyses suggest that this strain represents a novel species of the genus Domibacillus, for which the name Domibacillus iocasae sp. nov. is proposed. The type strain is S6T ( = DSM 29979T = CCTCC AB 2015183T). An emended description of the genus Domibacillus is also provided.
-
-
-
Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species
More LessThe genus Clostridium as presently constituted is phylogenetically and phenotypically incoherent. Data from polyphasic taxonomic studies indicate that the genus comprises a collection of very heterogeneous species. Numerous phylogenetic studies, principally based on sequencing of the 16S rRNA gene, indicate that the genus Clostridium should be restricted to Clostridium cluster I as Clostridium sensu stricto. Despite these findings, authors continue to add novel species to the genus Clostridium that do not fall within the radiation of cluster I and the type species Clostridium butyricum, thus perpetuating the confusion associated with the taxonomy of this group. Here, we formally propose that members of the genus Clostridium Prazmowski be restricted to the type species C. butyricum and cluster I species. Eubacterium moniliforme, Eubacterium tarantellae, Sarcina maxima and Sarcina ventriculi should be transferred to the genus Clostridium as Clostridium moniliforme comb. nov., Clostridium tarantellae comb. nov., Clostridium maximum comb. nov. and Clostridium ventriculi comb. nov. A novel genus, Hathewaya gen. nov., is proposed for the species Clostridium histolyticum, Clostridium limosum and Clostridium proteolyticum as Hathewaya histolytica gen. nov. comb. nov., Hathewaya limosa comb. nov. and Hathewaya proteolytica comb. nov. The type species of the genus Hathewaya is Hathewaya histolytica.
-
-
-
Bacillus cucumis sp. nov. isolated from the rhizosphere of cucumber (Cucumis sativus)
A facultative anaerobic, Gram-positive staining, endospore-forming bacterium, isolated from the rhizosphere of cucumber (Cucumis sativus), was taxonomically investigated. Based on 16S rRNA gene sequence similarity comparisons, strain AP-6T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus drentensis LMG 21831T (99.1 %), Bacillus vireti LMG 21834T (98.7 %) and Bacillus soli LMG 21838T (98.5 %). The 16S rRNA gene sequence similarity to the sequences of the type strains of other species of the genus Bacillus was 98.5 % or less. Chemotaxonomic features supported the grouping of the strain in the genus Bacillus; for example, the major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7 and the major compound in the polyamine pattern was spermidine. Additionally, DNA–DNA hybridization with B. drentensis LMG 21831T, B. vireti LMG 21834T and B. soli LMG 21838T resulted in relatedness values that were clearly below 70 %. Physiological and biochemical test results were also different from those of the most closely related species. As a consequence, AP-6T represents a novel species of the genus Bacillus, for which the name Bacillus cucumis sp. nov. is proposed, with AP-6T ( = CIP 110974T = CCM 8651T) as the type strain.
-
-
-
Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin
More LessA Gram-stain-positive, catalase-negative, coccus-shaped organism was isolated from the oral cavity of tufted capuchin (Cebus apella). Comparative 16S rRNA gene sequence analysis suggested classification of the organism within the genus Streptococcus. Strain M8T was related most closely to Streptococcus oralis ATCC 35037T (96.17 % similarity) followed by Streptococcus massiliensis CCUG 49690T (95.90 %) based on the 16S rRNA gene. Strain M8T was related most closely to S. massiliensis CCUG 49690T (86.58 %) based on the RNA polymerase β subunit-encoding gene (rpoB), and to Streptococcus tigurinus AZ_3aT (81.26 %) followed by S. massiliensis CCUG 49690T (80.45 %) based on the 60 kDa heat-shock protein gene (groEL). The phylogenetic trees of 16S rRNA, rpoB and groEL gene sequences showed that strain M8T was most closely related to S. massiliensis. Based on phenotypic characterization as well as 16S rRNA gene and housekeeping gene (rpoB and groEL) sequence data, a novel taxon, Streptococcus oricebi sp. nov. (type strain M8T = JCM 30719T = DSM 100101T), is proposed.
-
- Proteobacteria
-
-
Description of ‘Candidatus Berkiella aquae’ and ‘Candidatus Berkiella cookevillensis’, two intranuclear bacteria of freshwater amoebae
Two novel bacteria of the phylum Proteobacteria were isolated during searches for amoeba-resistant micro-organisms in natural and constructed water systems. Strain HT99 was isolated from amoebae found in the biofilm of an outdoor hot tub in Cookeville, Tennessee, USA, and strain CC99 was isolated from amoebae in the biofilm of a cooling tower in the same city. Both bacteria were Gram-stain-negative cocci to coccobacilli, unculturable on conventional laboratory media, and were found to be intranuclear when maintained in Acanthamoeba polyphaga. The genomes of both isolates were completely sequenced. The genome of CC99 was found to be 3.0 Mbp with a 37.9 mol% DNA G+C content, while the genome of HT99 was 3.6 Mbp with a 39.5 mol% DNA G+C content. The 16S rRNA gene sequences of the two isolates were 94 % similar to each other. Phylogenetic comparisons of the 16S rRNA, mip and rpoB genes, the DNA G+C content and the fatty acid composition demonstrated that both bacteria are members of the order Legionellales, and are most closely related to Coxiella burnetii. The phenotypic and genetic evidence supports the proposal of novel taxa to accommodate these strains; however, because strains HT99 and CC99 cannot be cultured outside of the amoeba host, the respective names ‘Candidatus Berkiella aquae’ and ‘Candidatus Berkiella cookevillensis’ are proposed.
-
-
-
Arcobacter pacificus sp. nov., isolated from seawater of the South Pacific Gyre
More LessA Gram-stain-negative, rod-shaped, slightly curved, non-spore-forming strain, designated SW028T, was isolated from surface seawater (26° 29′ S 137° 56′ W) of the South Pacific Gyre during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW028T belonged to the genus Arcobacter and it showed the highest sequence similarity with Arcobacter molluscorum LMG 25693T (95.50 %). The dominant fatty acids of strain SW028T were C18 : 1ω7c, C16 : 1ω7c and C16 : 0. The only respiratory quinone detected was menaquinone-6. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 27.1 mol%. The phylogenetic position of the novel strain was further confirmed by analysis of the housekeeping genes rpoB, gyrB and atpA. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain SW028T represents a novel species of the genus Arcobacter, for which the name Arcobacter pacificus is proposed. The type strain is SW028T ( = DSM 25018T = JCM 17857T = LMG 26638T = CGMCC NO.1.11011T).
-
-
-
Testudinibacter aquarius gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of freshwater turtles
A total of 13 Pasteurellaceae isolates from healthy freshwater turtles were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group. The closest related species based on 16S rRNA gene sequencing was Chelonobacter oris CCUG 55632T with 94.4 % similarity and the closest related species based on rpoB gene sequence comparison was [Pasteurella] testudinis CCUG 19802T with 91.5 % similarity. All the investigated isolates exhibited phenotypic characteristics of the family Pasteurellaceae. However, they could be separated from existing genera of the Pasteurellaceae by the following test results: indole, ornithine decarboxylase and Voges–Proskauer positive; and methyl red, urease and PNPG (α-glucosidase) negative. No X- or V-factor requirement was observed. A zone of β-haemolysis surrounded the colonies after 24 h of incubation on bovine blood agar at 37 °C. Acid was produced from l-arabinose, dulcitol, d-mannitol, sucrose and trehalose. Representative strain ELNT2xT had a fatty acid profile that was characteristic for members of the Pasteurellaceae. ELNT2xT expressed only one respiratory quinone, ubiquinone-8 (100 %). The DNA G+C content of strain ELNT2xT was 42.8 mol%. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the strains should be classified as representatives of a novel species of a new genus, Testudinibacter aquarius gen. nov., sp. nov. The type strain of Testudinibacter aquarius is ELNT2xT ( = CCUG 65146T = DSM 28140T), which was isolated from the oral cavity of a captive eastern long-necked turtle (Chelodina longicollis) in Denmark in 2012.
-
-
-
Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment
More LessA novel marine bacterial strain, designated JAMH 043T, was isolated from cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-motile and aerobic chemo-organotrophs. The isolate grew optimally at 25 °C, at pH 7.0–7.5 and with 3 % (w/v) NaCl. The major respiratory quinone was ubiquinone-10 (Q-10). The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated to members of the genus Thalassobius in the class Alphaproteobacteria, and 16S rRNA gene sequence similarity of the novel isolate with the type strain of its closest related species, Thalassobius aestuarii JC2049T, was 98.4 %. The DNA G+C content of the novel strain was 58.0 mol%. The hybridization values for DNA–DNA relatedness between strain JAMH 043T and reference strains belonging to the genus Thalassobius were less than 14.1 ± 2.2 %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Thalassobius, for which the name Thalassobius abyssi sp. nov. is proposed. The type strain is JAMH 043T ( = JCM 30900T = DSM 100673T).
-
-
-
Tagaea marina gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water
More LessA Gram-negative, heterotrophic, marine bacterium, designated strain TT1T, was isolated from seawater collected from the shallow coastal region of Anping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The isolate required NaCl for growth and exhibited optimal growth at 30–35 °C, 2–4 % NaCl and pH 7–8. Strain TT1T grew aerobically and was not capable of anaerobic growth by fermentation of glucose or other carbohydrates. Q-10 was the sole major isoprenoid quinone. Cellular fatty acids were dominated by C18 : 1ω7c (47.5 %), C18 : 1 2-OH (16.3 %) and C19 : 0ω8c cyclo (10.6 %). The DNA G+C content was 56.4 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain TT1T formed a distinct genus-level lineage in the family Rhodospirillaceae of the class Alphaproteobacteria and exhibited the highest sequence similarity with species of the genera Thalassobaculum (89.9–90.0 % 16S rRNA gene sequence similarity), Oceanibaculum (89.4–89.9 %) and Nisaea (89.1–89.7 %). Strain TT1T could be distinguished from species of these phylogenetically closest genera based on differences in DNA G+C contents (56.4 mol% vs 60.0–68.0 mol%), fatty acid profiles and some physiological characteristics. On the basis of the polyphasic taxonomic data from this study, strain TT1T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Tagaea marina gen. nov., sp. nov. is proposed. The type strain of the type species is TT1T ( = JCM 18659T = BCRC 80493T).
-
-
-
Roseovarius atlanticus sp. nov., isolated from surface seawater
A taxonomic study was carried out on strain R12BT, which was isolated from surface seawater of the Atlantic Ocean. The bacterium was observed to be rod-shaped, Gram-stain-negative, oxidase-positive and weakly positive for catalase. Growth was observed at salinities of 0.5–15 % and at temperatures of 4–45 °C. The isolate was incapable of nitrate reduction and hydrolysis of gelatin, Tween 80 and aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R12BT belonged to the genus Roseovarius, with highest sequence similarity to Roseovarius indicus B108T (97.2 % 16S rRNA gene sequence similarity), followed by Roseovarius halotolerans HJ50T (96.8 %); other species of genus Roseovarius shared 93.0–96.2 % sequence similarities. The DNA–DNA hybridization estimate value between strain R12BT and R. indicus B108T was 23.2 ± 2.4 %. The average nucleotide identity between strain R12BT and R. indicus B108T was 77.1 %. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and C16 : 0. The G+C content of the chromosomal DNA was 63.6 mol%. The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two aminolipids, two phospholipids and some unidentified lipids were present. The combined genotypic and phenotypic data show that strain R12BT represents a novel species of the genus Roseovarius, for which the name Roseovarius atlanticus sp. nov. is proposed, with the type strain R12BT ( = MCCC 1A09786T = KCTC 42506T).
-
-
-
Description of Luteimonas pelagia sp. nov., isolated from marine sediment, and emended descriptions of Luteimonas aquatica, Luteimonas composti, Luteimonas mephitis, Lysobacter enzymogenes and Lysobacter panaciterrae
An aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain CC-VAM-7T, was isolated from a marine sediment sample collected at Kending, Taiwan. The isolate grew optimally at pH 7.0 and 30 °C and in the presence of 4 % (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were the type strains of Luteimonas huabeiensis (95.2 %) and Lysobacter defluvii (95.0 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CC-VAM-7T clustered with members of the genus Luteimonas. Strain CC-VAM-7T possessed C15 : 1ω5c, C16 : 1ω5c, iso-C11 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0 3-OH and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c) as predominant fatty acids. The polar lipid profile contained major amounts of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate amounts of an unidentified phospholipid. The genomic DNA G+C content was 73.4 mol%. Ubiquinone 8 (Q-8) was the predominant respiratory quinone. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, which were in line with those of other members of the genus Luteimonas, strain CC-VAM-7T is proposed to represent a novel species within the genus Luteimonas, for which the name Luteimonas pelagia sp. nov. is proposed. The type strain is CC-VAM-7T ( = BCRC 80558T = JCM 18792T). In addition, we propose emended descriptions of Luteimonas aquatica Chou et al. 2008 , Luteimonas composti Young et al. 2007 , Luteimonas mephitis Finkmann et al. 2000 , Lysobacter enzymogenes Christensen and Cook 1978 and Lysobacter panaciterrae Ten et al. 2009 .
-
-
-
Marivivens donghaensis gen. nov., sp. nov., isolated from seawater
More LessA Gram-stain-negative, non-flagellated, aerobic and coccoid, ovoid or rod-shaped bacterium, designated AM-4T, was isolated from seawater collected from the East Sea, South Korea and subjected to a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30–35 °C, at pH 7.0–8.0 and in the presence of 1.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain AM-4T forms a distinct evolutionary lineage independent of other taxa of the family Rhodobacteraceae. Strain AM-4T exhibited 16S rRNA gene sequence similarities of 95.1–95.5 % to the type strains of Aestuariihabitans beolgyonensis, Donghicola eburneus and Pseudooctadecabacter jejudonensis, and of less than 94.9 % to the type strains of other taxa. Strain AM-4T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids detected in strain AM-4T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid, one unidentified aminolipid and one unidentified glycolipid. The fatty acid and polar lipid profiles of strain AM-4T were distinguished from those of the phylogenetically related taxa. The DNA G+C content of strain AM-4T was 57.2 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain AM-4T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Marivivens donghaensis gen. nov., sp. nov., is proposed. The type strain of the type species is AM-4T ( = KCTC 42776T = CECT 8947T).
-
-
-
Novosphingobium colocasiae sp. nov., isolated from a taro field
More LessA novel bacterial strain, designated Teta-03T, was isolated from a taro field in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain Teta-03T were aerobic, Gram-stain-negative, rod-shaped and non-motile and formed bright yellow colonies. Growth occurred at 10–37 °C (optimum, 20 °C), with 0–1.0 % (w/v) NaCl (optimum, 0 %) and at pH 3.0–9.0 (optimum, pH 7.0–8.0). The major fatty acids (>10 %) of strain Teta-03T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, an uncharacterized glycolipid and an uncharacterized aminolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.0 mol%. On the basis of 16S rRNA gene sequence analysis, strain Teta-03T was shown to belong to the genus Novosphingobium and showed highest similarity to Novosphingobium barchaimii LL02T (96.8 %). 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 Teta-03T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium colocasiae sp. nov. is proposed. The type strain is Teta-03T ( = LMG 27385T = KCTC 32255T).
-
-
-
Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent
A novel thermophilic, facultatively autotrophic bacterium, strain S2479T, was isolated from a thermal spring located in a tidal zone of a geothermally heated beach (Kuril Islands, Russia). Cells of strain S2479T were rod-shaped and motile with a Gram-negative cell-wall type. The temperature range for growth was 35–68 °C (optimum 65 °C), and the pH range for growth was pH 5.5–8.8 (optimum pH 6.5). Growth of strain S2479T was observed in the presence of NaCl concentrations ranging from 0.5 to 3.5 % (w/v) (optimum 1.5–2.0 %). The strain oxidized sulfur and thiosulfate as sole energy sources for autotrophic growth under anaerobic conditions with nitrate as electron acceptor. Strain S2479T was also capable of heterotrophic growth by reduction of nitrate with oxidation of low-chain fatty acids and a limited number of other carboxylic acids or with complex proteinaceous compounds. Nitrate was reduced to N2. Sulfur compounds were oxidized to sulfate. Strain S2479T did not grow aerobically during incubation at atmospheric concentration of oxygen but was able to grow microaerobically (1 % of oxygen in gas phase). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the family Ectothiorhodospiraceae, order Chromatiales, class Gammaproteobacteria. On the basis of phylogenetic and phenotypic properties, strain S2479T represents a novel species of a new genus, for which the name Inmirania thermothiophila gen. nov., sp. nov. is proposed. The type strain of the type species is S2479T ( = DSM 100275T = VKM B-2962T).
-
-
-
Massilia violacea sp. nov., isolated from riverbank soil
A bacterial strain designated CAVIOT was isolated during the course of a study of culturable bacteria in a riverbank soil sample from Tlaxcala, Mexico. The strain was subjected to a polyphasic taxonomic characterization. Strain CAVIOT was aerobic, Gram-stain-negative, non-spore-forming and rod-shaped. Colonies grown on R2A agar at 28 °C were pale violet, mucoid, rounded, smooth and glossy. The strain was motile and catalase- and oxidase-positive, and maximum growth temperature was 35 °C. Strain CAVIOT was classified within the genus Massilia as its 16S rRNA gene sequence was closely related to those of Massilia umbonata LP01T (97.5 % similarity), Massilia dura 16T (97.2 %) and Massilia plicata 76T (97.1 %). The predominant respiratory quinone was Q8. The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unknown phospholipid. The DNA G+C content was 65.0 mol% (Tm). DNA–DNA hybridization results showed values below 25 % with respect to the type strains of the closest related species. Therefore, strain CAVIOT can be differentiated from previously described species of the genus Massilia and represents a novel species, for which the name Massilia violacea sp. nov. is proposed. The type strain is CAVIOT ( = CECT 8897T = LMG 28941T).
-
-
-
Tianweitania sediminis gen. nov., sp. nov., a member of the family Phyllobacteriaceae, isolated from subsurface sediment core
More LessA bacterial strain, designated Z8T, was isolated from the terrestrial sediment of the Mohe Basin in north-east China. Phylogenetic analyses of 16S rRNA genes showed that this strain belonged to the family Phyllobacteriaceae, and was most closely related to Phyllobacterium bourgognense, with a sequence similarity of 96.9 %. The major cellular fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major respiratory quinone was ubiquinone-10. The three major polar lipids of strain Z8T consisted of glycolipids, phosphatidylethanolamine and phosphatidylmethylethanolamine. The DNA G+C content was 59.6 mol%. The chemotaxonomic characteristics of strain Z8T differed in some respects from those of members of the family Phyllobacteriaceae. Based on phylogenetic, phenotypic and chemotaxonomic data, strain Z8T is considered to represent a novel species of a novel genus within the family Phyllobacteriaceae, for which the name Tianweitania sediminis gen. nov., sp. nov. is proposed. The type strain is Z8T ( = CGMCC 1.12944T = JCM 30358T).
-
-
-
Halomonas garicola sp. nov., isolated from saeu-jeot, a Korean salted and fermented shrimp sauce
More LessA Gram-stain-negative, moderately halophilic and facultatively aerobic bacterium capable of respiration with nitrate, designated strain JJ-M1T, was isolated from saeu-jeot, a traditional Korean fermented shrimp sauce. Cells of the strain were non-motile short rods showing oxidase-negative and catalase-positive reactions and the production of pale-yellow pigments. Growth of strain JJ-M1T was observed at 20–37 °C (optimum, 30 °C), pH 5.5–9.5 (optimum, pH 7.0) and in the presence of 3–22.5 % (w/v) sea salts (optimum, 10 %). Strain JJ-M1T contained ubiquinone 9 (Q-9) as the predominant isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C12 : 0 3-OH as the major cellular fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content of strain JJ-M1T was 62.4 mol%. Phylogenetic and comparative analyses, based on 16S rRNA gene sequences, indicated that strain JJ-M1T formed a tight phyletic lineage with Halomonas jeotgali HwaT within the genus Halomonas and was most closely related to Halomonas jeotgali HwaT with 96.2 % 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic features, strain JJ-M1T represents a novel species of the genus Halomonas, for which the name Halomonas garicola sp. nov. is proposed. The type strain is JJ-M1T ( = KACC 18117T = JCM 30151T).
-
-
-
Glaciimonas frigoris sp. nov., a psychrophilic bacterium isolated from ancient Siberian permafrost sediment, and emended description of the genus Glaciimonas
More LessThe bacterial strain N1-38T was isolated from ancient Siberian permafrost sediment. The strain was Gram-reaction-negative, motile by gliding, rod-shaped and psychrophilic, and showed good growth over a temperature range of − 5 to 25 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain N1-38T was most closely related to members of the genus Glaciimonas and shared the highest 16S rRNA gene sequence similarities with the type strains of Glaciimonas alpina (99.3 %), Glaciimonas immobilis (98.9 %) and Glaciimonas singularis (96.5 %). The predominant cellular fatty acids of strain N1-38T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The major respiratory quinone was ubiquinone 8 and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genomic DNA G+C content was 53.0 mol%. Combined data of phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain N1-38T represents a novel species of the genus Glaciimonas, for which the name Glaciimonas frigoris sp. nov. is proposed. The type strain is N1-38T ( = LMG 28868T = CCOS 838T). An emended description of the genus Glaciimonas is also provided.
-
-
-
Comamonas piscis sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii
A novel Gram-stain-negative, obligately aerobic, non-motile and coccus-shaped bacterium, designated strain CN1T, was isolated from the intestine of a Korean rockfish, Sebastes schlegelii. The optimum growth condition for strain CN1T was 25 °C, pH 7 and 0–1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CN1T was in the genus Comamonas and that the nearest type strain was Comamonas koreensis YH12T with 98.65 % 16S rRNA gene sequence similarity. The primary cellular fatty acids of strain CN1T were summed feature 3 (comprised of C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprised of C18 : 1ω6c and/or C18 : 1ω7c). The predominant isoprenoid quinone was ubiquinone Q-8. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, an unidentified lipid, an unidentified phospholipid and two aminophospholipids. The DNA G+C content was 65.5 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain CN1T represents a novel species of the genus Comamonas, for which the name Comamonas piscis sp. nov. is proposed. The type strain is CN1T ( = KACC 18403T = JCM 30718T).
-
-
-
Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules
More LessIn total, 31 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora root nodules and authenticated as rhizobia on this host. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, with the representative strains ICMP 19560T, ICMP 19523T, ICMP 19535T, ICMP 19545T and ICMP 19512T being related most closely to Mesorhizobium sangaii SCAU7T (99.9–99.6 % similarity), Mesorhizobium cantuariense ICMP 19515T (99.7–99.6 %) and Mesorhizobium ciceri UMP-CA7T (99.7–99.5 %). Additionally, the novel strains formed distinct groups based on housekeeping gene sequence analysis and were closely related to Mesorhizobium waimense ICMP 19557T (93.5–94.9, 92.5–95.6 and 94.2–96.0 %), M. cantuariense ICMP 19515T (93.1–97.7, 93.5–95.4 and 94.8–96.8 %) and M. ciceri UMP-CA7T (93.2–97.2, 94.6–96.8 and 95.5–97.3 %) for glnII, recA and rpoB, respectively. Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium, and DNA–DNA hybridizations, matrix-assisted laser desorption/ionization time-of-flight MS analysis, enterobacterial repetitive intergenic consensus PCR, physiological and biochemical tests allowed the genotypic and phenotypic differentiation from their nearest neighbouring species. Therefore, these strains represent five novel species for which the names Mesorhizobium calcicola sp. nov. (type strain ICMP 19560T = LMG 28224T = HAMBI 3609T), Mesorhizobium waitakense sp. nov. (type strain ICMP 19523T = LMG 28227T = HAMBI 3605T), Mesorhizobium sophorae sp. nov. (type strain ICMP 19535T = LMG 28223T = HAMBI 3606T), Mesorhizobium newzealandense sp. nov. (type strain ICMP 19545T = LMG 28226T = HAMBI 3607T) and Mesorhizobium kowhaii sp. nov. (type strain ICMP 19512T = LMG 28222T = HAMBI 3603T) are proposed.
-
-
-
Bacillus cavernae sp. nov. isolated from cave soil
More LessA Gram-stain-positive, spore-forming, motile, strictly aerobic, rod-shaped bacterium, designated strain L5T, was isolated from soil of Tenglong cave, China. 16S rRNA gene sequence analysis showed that strain L5T was related most closely to Bacillus asahii MA001T (96.5 %) (the highest 16S rRNA gene sequence similarity), Bacillus kribbensis BT080T (96.4 %) and Bacillus deserti ZLD-8T (96.2 %). The DNA G+C content of strain L5T was 45.6 mol%. The major menaquinone was MK-7. The major fatty acids were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. In addition, strain L5T had different characteristics compared with the other Bacillus strains such as pink colony colour, low growth temperature and low nutrient requirement. The results indicate that strain L5T represents a novel species of the genus Bacillus, for which the name Bacillus cavernae sp. nov. is proposed. The type strain is L5T ( = KCTC 33637T = CCTCC AB 2015055T).
-
-
-
Vogesella facilis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella
More LessA bacterial strain, designated TTM-24T, was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-24T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, with rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 15–37 °C (optimum, 25 °C), at pH 6.0–8.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-24T belonged to the genus Vogesella and was most closely related to ‘Vogesella amnigena’ Npb-02 with sequence similarity of 97.1 %. Strain TTM-24T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The genomic DNA G+C content of strain TTM-24T was 67.4 mol%. The DNA–DNA hybridization value for strain TTM-24T with ‘V. amnigena’ Npb-02 was less than 45 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-24T should be classified as a novel species, for which the name Vogesella facilis sp. nov. is proposed. The type strain is TTM-24T ( = BCRC 80912T = KCTC 42742T = LMG 29003T).
-
-
-
Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea
More LessA novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l− 1 (optimum 15–20 g l− 1) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( − )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).
-
-
-
Marimicrobium arenosum gen. nov., sp. nov., a moderately halophilic bacterium isolated from sea sand
More LessA Gram-stain-negative, non-pigmented, non-spore-forming, non-motile, strictly aerobic bacterial strain, designated CAU 1038T, was isolated from a sea sand sample in Modo, Republic of Korea, and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1038T grew optimally at 30 °C, pH 7.5 in 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1038T formed a distinct lineage within the class Gammaproteobacteria as a separate deep branch, with 95.2 % or lower sequence similarity to representatives of the genera Haliea, Halioglobus and Chromatocurvus, and 92.3 % or lower with Luminiphilus, Pseudohaliea and Congregibacter. The major cellular fatty acids of strain CAU 1038T were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The polar lipid pattern of the isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The strain contained lipoquinone (Q-8) as the sole respiratory quinone. The G+C content of the genomic DNA was 65 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1038T represents a novel species of a new genus in the family Halieaceae, for which the name Marimicrobium arenosum gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1038T ( = KCTC 42300T = NBRC 110727T).
-
-
-
Ahrensia marina sp. nov., a dimethylsulfoniopropionate-cleaving bacterium isolated from seawater, and emended descriptions of the genus Ahrensia and Ahrensia kielensis
More LessA Gram-stain-negative, strictly aerobic, light-beige, rod-shaped, motile bacterium with peritrichous flagella that cleaves dimethylsulfoniopropionate (DMSP), designated strain LZD062T, was isolated from bottom seawater of the East China Sea. The isolate required sea salts for growth and grew optimally at pH 8.0 and 28 °C and in the presence of 2 % (w/v) NaCl. The major fatty acid (>10 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unidentified aminolipid and one unidentified glycolipid. Ubiquinone Q-10 was the only quinone detected. Phylogenetic analyses based on 16S rRNA and atpD gene sequences placed LZD062T within the genus Ahrensia of the family Phyllobacteriaceae in the class Alphaproteobacteria. The most closely related type strain was, in both cases, Ahrensia kielensis JCM 20689T ( = IAM 12618T = DSM 5890T), which gave sequence similarities of 97.7 % in the 16S rRNA gene and 90.4 % in the atpD gene. Genome relatedness between strain LZD062T and A. kielensis JCM 20689T was computed using both genome-to-genome distance analysis and average nucleotide identity, giving values of 22.10 ± 2.35 and 79.55 %, respectively. The genomic DNA G+C content calculated from the genome sequence was 50.1 mol%. On the basis of our polyphasic analyses, strain LZD062T is considered to represent a novel species of the genus Ahrensia, for which the name Ahrensia marina sp. nov. is proposed. The type strain is LZD062T ( = MCCC 1K00254T = JCM 30117T = DSM 28886T). Emended descriptions of the genus Ahrensia and Ahrensia kielensis are also proposed.
-
-
-
Acinetobacter equi sp. nov., isolated from horse faeces
The taxonomic position of five strains isolated from horse faeces, and which shared identical 16S rRNA gene sequences, were studied. Cells of all isolates are Gram-stain-negative, obligately aerobic and have a rod-shaped appearance. The strains show highest 16S rRNA gene sequence similarities to Acinetobacter lwoffii (98.3 %), Acinetobacter haemolyticus (98.0 %), Acienetobacter johnsonii (97.9 %) and Acinetobacter brisouii (97.9 %). Whole-genome sequencing of strain 114T and phylogeny reconstruction based on a core set of 1061 Acinetobacter genes indicated that A. bouvetii CIP 107468T was the closest relative among species of the genus Acinetobacter for which whole genome sequences are available. The genomic DNA G+C content of strain 114T is 34.9 mol%, which is lower than any other value reported for the genus Acinetobacter. The predominant polyamine is 1,3-diaminopropane, which is typical for the genus Acinetobacter. The most abundant fatty acids are C16 : 1ω7c and/or iso-C15 : 0 2-OH (36 %) and C16 : 0 (28 %). The proportion of C18 : 1ω9c (7 %) is distinctively low compared to most species of the genus. The major ubiquinone of strain 114T is Q-9. Microscopic studies revealed the presence of pili and the absence of flagella. The capability of all five strains to utilize l-arabinose and gentisate as well as their lack of growth at temperatures of 41 °C and above provide sufficient criteria to distinguish the isolates from all species of the genus Acinetobacter with validly published names. Based on these combined data, the five isolates represent a novel species of the genus Acinetobacter, for which the name Acinetobacter equi sp. nov. is proposed. The type strain is 114T ( = DSM 27228T = CCUG 65204T).
-
-
-
Aetherobacter fasciculatus gen. nov., sp. nov. and Aetherobacter rufus sp. nov., novel myxobacteria with promising biotechnological applications
More LessBacterial strains SBSr002T and SBSr003T were isolated in 2007 from dried soil samples containing decaying plant material. The organisms were recognized as myxobacteria by growth-stage characteristics, forming swarming colonies and fruiting bodies on agar and on filter paper. These strains were unusual for their ring-like or halo colony appearance in an agar. Both isolates were characterized as bacteriolytic, non-cellulolytic, mesophilic, aerobic and chemoheterotrophic and showed resistance to various antibiotics. GC-MS analysis of their cellular fatty acids revealed rather large quantities of docosahexaenoic acid, and they also both contained eicosapentaenoic acid, arachidonic acid and docosapentaenoic acid. Strain SBSr003T was previously identified as the producer organism of a novel class of potent antiviral metabolites that were called aetheramides. The G+C content of the genomic DNA was 68.0–68.9 mol%. Phylogenetic analysis revealed that both strains belong within the family Polyangiaceae, suborder Sorangiineae, order Myxococcales. Their 16S rRNA gene sequences showed the highest similarity (97–99 %) to sequences derived from clones of uncultured bacteria, 95–96 % similarity to Byssovorax cruenta and Sorangium cellulosum and 94 % similarity to Chondromyces apiculatus. The results of a polyphasic taxonomic characterization suggested that strains SBSr002T and SBSr003T represent two distinct species of a novel genus, Aetherobacter gen. nov., for which the names Aetherobacter fasciculatus sp. nov. (type strain SBSr002T = DSM 24601T = NCCB 100377T) and Aetherobacter rufus sp. nov. (type strain SBSr003T = DSM 24628T = NCCB 100378T) are proposed. The type species of Aetherobacter is Aetherobacter fasciculatus.
-
-
-
Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere
A Gram-staining-negative, yellow-pigmented strain, designated SYP-B804T, was isolated from the rhizosphere of Panax notoginseng. The strain was rod-shaped with a single polar flagellum. The optimum temperature and pH required for growth of the strain were 28–32 °C and pH 7–8, respectively. 16S rRNA gene sequence analysis indicated that strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0 %). However, the DNA–DNA relatedness value between them (38.1 ± 0.6 %) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71 %. On the basis of phenotypic, chemotaxonomic and molecular characteristics, strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed, with SYP-B804T ( = KCTC 42211T = JCM 30329T) as the type strain.
-
-
-
Acetobacter musti sp. nov., isolated from Bobal grape must
More LessAn acetic acid bacterium (strain Bo7T), obtained during a study of the microbial diversity of spontaneous fermentations of Bobal grape must, was subjected to a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain Bo7T to the genus Acetobacter, and revealed Acetobacter aceti and Acetobacter oeni to be nearest neighbours (99.57 % 16S rRNA gene sequence similarity between strain Bo7T and A. oeni CECT 5830T, and 98.76 % between strain Bo7T and A. aceti CECT 298T). Cells of strain Bo7T are Gram-negative, motile rods, catalase-positive and oxidase-negative. The DNA G+C content of strain Bo7T was 58.0 mol%. DNA–DNA hybridizations demonstrated that strain Bo7T belongs to a single novel genospecies that can be differentiated from its nearest phylogenetic neighbours by the following phenotypic characteristics: no production of 5-keto-d-gluconic acid from d-glucose, growth with glycerol but not with methanol or maltose as sole carbon sources, and growth on yeast extract with 30 % d-glucose. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c (summed feature 8; approx. 56 %); other fatty acids in significant amounts (>5 %) were C16 : 0 2-OH (11 %), C16 : 0 (7 %), C14 : 0 2-OH (7 %) and C14 : 0 3-OH/iso-C16 : 1 I (summed feature 2; 6 %). The results obtained indicate that strain Bo7T represents a novel species of the genus Acetobacter, for which the name Acetobacter musti sp. nov. is proposed. The type strain is Bo7T ( = DSM 23824T = CECT 7722T).
-
-
-
Aquitalea pelogenes sp. nov., isolated from mineral peloid
Strain P1297T was isolated in the frame of a project aimed on the psychrotolerant microbiota occurring in water sources. The strain initially identified as a tentative species of the genus Aeromonas was rod-shaped, Gram-stain-negative, facultatively anaerobic and oxidase-positive. Subsequently, 16S rRNA gene sequence analysis placed strain P1297T within the class Betaproteobacteria and showed Aquitalea magnusonii TRO-001DR8T as the closest phylogenetic relative with 99.28 % 16S rRNA gene sequence similarity. Digital DDH and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain P1297T and Aquitalea magnusonii CCM 7607T. Digital DDH estimation (31.3 ± 2.46 %) as well as ANI (85.6001 %; reciprocal value 85.3277 %) proved the dissimilarity of strain P1297T. Further investigation using phenotyping, automated ribotyping, whole-cell protein profiling and PCR-fingerprinting methods showed a distinct taxonomic position of strain P1297T among hitherto described species of the genus Aquitalea. DNA–DNA hybridization experiments revealed low binding values between strain P1297T and Aquitalea magnusonii CCM 7607T (57 ± 3 %) and Aquitalea denitrificans CCM 7935T (41 ± 5 %). The DNA G+C content of strain P1297T was 60.3 mol%. The predominant fatty acids were C16 : 1ω7c/ iso-C15 : 0 2-OH (47.0 %), C16 : 0 (24.5 %) and C18 : 1ω7c (10.6 %), and the quinone system contained predominantly ubiquinone Q-8. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and one unidentified aminophospholipid. Obtained results of genotypic and chemotaxonomic methods clearly proved that strain P1297T represents a novel species of the genus Aquitalea, for which the name Aquitalea pelogenes sp. nov. is proposed. The type strain is P1297T ( = CCM 7557T = LMG 28989T = CCUG 67440T).
-
-
-
Enterobacter bugandensis sp. nov., isolated from neonatal blood
A total of 17 Enterobacter-like isolates were obtained from blood during a septicaemia outbreak in a neonatal unit, Tanzania, that could not be assigned based on phenotypic test to any existing Enterobacter species. Eight representative outbreak isolates were investigated in detail. Fermentation characteristics, biochemical assays and fatty acid profiles for taxonomic analysis were determined and supplemented with information derived from whole genome sequences. Phenotypic and morphological tests revealed that these isolates were Gram-stain-negative, rod-shaped, highly motile and facultatively anaerobic. The fatty acid profile was similar to those of the type strains for all recognized Enterobacter species, with quantitative differences in C17 : 0, C18 : 1ω7c and C17 : 0 cyclo fatty acids. Whole genome sequencing was used to identify taxonomically relevant characteristics, i.e. for 16S rRNA gene sequence analysis, multi-locus sequence analysis (MLSA), in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI). Draft genomes were approximately 4.9 Mb in size with a G+C content of 56.0 mol%. The 16S rRNA gene sequence of these eight isolates showed >97 % similarity to all Enterobacter species, while MLSA clustered them closely with the type strains of Enterobacter xiangfangensis and Enterobacter hormaechei. These eight strains showed less than 70 % isDDH identity with the type strains of Enterobacter species. In addition, less than 95 % ANI to the type strains of Enterobacter species was observed. From these results, it is concluded that these isolates possess sufficient characteristics to differentiate them from all recognized Enterobacter species, and should therefore be considered as representing a novel species. The name Enterobacter bugandensis sp. nov. is proposed with EB-247T ( = DSM 29888T = NCCB 100573T) as the type strain.
-
-
-
Erwinia endophytica sp. nov., isolated from potato (Solanum tuberosum L.) stems
We analysed, using a polyphasic taxonomic approach, two bacterial strains coded BSTT30T and BSTT40, isolated in the course of a study of endophytic bacteria occurring in the stems and roots of potatoes growing in soil from Salamanca, Spain. The 16S rRNA gene sequence was identical in both strains and had 98.4 % identity with respect to the closest relatives Erwinia tasmaniensis Et1/99T and Erwinia rhapontici ATCC29283T. Erwinia billingiae E63T and Erwinia toletana A37T were also closely related with 98.2 % sequence similarities, so the novel strains were classified within the genus Erwinia. The analysis of the housekeeping genes gpd, gyrB and rpoD confirmed the phylogenetic affiliation of strains BSTT30T and BSTT40 with similarities of lower than 90 % in all cases with respect to the closest relatives mentioned above. The respiratory quinone of strain BSTT30T was Q8. The major fatty acids were C16 : 0, C16 : 1ω7c/16 : 1ω6c in summed feature 3 and C18 : 1ω7c/18 : 2ω6,9c in summed feature 8. The novel strains were oxidase-negative and catalase-positive. Glucose was fermented without gas production. They were negative for arginine dihydrolase, urease and indole production. The strains could grow at 35 °C and at pH 10. DNA G+C content was 50.1 mol%. DNA–DNA hybridization results showed values of lower than 29 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strains BSTT30T and BSTT40 into a novel species of the genus Erwinia, for which the name Erwinia endophytica sp. nov. is proposed. The type strain is BSTT30T ( = LMG 28457T, CECT 8692T).
-
-
-
Niveibacterium umoris gen. nov., sp. nov., isolated from wetland freshwater
More LessA taxonomic study was carried out on a novel bacterial strain, designated MIC2059T, which was isolated from Ungok Wetland of Gochang in Korea. Cells of the isolate were found to be Gram-stain-negative, rod-shaped and motile. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the family Rhodocyclaceae, with Uliginosibacterium gangwonense as its closest relative, with a similarity of 94.8 %. It contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C12 : 0 3-OH as the major fatty acids and Q8 as the respiratory ubiquinone. The polar lipid profile of strain MIC2059T revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major polar lipids. In addition, phosphatidylserine, an unidentified aminophospholipid and unidentified lipids were present in small amounts. The DNA G+C content of the strain was 65.1 mol%. On the basis of the evidence presented, it is concluded that strain MIC2059T represents a novel species of a novel genus within the family Rhodocyclaceae, for which the name Niveibacterium umoris gen. nov., sp. nov. is proposed. The type strain is MIC2059T ( = KACC 17062T = JCM 18716T).
-
-
-
Dissulfurimicrobium hydrothermale gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating deltaproteobacterium isolated from a hydrothermal pond
A thermophilic, anaerobic, chemolithoautotrophic bacterium (strain Sh68T) was isolated from a hydrothermal pond at Uzon Caldera, Kamchatka, Russia, using anoxic medium with elemental sulfur as the only energy source. Cells of strain Sh68T were Gram-stain-negative rods, 0.5–0.8 μm in diameter and 1.2–2.0 μm in length, motile by means of flagella. The temperature range for growth was 30–65 °C, with an optimum at 50–52 °C. The pH range for growth was 5.2–7.5, with optimum growth at pH 6.0–6.2. Growth of strain Sh68T was observed at NaCl concentrations ranging from 0 to 2.3 % (w/v). Strain Sh68T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline Fe(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain Sh68T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor either with H2 or with organic electron donors. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the class Deltaproteobacteria and is related most closely to Dissulfuribacter thermophilus S69T (90.0 % similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain Sh68T is considered to represent a novel species of a new genus, for which the name Dissulfurimicrobium hydrothermale gen. nov., sp. nov. is proposed. The type strain of Dissulfurimicrobium hydrothermale is Sh68T ( = JCM 19990T = VKM B-2854T). This is the first description of a sulfur-disproportionating thermophile from a terrestrial ecosystem.
-
-
-
Ideonella paludis sp. nov., isolated from a marsh
More LessA bacterial strain, designated KBP-31T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-31T were Gram-stain-negative, strictly aerobic, motile, light-yellow rods. Growth occurred at 10–37 °C (optimum 25 °C), at pH 6–8 (optimum pH 6) and with 0–1 % NaCl (w/v, optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-31T belonged to the genus Ideonella and was most closely related to Ideonella dechloratans ATCC 51718T with a sequence similarity of 98.2 %. Strain KBP-31T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The major hydroxyl fatty acid was C10 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The DNA G+C content of the genomic DNA was 67.9 mol%. The DNA–DNA relatedness of strain KBP-31T with respect to recognized species of the genus Ideonella was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain KBP-31T should be classified as a novel species, for which the name Ideonella paludis sp. nov. is proposed. The type strain is KBP-31T ( = BCRC 80524T = KCTC 32238T).
-
-
-
Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter
More LessA Gram-stain-negative, facultatively aerobic, cream-coloured, ovoid-shaped, non-motile and psychrotolerant bacterial strain, PAMC 27389T, was isolated from terrestrial soil collected on King George Island, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27389T belongs to the genus Pseudorhodobacter, sharing highest similarities with the type strains of Pseudorhodobacter wandonensis (96.9 %), Pseudorhodobacter antarcticus (96.8 %), Pseudorhodobacter ferrugineus (96.5 %) and Pseudorhodobacter aquimaris (95.4 %). Average nucleotide identity values between strain PAMC 27389T and the type strains of P. wandonensis, P. antarcticus, P. ferrugineus and P. aquimaris were 70.8, 70.9, 71.0 and 70.5 %, respectively and the genome-to-genome distances were 18.4–19.1 %, indicating PAMC 27389T is clearly distinguished from the most closely related Pseudorhodobacter species. The genomic DNA G+C content was 60.1 mol%. Strain PAMC 27389T grew at 0–37 °C (optimally at 15–20 °C), at pH 5.5–9.0 (optimally at pH 6.5–7.0) and in the presence of 0.5–3.0 % (w/v) sea salt (optimally with 0.5 %). It lacked bacteriochlorophyll a. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 1ω7c 11-methyl. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid, an unidentified lipid and three unidentified aminophospholipids. The major respiratory quinone was Q-10. Based on the phenotypic, chemotaxonomic and genomic data presented, we propose the name Pseudorhodobacter psychrotolerans sp. nov. with the type strain PAMC 27389T ( = KCTC 42640T = JCM 30764T).
-
-
-
Pontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil
More LessA Gram-stain-negative, pinkish-red, rod-shaped bacterium designated strain NKM1T was isolated from soil samples contaminated with hexachlorocyclohexane isomers, collected from Ummari village, Lucknow, Uttar Pradesh, India. The strain was characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that strain NKM1T clustered exclusively with members of the genus Pontibacter of the family Cytophagaceae, phylum Bacteroidetes. The 16S rRNA gene sequence similarity to type strains of the genus Pontibacter ranged from 96.7 to 93.8 %, with the highest sequence similarity found with Pontibacter odishensis JC130T (96.7 %). Cells of strain NKM1T were aerobic, non-flagellated and non-motile. Strain NKM1T was catalase- and oxidase-positive but negative for nitrate reduction and hydrolysis of gelatin. The major fatty acids in strain NKM1T were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile of strain NKM1T showed the presence of phosphatidylethanolamine and unknown glycolipids as well as aminolipids. sym-Homospermidine was found to be the major polyamine and menaquinone 7 (MK-7) was the major respiratory quinone. The DNA G+C content of strain NKM1T was determined to be 58.6 mol%. Based on phenotypic, chemotaxonomic, physiological and biochemical evidence, it is proposed that isolate NKM1T represents a novel species that belongs to the genus Pontibacter, for which the name Pontibacter ummariensis sp. nov. is proposed. The type strain is NKM1T ( = DSM 100161T = KCTC 42944T = MCC 2777T).
-
- Bacteroidetes
-
-
Flavitalea soli sp. nov. isolated from soil
A Gram-stain-negative, rod-shaped, non-flagellated, mesophilic, yellow-pigmented, aerobic bacterium, designated strain KIS20-3T, was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Flavitalea populi HY-50RT (94.5 %), Niastella populi THYL-44T (94.2 %) and Flavitalea gansuensis JCN-23T (93.7 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain KIS20-3T formed a subcluster with members of the genus Flavitalea, and this subcluster was closely related to members of the genera Niastella, Segetibacter and Parasegetibacter within the family Chitinophagaceae. The major fatty acids of strain KIS20-3T were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G, and the predominant isoprenoid quinone was menaquinone 7. The polar lipid profile comprised large amounts of phosphatidylethanolamine and one unknown polar lipid, and moderate or small amounts of four unknown aminophospholipids, two unknown aminolipids, three unknown lipids and one unknown phospholipid. The G+C content of the DNA of strain KIS20-3T was 55.7 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain KIS20-3T represents a novel species of the genus Flavitalea, for which the name Flavitalea soli sp. nov. is proposed. The type strain is KIS20-3T ( = KACC 17319T = JCM 19937T).
-
-
-
Ichthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum ‘Bacteroidetes’, isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.
A novel Gram-stain-negative, rod-shaped (0.3 × 4–6 μm), non-flagellated, aerobic strain with gliding motility, designated JBKA-6T, was isolated in 1991 from a yellowtail fish, Seriola quinqueradiata, showing symptoms of bacterial haemolytic jaundice. 16S rRNA gene sequence analysis showed that strain JBKA-6T was related most closely to members of the family Flavobacteriaceae in the phylum ‘Bacteroidetes’. Furthermore, based on gyrB gene sequence analysis, JBKA-6T was classified into a single clade within the order Flavobacteriales, which was distinct from the known clades of the families Flavobacteriaceae, Blattabacteriaceae and Cryomorphaceae. The predominant isoprenoid quinone was identified as MK-6 (97.9 %), and the major cellular fatty acids (>10 %) were C14 : 0 and iso-C15 : 0. The main polar lipids were phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminophospholipids and two unidentified polar lipids. The DNA G+C content of JBKA-6T, as derived from its whole genome, was 33.4 mol%. The distinct phylogenetic position and phenotypic traits of strain JBKA-6T distinguish it from all other described species of the phylum ‘Bacteroidetes’, and therefore it was concluded that strain JBKA-6T represents a new member of the phylum ‘Bacteroidetes’, and the name Ichthyobacterium seriolicida gen. nov., sp. nov. is proposed. The type strain of Ichthyobacterium seriolicida is JBKA-6T ( = ATCC BAA-2465T = JCM 18228T). We also propose that Icthyobacterium gen. nov. is the type genus of a novel family, Ichthyobacteriaceae fam. nov.
-
-
-
Lacinutrix gracilariae sp. nov., isolated from the surface of a marine red alga Gracilaria sp.
More LessA Gram-stain-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain Lxc1T, was isolated from the surface of a marine red alga, Gracilaria sp., which was collected from the coastal regions in Jinjiang, Fujian Province, China. Colonies of the strain were orange–yellow, circular and smooth. The 16S rRNA gene of strain Lxc1T had maximum sequence similarity with Lacinutrix himadriensis E4-9aT (97.1 %), followed by Lacinutrix jangbogonensis PAMC 27137T, Lacinutrix copepodicola DJ3T, Lacinutrix algicola AKS293T and Lacinutrix mariniflava AKS 432T (similarities < 96.4 %). Phylogenetic analysis showed strain Lxc1T formed a tight cluster with L. himadriensis E4-9aT and L. copepodicola DJ3T, but represented a novel lineage belonging to the genus Lacinutrix. The predominant fatty acids were iso-C15 : 1 G (18.3 %), iso-C15 : 0 (16.7 %), iso-C17 : 0 3-OH (10.6 %) and iso-C15 : 0 3-OH (8.6 %). Menaquinone-6 (MK-6) was the only respiratory quinone present. The DNA G+C content of strain Lxc1T was 31.7 mol%. Combining the results above, it was ascertained that strain Lxc1T represented a novel species of the genus Lacinutrix, for which the name Lacinutrix gracilariae sp. nov. is proposed. The type strain is Lxc1T ( = MCCC 1A01567T = KCTC 42808T).
-
-
-
Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense
A yellow, Gram-reaction-negative, non-motile, aerobic bacterium, designated D07T, was isolated from a tundra soil near Ny-Ålesund, Svalbard archipelago, Norway (78° N). Growth occurred at 4–37 °C (optimum 28–30 °C) and at pH 6.0–9.0 (optimum pH 7.0–8.0). The strain produced flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D07T belonged to the genus Chryseobacterium in the family Flavobacteriaceae. The 16S rRNA gene sequence of this strain showed 93.83 and 93.31 % sequence similarity, respectively, to those of Chryseobacterium contaminans C26T and Chryseobacterium taklimakanense X-65T. Strain D07T contained anteiso-C15 : 0 (25.91 %), iso-C15 : 0 (16.05 %), iso-C16 : 0 3-OH (9.64 %), iso-C16 : 0 (9.42 %) and iso-C14 : 0 (7.36 %) as the predominant cellular fatty acids, MK-6 as the major respiratory quinone and phosphatidylethanolamine, five unknown aminolipids and three unknown lipids as the main polar lipids. The DNA G+C content was 49.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D07T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium frigidum sp. nov. is proposed. The type strain is D07T ( = CCTCC AB 2011160T = KCTC 42897T). Emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense are also provided.
-
-
-
Paenibacillus radicis sp. nov., an endophytic bacterium isolated from maize root
More LessA novel Gram-stain-positive, aerobic, endospore-forming, and rod-shaped strain designated 694T was isolated from surface-sterilized root tissue of a maize planted in the Fangshan District of Beijing, People's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain 694T and Paenibacillus xinjiangensis DSM 30034T (98.5 %) and Paenibacillus glycanilyticus (98.1 %), respectively. However, the DNA–DNA hybridization values between strain 694T and its close relatives P. xinjiangensis 16970T and Paenibacillus algorifonticola CGMCC 1.10223T were 30.0 % and 36.7 % respectively. The DNA G+C content of strain 694T was determined to be 46.9 mol%. The predominant respiratory quinone was identified as menaquinone-7 and the polar lipid profile was found to be composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were found to be anteiso-C15 : 0 (42.1 %), iso-C15 : 0 (18.4 %), iso-C16 : 0 (11.2 %) and C16 : 0 (12.1 %). The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 694T from the closely related species in the genus Paenibacillus. Strain 694T is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus radicis sp. nov. is proposed, with the type strain 694T ( = CGMCC 1.15286T = DSM 100762T).
-
-
-
Hymenobacter monticola sp. nov., isolated from mountain soil
More LessA Gram-reaction-negative, aerobic, non-motile, red-pigmented and rod-shaped bacterium, designated XF-6RT, was isolated from mountain soil in the Sichuan province of China. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that XF-6RT belonged to the genus Hymenobacter. The greatest 16S rRNA gene sequence similarities of strain XF-6RT were with Hymenobacter soli PB17T (96.4 %) and Hymenobacter saemangeumensis GSR0100T (95.8 %). Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c and anteiso-C15 : 0 were the major fatty acids (>10 %). The only menaquinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine, four aminolipids, four phosphoaminolipids and three lipids. The DNA G+C content was 62 mol%. On the basis of the polyphasic taxonomic analysis, strain XF-6RT is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter monticola sp. nov. is proposed. The type strain is XF-6RT ( = KCTC 42733T = CCTCC AB 2015206T).
-
-
-
Confluentibacter lentus gen. nov., sp. nov., isolated from the junction between the ocean and a freshwater lake
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped bacterium, designated HJM-3T, was isolated from the place where the ocean and a freshwater lake meet at Hwajinpo on the East Sea, South Korea, and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30–35 °C, at pH 7.0–7.5 and in the presence of 1.0–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain HJM-3T clustered with the type strain of Yeosuana aromativorans and the proposed type strain of Mariniflexile ostreae. Strain HJM-3T exhibited the highest 16S rRNA gene sequence similarity values (each 95.1 %) to these representative strains of Y. aromativorans and M. ostreae, and sequence similarities of less than 94.9 % to the type strains of other recognized species. Strain HJM-3T contained menaquinone-6 as the predominant isoprenoid quinone, and iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain HJM-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain HJM-3T was 34.7 mol%. The fatty acid and polar lipid profiles and DNA G+C content of strain HJM-3T could be distinguished from those of the phylogenetically related taxa. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain HJM-3T is considered to represent a novel genus and species within the family Flavobacteriaceae, for which the name Confluentibacter lentus gen. nov., sp. nov., is proposed. The type strain is HJM-3T ( = KCTC 42777T = NBRC 111588T).
-
-
-
Salinicola rhizosphaerae sp. nov., isolated from the rhizosphere of the mangrove Avicennia marina L.
More LessA Gram-stain-negative, motile, rod-shaped bacterium, designated MSSRFH1T, was isolated from the rhizosphere of the mangrove, Avicennia marina, in Pichavaram, Tamil Nadu, India. Phylogenetic analysis, based on the 16S rRNA gene sequence of MSSRFH1T, indicated that it clustered in the genus Salinicola and was most closely related to Salinicola peritrichatus JCM18795T (96.7 % similarity). The 16S rRNA gene sequence similarity was < 96.5 % with other strains of species of the genus Salinicola. The distinctiveness of strain MSSRFH1T was also shown by low similarities of its rpoD ( < 87 % similarity) and gyrB ( < 85 %) gene sequences with those of other members of the genus Salinicola. Strain MSSRFH1T could tolerate NaCl concentrations of up to 30 % (w/v). The main fatty acids of MSSRFH1T included C18 : 1ω7c, C16 : 0 and C19 : 0ω8c. The polar lipids present included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified amino lipid and unidentified phospholipids. Comparison of BOX-PCR fingerprints indicated that MSSRFH1T showed a unique DNA profile and its genomic G+C content was 64 mol%. On the basis of the data presented, strain MSSRFH1T represents a novel species of the genus Salinicola, for which the name Salinicola rhizosphaerae sp. nov. is proposed. The type strain is MSSRFH1T ( = KCTC 32998T = NBRC 110222T).
-
-
-
Mongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake
A novel haloalkalitolerant, rod-shaped bacterium, designated strain YIM 4-4T, was isolated from the surface water of the Dugerno lake, a haloalkaline lake in Inner Mongolia. The taxonomy of strain YIM 4-4T was investigated by a polyphasic approach. Strain YIM 4-4T was Gram-stain-negative, strictly aerobic, non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.0–11.0 and 0.5–2 % NaCl. The major respiratory quinone was menaquinone-7 (MK-7). The polar lipid profile was composed predominantly of phosphatidylethanolamine, six unidentified polar lipids, one phospholipid and one aminolipid. The predominant cellular fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 1I/anteiso-C17 : 1B, iso-C16 : 1G, iso-C17 : 0 3-OH, C16 : 1ω7c/C16 : 1ω6c and iso-C16 : 1. The genomic DNA G+C content was 43.0 mol%. 16S rRNA gene sequence analysis indicated that the members of the genera Cecembia, Fontibacter, Aquiflexum and Indibacter of the family Cyclobacteriaceae (phylum Bacteroidetes) were the most closely related, with 16S rRNA gene sequence similarities ranging from 93.6 to 94.2 %. Other members of the family Cyclobacteriaceae showed sequence similarities < 93.0 %. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain YIM 4-4T represents a novel species of a new genus, for which the name Mongoliibacter ruber gen. nov., sp. nov. is proposed. The type strain is YIM 4-4T ( = CCTCC AB 2012966T = DSM 27929T).
-
-
-
Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium
More LessA Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T).
-
- Other bacteria
-
-
Thermostilla marina gen. nov., sp. nov., a thermophilic, facultatively anaerobic planctomycete isolated from a shallow submarine hydrothermal vent
A novel thermophilic planctomycete (strain SVX8T) was isolated from a shallow submarine hydrothermal vent, Vulcano Island, Italy. The temperature range for growth was 30–68 °C, with an optimum at 55 °C. The pH range for growth was 5.0–9.0, with an optimum at pH 7.0–8.0. Growth was observed at NaCl concentrations ranging from 0.8 to 4.5 % (w/v) with an optimum at 2.5–3.5 % (w/v). The isolate grew anaerobically using a number of mono-, di- and polysaccharides as electron donors and nitrate or elemental sulfur as electron acceptors or by fermentation. Nitrate was reduced to nitrite; sulfur was reduced to sulfide. Strain SVX8T did not grow at atmospheric concentration of oxygen but grew microaerobically (up to 2 % oxygen in the gas phase). The G+C content of the DNA of strain SVX8T was 58.5 mol%. Based on phylogenetic position and phenotypic features, the new isolate is considered to represent a novel species belonging to a new genus in the order Planctomycetales, for which the name Thermostilla marina gen. nov., sp. nov. is proposed. The type strain of Thermostilla marina is SVX8T ( = JCM 19992T = VKM B-2881T). Strain SVX8T is the first thermophilic planctomycete isolated from a marine environment.
-
-
-
Phyllonema aviceniicola gen. nov., sp. nov. and Foliisarcina bertiogensis gen. nov., sp. nov., epiphyllic cyanobacteria associated with Avicennia schaueriana leaves
Cyanobacteria dwelling on the salt-excreting leaves of the mangrove tree Avicennia schaueriana were isolated and characterized by ecological, morphological and genetic approaches. Leaves were collected in a mangrove with a history of oil contamination on the coastline of São Paulo state, Brazil, and isolation was achieved by smearing leaves on the surface of solid media or by submerging leaves in liquid media. Twenty-nine isolated strains were shown to belong to five cyanobacterial orders (thirteen to Synechococcales, seven to Nostocales, seven to Pleurocapsales, one to Chroococcales, and one to Oscillatoriales) according to morphological and 16S rRNA gene sequence evaluations. More detailed investigations pointed six Rivulariacean and four Xenococcacean strains as novel taxa. These strains were classified as Phyllonema gen. nov. (type species Phyllonema aviceniicola sp. nov. with type strain CENA341T) and Foliisarcina gen. nov. (type species Foliisarcina bertiogensis sp. nov. with type strain CENA333T), according to the International Code of Nomenclature for Algae, Fungi, and Plants. This investigation shows some of the unique cyanobacteria inhabiting the phyllosphere of Avicennia schaueriana can be retrieved by culturing techniques, improving current taxonomy and providing new insights into the evolution, ecology, and biogeography of this phylum.
-
-
-
Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.
Two isolates of aerobic, budding, pink-pigmented bacteria, designated strains PX4T and PT1, were isolated from a boreal Sphagnum peat bog and a forested tundra wetland. Cells of these strains were non-motile spheres that occurred singly or in short chains. Novel isolates were capable of growth at pH values between 3.5 and 6.5 (optimum at pH 5.0–5.5) and at temperatures between 6 and 30 °C (optimum at 15–25 °C). Most sugars and a number of polysaccharides including pectin, xylan, lichenin and Phytagel were used as growth substrates. The major fatty acids were C16 : 0, C18 : 1ω9 and C18 : 0; the major polar lipids were phosphocholine and trimethylornithine. The quinone was menaquinone-6, and the G+C content of the DNA was 66 mol%. Strains PX4T and PT1 were members of the order Planctomycetales and displayed 93–94 % 16S rRNA gene sequence similarity to Aquisphaera giovannonii, 91–92 % to species of the genus Singulisphaera and 90–91 % to Isosphaera pallida. The two novel strains, however, differed from members of these genera by cell morphology, 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 Paludisphaera borealis gen. nov., sp. nov., is proposed. The type strain is PX4T ( = DSM 28747T = VKM B-2904T). We also suggest the establishment of a novel family, Isosphaeraceae fam. nov., to accommodate stalk-free planctomycetes with spherical cells, which can be assembled in short chains, long filaments or shapeless aggregates. This family includes the genera Isosphaera, Aquisphaera, Singulisphaera and Paludisphaera.
-
-
-
Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi
A novel obligately anaerobic bacterium, designated strain TC1T, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based wastewater. Cells had a multicellular filamentous morphology, stained Gram-negative and were non-motile. The filaments were flexible, generally >100 μm long and 0.3–0.4 μm wide. Growth of the isolate was observed at 25–43 °C (optimum 37 °C) and pH 6.0–8.5 (optimum pH 7.0). Strain TC1T grew chemo-organotrophically on a range of carbohydrates under anaerobic conditions. Yeast extract was required for growth. The major fermentative end products of glucose, supplemented with yeast extract, were acetate, lactate, succinate, propionate, formate and hydrogen. Co-cultivation with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864T enhanced growth of the isolate. The DNA G+C content was determined experimentally to be 42.1 mol%. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C17 : 0 3-OH. Based on 16S rRNA gene sequence analysis, strain TC1T belonged to the class Anaerolineae in the phylum Chloroflexi, in which Ornatilinea apprima P3M-1T was its closest phylogenetic relative (88.3 % nucleotide identity). Phylogenomic analyses using 38 and 83 single-copy marker genes also supported the novelty of strain TC1T at least at the genus level. Based on phylogenetic, genomic and phenotypic characteristics, we propose that strain TC1T represents a novel species of a new genus, for which we suggest the name Flexilinea flocculi gen. nov., sp. nov. The type strain of Flexilinea flocculi is strain TC1T ( = JCM 30897T = CGMCC 1.5202T).
-
-
-
Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside
Three Gram-stain-positive, catalase- and oxidase-positive coccus- or rod-shaped bacterial strains, designated BM2T, BM4 and BM5, were isolated from soil in South Korea. They showed strong resistance to gamma radiation with a D 10 value of 9 kGy but weak UVC resistance. The 16S rRNA sequences of strains BM2T, BM4 and BM5 represent a novel subline within the genus Deinococcus in the family Deinococcaceae. The 16S rRNA gene sequences of strains BM2T, BM4 and BM5 were indistinguishable and showed 98.1–87.3 % similarity with other species of the genus Deinococcus. Strain BM2T exhibited relatively high levels of DNA–DNA hybridization with BM4 (87 ± 0.8 %) and BM5 (92 ± 1.2 %). Meanwhile, it showed a low level of DNA–DNA hybridization ( < 30 %) with other closely related species of the genus Deinococcus. The strains showed the typical chemotaxonomic characteristics of the genus Deinococcus, with the presence of menaquinone 8 as the respiratory quinone; the major fatty acids were summed feature 3 (composed of C16 : 1ω7c/C16 : 1ω6c), C15 : 1ω6c and C16 : 0. The DNA G+C content of strain BM2T was 69.7 mol%. The polar lipid profile included major amounts of phosphatidylglycerol, phosphatidylcholine and an unknown aminolipid. On the basis of phenotypic and genotypic properties, and phylogenetic distinctiveness, strains BM2T, BM4 and BM5 should be classified in a novel species in the genus Deinococcus, for which the name Deinococcus actinosclerus sp. nov. is proposed. The type strain is BM2T ( = KEMB 5401-184T = JCM 30700T); reference strains are BM4 ( = JCM 30701) and BM5 ( = JCM 30702).
-
-
-
Athalassotoga saccharophila gen. nov., sp. nov., isolated from an acidic terrestrial hot spring, and proposal of Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov. in the phylum Thermotogae
A novel moderately thermophilic, weakly acidophilic, heterotrophic, anaerobic, short-rod bacterium having an outer sheath-like structure (toga) was isolated from a low-salt acidic terrestrial hot spring in Oku-Shiobara, Tochigi, Japan. The strain, designated NAS-01T, grew between 30 and 60 °C (optimum 55 °C), and at pH 4.5 and 7.5 (optimum pH 5.5 to 6.0) and could not grow in media with ≥ 1 % NaCl (optimum 0 % NaCl). It utilized Fe(III), thiosulfate or l-cystine as electron acceptor for growth, and yeast extract, peptone or a variety of sugars as carbon and energy sources. The major cellular fatty acid was C16 : 0, and no lipoquinone was detected. Strain NAS-01T contained phospholipids and glycolipids, but not aminolipids. The DNA G+C content was 41.1 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was included in the phylum Thermotogae, and was closely related to Mesoaciditoga lauensis. The 16S rRNA gene sequence similarity between them was 90 %, and they were deeply branched off the rest of the known Thermotogae species. On the basis of the phylogenetic and ecophysiological properties, strain NAS-01T represents a novel species of a new genus in the phylum Thermotogae, for which we propose the name Athalassotoga saccharophila gen. nov., sp. nov. The type strain of the type species is NAS-01T ( = JCM 19762T = DSM 28954T). In addition, we propose a new order and family, Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov., respectively, to accommodate the novel genus and the closely related genus Mesoaciditoga.
-
- Eukaryotic micro-organisms
-
-
Spencermartinsiella silvicola sp. nov., a yeast species isolated from rotting wood
More LessThree strains of a new xylanase-producing yeast species were isolated from rotting wood samples collected in the Atlantic Rain Forest of Brazil. The sequences of the internal transcribed spacer region and D1/D2 domains of the large subunit of the rRNA gene showed that this novel yeast species belongs to the genus Spencermartinsiella, and its closest relatives among recognized species are Spencermartinsiella europaea and Spencermartinsiella ligniputridi. A novel species, named Spencermartinsiella silvicola sp. nov., is proposed to accommodate these isolates. The type strain is UFMG-CM-Y274T ( = CBS 13490T). The MycoBank number is MB 813053. In addition, Candida cellulosicola is reassigned to the genus Spencermartinsiella as a new combination.
-
-
-
Jaminaea phylloscopi sp. nov. (Microstromatales), a basidiomycetous yeast isolated from migratory birds in the Mediterranean basin
During a survey of yeasts vectored by migratory birds in the Mediterranean basin, isolations from the cloacae of members of the order Passeriformes collected in Ustica (Italy) were performed. Based on phylogenetic analysis of the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacer ITS1-5.8S rRNA gene-ITS2 region, five yeast isolates clustered in a new lineage within the Microstromatales clade. The DNA sequences of these isolates differed from those of their closest relatives, Jaminaea angkorensis and Jaminaea lanaiensis, by 20 and 25 nt substitutions in the D1/D2 domain and 119 and 131 nt substitutions in the complete ITS region, respectively. In addition, the five isolates showed phenotypic characteristics not observed in their closest relatives, such as the ability to grow at 44 °C and at pH 2.5, which suggests a possible adaptation to the bird gastrointestinal tract. On the basis of the isolation source, phenotypic features and molecular strain typing carried out with randomly amplified polymorphic DNA (RAPD)-PCR and mini-satellite-primed (MSP)-PCR analysis, the five isolates were characterized as five distinct strains of a novel species formally described as Jaminaea phylloscopi sp. nov., with 551B6T ( = PYCC 6783T = CBS 14087T) as the type strain. The Mycobank accession number is MB811984.
-
-
-
A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA
More LessA novel species of the genus Phytophthora was recovered during surveys of stream and nursery irrigation water in Maryland, Massachusetts, North Carolina, Virginia and West Virginia in the USA. The novel species is heterothallic, and all examined isolates were A1 mating type. It produced rare ornamented oogonia and amphigynous antheridia when paired with A2 mating type testers of Phytophthora cinnamomi and Phytophthora cryptogea. Sporangia of this novel species were non-papillate and non-caducous. Thin-walled intercalary chlamydospores were abundant in hemp seed agar and carrot agar, while they were produced only rarely in aged cultures grown in clarified V8 juice agar. Phylogenetic analyses based on sequences of the internal transcribed spacer region and the β-tubulin and mitochondrial cytochrome-c oxidase 1 (cox1) genes indicated that the novel species is phylogenetically close to Phytophthora gallica in Phytophthora clade 10. The novel species has morphological and molecular features that are distinct from those of other species in Phytophthora clade 10. It is formally described here as Phytophthora intercalaris sp. nov. Description of this unique clade-10 species is important for understanding the phylogeny and evolution of Phytophthora clade 10.
-
-
-
Cystofilobasidium intermedium sp. nov. and Cystofilobasidium alribaticum f.a. sp. nov., isolated from Mediterranean forest soils
Multiple isolates belonging to the basidiomycetous genus Cystofilobasidium were obtained from forest soils in Serra da Arrábida Natural Park in Portugal. Phylogenetic analyses employing concatenated sequences of the D1/D2 domain and ITS region support the recognition of two novel species: Cystofilobasidium alribaticum f.a., sp. nov. (type strain CBS 14164T = PYCC 6956T = DSM 101473T) and Cystofilobasidium intermedium sp. nov. (type strain CBS 14089T = PYCC 6856T = DSM 101474T). Whereas C. alribaticum f. a. sp. nov. does not form hyphae, even when different strains are crossed, C. intermedium sp. nov. is self-fertile and forms mycelium with teliospores that upon germination give rise to slender basidia. The most remarkable physiological trait of the two novel species is their ability to grow at 35 °C, a property not observed for remaining species of the genus.
-
- EVOLUTION, PHYLOGENY AND BIODIVERSITY
-
-
-
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
More LessSpecies demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA–DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, a new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.
-
-
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)