- Volume 67, Issue 11, 2017
Volume 67, Issue 11, 2017
- New taxa
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- Other Bacteria
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Deinococcus taklimakanensis sp. nov., isolated from desert soil
A gamma- and UV radiation-tolerant, Gram-negative, short-rod-shaped bacterial strain, designated X-121T, was isolated from soil samples collected from the Taklimakan desert in Xinjiang, China. Strain X-121T showed the highest 16S rRNA gene sequence similarity with Deinococcus depolymerans TDMA-24T (94.7 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain X-121T is a member of a novel species belonging to the clade formed by members of the genus Deinococcus in the family Deinococcaceae . The DNA G+C content of strain X-121T was 63.6 mol%. The chemotaxonomic charateristics of strain X-121T were typical of members of the genus Deinococcus , with MK-8 being the predominant respiratory quinone, summed feature 3 (16 : 1ω7c,16 : 1ω6c), 16 : 0 and 17 : 1ω8c as major cellular fatty acid, several unidentified phosphoglycolipids and glycolipids as the dominant polar lipids, galactose as the predominant cell-wall sugar and the presence of peptidoglycan with l-ornithine. Strain X-121T is therefore identified as representing a novel species, for which the name Deinococcus taklimakanensis sp. nov. is proposed, with the type strain X-121T(=CCTCC AB 207228T=KCTC 33842T).
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Aridibacter nitratireducens sp. nov., a member of the family Blastocatellaceae, class Blastocatellia, isolated from an African soil
Members of the class Blastocatellia are frequently found in soils with a neutral and (slightly) basic pH where they constitute an important fraction of the microbial community. A novel representative of the class Blastocatellia was isolated from a Ghanaian soil and was characterized in detail. Cells of strain A24_SHP_−5_238T were non-motile rods that divided by binary fission and formed orange to salmon-coloured colonies on agar plates. Strain A24_SHP_−5_238T tolerated pH values of pH 6.0–9.0 (best growth at pH 7.0–8.5) and temperature values of 8–45 °C (best growth at 33–40 °C). It grew chemo-organoheterotrophically on several sugars, a few amino acids, organic acids and different complex protein substrates. In addition, strain A24_SHP_−5_238T was able to use nitrate as an alternative electron acceptor in the absence of oxygen. Major fatty acids of A24_SHP_−5_238T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The major quinone was MK-8, and the DNA G+C content was 53.5 mol%. The closest described phylogenetic relatives were Aridibacter famidurans A22_HD_4HT and Aridibacter kavangonensis Ac_23_E3T with a 16S rRNA gene sequence identity of 97.6 and 97.2 %, respectively. The DNA–DNA hybridization values (<28.5 %) confirmed that A24_SHP_−5_238T represents a novel species within the genus Aridibacter . Based on its morphological, physiological and molecular characteristics, we propose the novel species Aridibacter nitratireducens sp. nov. (type strain A24_SHP_−5_238T = DSM 102177T = CECT 9235T).
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- Proteobacteria
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Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat
Strain Hb3T was isolated from a tidal flat in Jeollabuk-do Gunsan, Republic of Korea. Cells were Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and motile. The strain grew optimally at 25–35 °C, at pH 6.0–6.5 and with 3.0–10.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Hb3T belonged to the genus Halomonas . Strain Hb3T was related most closely to Halomonas ventosae Al12T (98.6 % 16S rRNA gene sequence similarity), Halomonas denitrificans M29T (98.6 %) and Halomonas saccharevitans AJ275T (98.4 %). Moreover, multilocus sequence analysis using the gyrB, rpoD and secA genes supported the phylogenetic position of strain Hb3T. The genomic G+C content of strain Hb3T was 67.9 mol%. DNA–DNA hybridization values for strain Hb3T versus H. ventosae Al12T, H. denitrificans M29T and H. saccharevitans AJ275T were 38.0, 54.5 and 47.4 %, respectively. The major quinone was ubiquinone Q-9 and the major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, amino lipid, six unidentified phospholipids and an unidentified lipid comprised the polar lipid profile. On the basis of the data presented in this report, strain Hb3T represents a novel species of the genus Halomonas . The name Halomonas aestuarii sp. nov. is proposed for this novel species. The type strain is Hb3T (=KCTC 52253T=JCM 31415T).
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Neisseria dumasiana sp. nov. from human sputum and a dog’s mouth
Three independent isolates of Gram-reaction-negative cocci collected from two New York State patients and a dog’s mouth in California were subjected to a polyphasic analysis. The 16S rRNA gene sequence similarity among these isolates is 99.66 to 99.86 %. The closest species with a validly published name is Neisseria zoodegmatis (98.7 % 16S rRNA gene sequence similarity) with six additional species of the genus Neisseria with greater than 97 % similarity. Average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC 2.0) analysis on whole genome sequence data support the three novel isolates as being from a single species that is distinct from all other closely related species of the genus Neisseria . Phylogenetic analysis of 16S rRNA gene sequences and ribosomal multilocus sequence typing (rMLST) indicate the novel species belongs in the genus Neisseria . This assignment is further supported by the predominant cellular fatty acids composition of C16 : 0, summed feature 3 (C16 : 1ω7c/C15 : 0iso 2-OH), and C18 : 1ω7c, and phenotypic characters. The name Neisseria dumasiana sp. nov. is proposed, and the type strain is 93087T (=DSM 104677T=LMG 30012 T).
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Izhakiella australiensis sp. nov. isolated from an Australian desert soil
More LessA Gram-stain-negative, rod-shaped, non-motile bacterium, designated D4N98T, was isolated from a desert soil near Glendambo, Australia. The taxonomic position of strain D4N98T was investigated using a polyphasic approach. Strain D4N98T shared 97 % 16S rRNA gene sequence similarity with the only reference strain of the genus Izhakiella ( Izhakiella capsodis N6PO6T), and less than 96 % similarity with other species of genera in the family Enterobacteriaceae with validly published names. Phylogenetic analysis, based on 16S rRNA, rpoB, atpD, gyrB genes and a concatenated sequence comprising 37 single copy marker genes, as well as chemotaxonomic data (major polar lipids: phosphatidyl ethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a neutral lipid, and a glycolipid. Major fatty acids (>10 %): C16 : 0, C17 : 0 cyclo, summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) support the affiliation of this strain to the genus Izhakiella . The results of in silico DNA–DNA hybridisation plus physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain D4N98T from the other species of the genus Izhakiella with validly published names. Therefore, strain D4N98T represents a novel species, for which the name Izhakiella australiensis sp. nov. is proposed. The type strain is D4N98T (LMG 30066T=DSM 105030T).
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Chitinimonas lacunae sp. nov., isolated from artificial pond in Korea
More LessA gram-negative, rod shaped bacterium designated as strain H2T was isolated from an artificial pond in Korea. The strain H2T was able to grow aerobically and anaerobically with optimal growth occurring at 30 °C and pH 7.0 under aerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain H2T belonged to the genus Chitinimonas of the family Burkholderiaceae . Phylogenetic similarity calculated from 16S rRNA gene sequences of strain H2T and valid species belongs to the genus Chitinimonas ranged from 93.2 % (for Chitinimonas taiwanensis cfT) to 94.4 % (for Chitinimonas prasina LY03T), and strain H2T formed a tight monophyletic group with them. Predominant fatty acids were C16 : 0 and summed feature 3, which consisted of C16 : 1 ω6c and/or C16 : 1 ω7c. The major respiratory quinone of the strain H2T was ubiquinone-8, and DNA G+C content was 60.2 %. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, unidentified aminolipid, and unidentified phospholipid. The biochemical characteristics that distinguished strain H2T from other Chitinimonas species included positive cystine arylamidase activity and lacked α-chymotrypsin and β-glucosidase (aesculin hydrolysis) activity. In addition, reciprocal DNA–DNA relatedness between H2T and three Chitinimonas strains ranged from 32.0 to 43.7 %. On the basis of its phylogenetic, chemotaxonomic, and genotypic characteristics, strain H2T represents a novel species of the genus Chitinimonas. Chitinimonas lacunae sp. nov. is proposed with the type strain H2T (=KCTC 52574T=LMG 29894T).
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Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus
More LessWith the description of the genus Sphingorhabdus , the taxonomic position of Sphingopyxis contaminans was re-evaluated based on analyses of 16S rRNA gene sequences and phenotypic and chemotaxonomic characteristics. The results revealed that Sphingopyxis contaminans is clearly a member of the genus Sphingorhabdus and we proposed that Sphingopyxis contaminans (Subhash Y, Sasikala C, Ramana CV. Int J Syst Evol Microbiol 2014;64:2238–2243) should be reclassified as Sphingorhabdus contaminans comb. nov. An emended description of the genus Sphingorhabdus is also provided.
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Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae
Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine–seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5–0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30–33 °C, pH 7.0–7.5, and in the presence of 9.0–12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae . Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA–DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1 ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus , for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).
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Paracoccus sordidisoli sp. nov., isolated from an agricultural field contaminated with hexachlorocyclohexane isomers
More LessA novel bacterial strain, designated LP91T, was isolated from an agricultural field contaminated with hexachlorocyclohexane (HCH) isomers at Ummari Village, Lucknow, Uttar Pradesh, India. Cells of the strain were aerobic, short rod or coccoid, Gram-stain-negative and non-motile. Colonies of the strain were initially transparent but with time changed to a creamy white colour. Phylogenetic analysis based on the 16S rRNA marker gene showed that it was closely associated with Paracoccus aestuariivivens GHD-30T (99.1 %) and Paracoccus limosus NB88T (98.0 %), followed by Paracoccus laeviglucosivorans 43PT (97.9 %) and Paracoccus marinus KKL-A5T (97.0 %). The DNA–DNA hybridization values of strain LP91T with the closely related type strains mentioned above were below 51.2±0.64 %, confirming it as a distinct species from other known species of the genus Paracoccus . The major cellular fatty acids of strain LP91T were C18 : 0 ω7c/C18 : 0 ω6c and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and aminophospholipid, along with other lipids including glycolipids, aminolipids and other unknown phosphoglycolipids. Spermine was the major polyamine, along with putrescine in a minor amount. Ubiquinone (Q-10) was the sole isoprenoid quinone. Based on the results of phylogenetic, phenotypic and chemotaxonomic analysis, it is proposed that the isolate represents a new species of the genus Paracoccus , for which the name Paracoccus sordidisoli sp. nov. is proposed. The type strain is LP91T (=KCTC 42938T=CCM 8696T=MCC 3128T).
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Massilia buxea sp. nov., isolated from a rock surface
More LessA Gram-stain-negative, rod-shaped and motile bacterial strain, designated A9T, was isolated from the surface of rock collected from the shore of Nvshan lake in Mingguang, Anhui province, China. Phylogenetic analysis based on 16S rDNA sequence data showed that strain A9T was affiliated with the genus Massilia and showed the highest sequence similarities to Massilia plicata KCTC 12344T (98.8 %) and Massilia lurida CGMCC 1.10822T (97.9 %). The major fatty acids (>5 %) were summed feature 3 (C16 : 1ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1ω7c. Strain A9T contained Q-8 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid as the predominant polar lipids. The DNA G+C content was 69.9 mol%. Mean DNA–DNA relatedness values between strain A9T and its closest phylogenetic relatives, M. plicata KCTC 12344T and M. lurida CGMCC 1.10822T, were 38.8 % and 23.23 %, respectively. On the basis of the results obtained in this study, strain A9T is considered to represent a novel species of the genus Massilia , for which the name Massilia buxea sp. nov. is proposed. The type strain is A9T (=DSM 103547T=CGMCC 1.15931T=KCTC 52429T).
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Wohlfahrtiimonas populi sp. nov., isolated from symptomatic bark of a Populus × euramericana canker
More LessA Gram-stain-negative, facultatively anaerobic, motile, bacterial strain, 34C10-3-10T, was isolated from symptomatic bark tissue of a Populus × euramericana canker. The isolate could grow between 10 and 37 °C, at pH 5 to 11, and in 0–3 % (w/v) NaCl. The strain was oxidase and catalase positive. The ubiquinone of strain 34C10-3-10T was Q-8. The polar lipid profile of strain 34C10-3-10T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, phosphatidylmonomethylethanolamine, phosphatidylserine; the major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 1ω7c/C16 : 1ω6c. The average nucleotide identity (ANI) values between strain 34C10-3-10T and the type strains of reference species Wohlfahrtiimonas chitiniclastica S5T and Wohlfahrtiimonas larvae KBL006T were lower than the proposed species boundary cut-off for ANI. The DNA G+C content was 37.1 mol%. Based on phenotypic and genotypic characteristics, strain 34C10-3-10T represents a novel species of genus Wohlfahrtiimonas ; the name Wohlfahrtiimonas populi sp. nov. is proposed. The type strain is 34C10-3-10T (=CFCC 12747T=KCTC 52796T).
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Sphingomonas agri sp. nov., a bacterium isolated from soil
More LessA Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06T) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06T was observed to grow optimally at 30 °C and at pH 6.5–7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06T belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5T (97.4 % similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C18 : 1ω6c, C18 : 0 3-OH and C16 : 0)] supported the affiliation of strain HKS-06T to the genus Sphingomonas . Moreover, the physiological and biochemical results and low level of DNA–DNA relatedness [between strain HKS06T and S . lutea JS5T (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06T from recognized species of the genus Sphingomonas . The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06T (=KACC 18880T=LMG 29563T).
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Asprobacter aquaticus gen. nov., sp. nov., a prosthecate alphaproteobacterium isolated from fresh water
More LessA novel Gram-negative bacterium strain, DRW22-8T, was isolated from fresh water taken at a depth of 22 m at Daechung Reservoir, Republic of Korea. The cells of strain DRW22-8T were aerobic and motile with a single polar flagellum or non-motile (stalked), and formed creamy-white colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the order Rhodobacterales , showing similarity values under 91.8 % with its closest phylogenetic neighbours, Hirschia litorea , Hirschia baltica and Hirschia maritima . The chemotaxonomic results showed Q-10 as the predominant respiratory ubiquinone, three unidentified glycolipids, an unidentified lipid and phosphatidylglycerol as the major polar lipids, and C16 : 0, 11-methyl C18 : 1, C18 : 1 ω7c and/or C18 : 1 ω6c as the major fatty acids. The DNA G+C content was 64.4 mol%. The combined genotypic and phenotypic data showed that strain DRW22-8T could be distinguished from all genera within the family Hyphomonadaceae and represented a novel genus, Asprobacter gen. nov., with the name Asprobacter aquaticus sp. nov., in the family Hyphomonadaceae . The type strain is DRW22-8T (=KCTC 42356T=JCM 30469T).
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Ramlibacter monticola sp. nov., isolated from forest soil
More LessDuring a study of bacterial diversity in forest soil, strain G-3-2T, a Gram-stain-negative, light brown-coloured, non-motile, rod- or coccoid-shaped bacterium, was isolated. It was able to grow at 15–37 °C, at pH 5.5–10.0 and at 0–0.5 % (w/v) NaCl concentration. The strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain G-3-2T belongs to the genus Ramlibacter and is closely related to Ramlibacter ginsenosidimutans BXN5-27T (98.69 % sequence similarity), Ramlibacter henchirensis TMB834T (96.98 %), Ramlibacter tataouinensis TTB310T (96.49 %) and Ramlibacter solisilvae 5-10T (96.42 %). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain G-3–2T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C10 : 0 3-OH. The genomic DNA G+C content of this novel strain was 68.9 mol%. The DNA–DNA relatedness between strain G-3-2T and R. ginsenosidimutans BXN5-27T was 44.7 %, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain G-3-2T represents a novel species of the genus Ramlibacter , for which the name Ramlibacter monticola sp. nov. is proposed. The type strain is G-3-2T (=KEMB 9005-573T=KACC 19175T=JCM 31918T).
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Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg.
More LessA Gram-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5–5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter , sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1 ω7c and C19 : 0cyclo ω8c. The DNA–DNA relatedness of E130T to A. rudongensis DSM 17131T , A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).
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Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai
More LessThree gammaproteobacterial methanotrophic strains (73aT, 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73aT contains high quantities of C16 : 1ω5c. 16S rRNA gene sequence analyses showed that strains 114 and 175 are most closely related to Methylomagnum ishizawai (≥99.6 % sequence identity). Strain 73aT is representing a new genus within the family Methylococcaceae , most closely related to Methylococcus capsulatus (94.3 % sequence identity). Phylogenetic analysis of the PmoA sequence indicates that strain 73aT represents rice paddy cluster I (RPCI), which has almost exclusively been detected in rice ecosystems. The G+C content of strain 73aT is 61.0 mol%, while strains 114 and 175 have a G+C content of 63.3 mol%. Strain 73aT (=LMG 29185T, =VKM B-2986T) represents the type strain of a novel species and genus, for which the name Methyloterricola oryzae gen. nov., sp. nov. is proposed and a description is provided. Strains 175 (=LMG 28717, VKM B-2989) and 114 are members of the species Methylomagnum ishizawai . This genus was so far only represented by one isolate, so an amended description of the species is given.
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Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish
Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium , showing high similarity (98.6–99.3 %) to the type strains of Photobacterium iliopiscarium , P. piscicola , P. kishitanii , P. aquimaris and P. phosphoreum . Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species. To confirm this, we used whole genome sequencing and genomic analysis (ANIb, ANIm and in silico DNA–DNA hybridization) obtaining values well below the thresholds for species delineation. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strains from related taxa. Cells were Gram-stain-negative, motile bacilli, chemo-organotrophic and facultatively anaerobic. They fermented glucose, as well as galactose and d-mannose, without production of gas. Oxidase and catalase were positive. The predominant cellular fatty acids were C16 : 1ω7c/C16 : 1ω6c and C16 : 0. The predominant respiratory quinone (Q-8) and major polar lipids (phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol) were inferred from annotated genes in the genome of strain H01100410BT, which had a G+C content of 38.6 mol%. The results obtained demonstrate that the three strains represent a novel species, for which the name Photobacterium toruni sp. nov. is proposed. The type strain is H01100410BT (=CECT 9189T=LMG 29991T).
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Porphyrobacter algicida sp. nov., an algalytic bacterium isolated from seawater
More LessA novel Gram-stain-negative, yellow-pigmented, catalase- and oxidase-positive, non-endospore-forming, flagellated bacterium, designated strain Yeonmyeong 2-22T, was isolated from surface seawater of Geoje Island, Republic of Korea. Strain Yeonmyeong 2-22T showed algalytic activity against the seven strains tested: Cochlodinium polykrikoides, Chattonella marina, Heterosigma akashiwo, Scrippsiella trochoidea, Heterocapsa triquetra, Prorocentrum minimum and Skeletonema costatum. A taxonomic study was carried out based on a polyphasic approach to characterize the exact taxonomic position of strain Yeonmyeong 2-22T. The bacterium was able to grow at 10–40 °C, at salinities from 0 to 9 %, at pH from 4.0 to 9.0 and was not able to degrade gelatin or casein. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain Yeonmyeong 2-22T was considered to represent a novel species of the genus Porphyrobacter , which belongs to the family Erythrobacteraceae, and was related most closely to Porphyrobacter dokdonensis DSW-74T with 97.23 % 16S rRNA gene sequence similarity. The dominant cellular fatty acids of strain Yeonmyeong 2-22T were C18 : 1ω7c (49.7 %), C16 : 0 (12.0 %) and 11-methyl C18 : 1ω7c (11.5 %), and ubiquinone-10 (Q-10) was the predominant respiratory lipoquinone. The genomic DNA G+C content of strain Yeonmyeong 2-22T was calculated to be 63.0 mol%. Phenotypic characteristics of the novel strain also differed from other members of the genus Porphyrobacter . On the basis of polyphasic taxonomic data, strain Yeonmyeong 2-22Trepresents as a novel species of the genus Porphyrobacter , for which the name of Porphyrobacter algicida sp. nov. is proposed. The type strain is Yeonmyeong 2-22T (=KEMB 9005-328T=JCM 31499T).
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Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frоm roots of Sonchus arvensis L.
More LessAn aerobic facultatively methylotrophic bacterium was isolated from roots of Sonchus arvensis L. and designated strain OsotT The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fisson. They utilized methanol, methylamines and a variety of polycarbon compounds as the carbon and energy sources. Methanol was assimilated after sequential oxidation to formaldehyde and CO2 via the ribulose bisphosphate pathway. The organism grew optimally at 22–29 °C and pH 7.5–8.0. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The major cellular fatty acids of strain OsotT cells grown in R2A medium were C18 : 1 ω7c (49.0 %), C19 : 0 ω8c cyclo (38.3 %) and C16 : 0 (8.4 %). The major ubiquinone was Q-10. The DNA G+C content of strain OsotT was 66.1 mol% (T m). On the basis of 16S rRNA gene sequence analysis strain OsotT is phylogenetically related to the members of genus Ancylobacter (97.1–98.8 % sequence similarity). Based on 16S rRNA gene sequence analysis and DNA–DNA relatedness (27–29 %) with type strains of the genus Ancylobacter , the novel isolate is classified as a new species of this genus and named Ancylobacter sonchi sp. nov.; the type strain is OsotT (=VKM B-3145T=JCM 32039T).
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Phaeobacter piscinae sp. nov., a species of the Roseobacter group and potential aquaculture probiont
Four heterotrophic, antimicrobial, motile, marine bacterial strains, 27-4T, 8-1, M6-4.2 and S26, were isolated from aquaculture units in Spain, Denmark and Greece. All four strains produced the antibiotic compound tropodithietic acid, which is a key molecule in their antagonism against fish pathogenic bacteria. Cells of the strains were Gram-reaction-negative, rod-shaped and formed star-shaped aggregates in liquid culture and brown-coloured colonies on marine agar. The predominant cellular fatty acids were C18 : 1 ω7c, C16 : 0, C11 methyl C18 : 1 ω7c and C16 : 0 2-OH, and the polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminolipid, a phospholipid and an unidentified lipid. The strains grew optimally at 31–33 °C. Growth was observed at a salt concentration between 0.5 and 5–6 % NaCl with an optimum at 2–3 %. The pH range for growth of the strains was from pH 6 to 8–8.5 with an optimum at pH 7. Based on 16S rRNA gene sequence analysis, the strains are affiliated with the genus Phaeobacter . The genome sequences of the strains have a DNA G+C content of 60.1 % and share an average nucleotide identity (ANI) of more than 95 %. The four strains are distinct from the type strains of the closely related species Phaeobacter gallaeciensis and Phaeobacter inhibens based on an ANI of 90.5–91.7 and 89.6–90.4 %, respectively, and an in silico DNA–DNA hybridization relatedness of 43.9–46.9 and 39.8–41.9 %, respectively. On the basis of phylogenetic analyses as well as phenotypic and chemotaxonomic properties, the isolates are considered to represent a novel species, for which the name Phaeobacter piscinae sp. nov. is proposed. The type strain is 27-4T (=DSM 103509T=LMG 29708T).
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Gellertiella hungarica gen. nov., sp. nov., a novel bacterium of the family Rhizobiaceae isolated from a spa in Budapest
More LessA novel alphaproteobacterium, strain RAM11T, belonging to the family Rhizobiaceae was isolated from the pool water of a thermal bath in Budapest, Hungary. Based on the 16S rRNA gene sequence strain RAM11T shows the highest sequence similarity values to Ensifer adhaerens Casida A (97.44 %), to Ensifer (syn. Sinorhizobium ) americanus CFNEI 156T (96.87 %) and to Rhizobium azooxidifex Po 20/26T (96.76 %). The new bacterium is strictly aerobic, its optimum growth occurs at 20–37 °C, between pH 7 and 9 and without NaCl. It is motile due to a single polar flagellum, capable of budding and forms rosettes in liquid culture. The major isoprenoid quinone of strain RAM11T is Q-10, the major cellular fatty acids are C18 : 1 ω7c and 11-MeC18 : 1 ω7c. The polar lipid profile contains phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of DNA of the type strain is 62.9 mol%. Strain RAM11T (=DSM 29853T=NCAIM B.02618T) is proposed as type strain of a new genus and species with the proposed name Gellertiella hungarica gen. nov., sp. nov.
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Marinobacter salexigens sp. nov., isolated from marine sediment
More LessA novel bacterium, designated as strain HJR7T, was isolated from a marine sediment sample collected from the coastal area of Weihai, China (121° 57′ E, 37° 29′ N). Cells were Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped. The temperature, pH and NaCl ranges for growth were determined as 4–40 °C, pH 6.5–9.5 and 0.5–15.0 % (w/v), respectively. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain HJR7T belongs to the genus Marinobacter in the family Alteromonadaceae . The most closely related species were Marinobacter aromaticivorans (97.6 % 16S rRNA gene sequence similarity) and Marinobacter maritimus (97.3 % similarity). Ubiquinone 9 (Q-9) was the only respiratory quinone detected in strain HJR7T. The major fatty acids of strain HJR7T were C12 : 0, C16 : 0, C16 : 0 N alcohol, C18 : 1ω9c and C18 : 3ω6, 9, 12c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The DNA G+C content of strain HJR7T was 53.7 mol%. On the basis of phylogenetic, genotypic, phenotypic, and chemotaxonomic analyses, strain HJR7T represents a novel species within the genus Marinobacter , for which the name Marinobacter salexigens sp. nov. is proposed. The type strain is HJR7T (=KCTC 52545T=MCCC 1H00176T).
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Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng
More LessA novel bacterial strain, designated CJ661T, was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661T grew optimally at 30 °C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276T (98.1 %), followed by Ramlibacter henchirensis DSM 14656T (97.1 %). DNA–DNA relatedness levels of strain CJ661T were 40.6 % to R. ginsenosidimutans KCTC 22276T and 25.0 % to R. henchirensis DSM 14656T. The major isoprenoid quinone was ubiquinone (Q-8). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain CJ661T were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The G+C content of the genomic DNA was 65.4 mol%. On the basis polyphasic taxonomic data, strain CJ661T represents a novel species in the genus Ramlibacter , for which name Ramlibacter alkalitolerans sp. nov. is proposed; the type strain is CJ661T (=KACC 19305T=JCM 32081T).
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Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine–seawater interface at Erba Deep in the Red Sea
Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae , designated ZGT108T and ZGT118T, were isolated from the brine–seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108T and ZGT118T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108T to its closest relative, Ruegeria conchae JCM 17315T, was 98.9 %, while the 16S rRNA gene of ZGT118T was most closely related to that of Ruegeria intermedia LMG 25539T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108T) and 4 012 109 bp (strain ZGT118T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108T) and 62.94 mol% (ZGT108T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria . This was also confirmed by low DNA–DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeria profundi sp. nov. (type strain ZGT108T=JCM 19518T=ACCC 19861T) and Ruegeria marisrubri sp. nov. (type strain ZGT118T=JCM 19519T=ACCC 19862T).
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Polynucleobacter aenigmaticus sp. nov. isolated from the permanently anoxic monimolimnion of a temperate meromictic lake
More LessThe bacterial strain MWH-K35W1T was isolated from a permanently anoxic water layer of a meromictic lake located in the Austrian Salzkammergut area. The basically chemo-organoheterotrophic strain was isolated and maintained under aerobic conditions. Phylogenetic analyses of the 16S rRNA gene and the glutamine synthetase gene (glnA) of the strain suggested an affiliation to the genus Polynucleobacter and the cryptic species complex PnecC. Strain MWH-K35W1T shares with the type strains of the six free-living species of the genus Polynucleobacter affiliated with this species complex 16S rRNA gene sequence similarities of 99.6–99.9 %, while the type material of the obligate endosymbiont Polynucleobacter necessarius, which is also affiliated with this species complex, shares a gene sequence similarity of 99.1 %. Genome sequencing resulted in a genome size of 2.14 Mbp and a DNA G+C content of 45.98 mol%. Major fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. This strain is the first strain of the genus Polynucleobacter found to encode a proteorhodopsin-like protein but, in contrast to some other strains affiliated to this genus, it does not encode a putative anoxygenic photosynthesis system. Multilocus sequence analysis based on partial sequences of eight housekeeping genes, as well as average nucleotide identity (ANI) analyses, did not suggest that strain MWH-K35W1T belongs to a previously described species. We propose the name Polynucleobacter aenigmaticus for a novel species with strain MWH-K35W1T (=DSM 24006T=LMG 29706T) as the type strain.
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Lysobacter olei sp. nov., isolated from oil-contaminated soil
More LessStrain D-14T, a brown-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from oil-contaminated soil. It was able to grow at 20–40 °C, at pH 6.0–10.0 and at 0–1 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain D-14T belonged to the genus Lysobacter and was closely related to Lysobacter caeni BUT-8T (99.0 % sequence similarity), Lysobacter ruishenii CTN-1T (98.5 %), Lysobacter daejeonensis GH1-9T (98.2 %) and Lysobacter panacisoli CJ29T (97.2 %). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl-N-methyl-ethanolamine. The predominant fatty acids of strain D-14T were iso-C15 : 0, iso-C16 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C14 : 0, C11 : 0iso 3-OH, C15 : 1iso F and C16 : 0. The genomic DNA G+C content of this novel strain was 68.7 mol%. The DNA–DNA relatedness values between strain D-14T and L. caeni BUT-8T, L. ruishenii CTN-1T, L. daejeonensis GH1-9T and L. panacisoli CJ29T were 56.0, 46.3, 48.7 and 41.7 %, respectively, which fall below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain D-14T represents a novel species of the genus Lysobacter , for which the name Lysobacter olei sp. nov. is proposed. The type strain is D-14T (=KEMB 9005-572T=KACC 19173T=JCM 31917T).
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Elevation of three subspecies of Lonsdalea quercina to species level: Lonsdalea britannica sp. nov., Lonsdalea iberica sp. nov. and Lonsdalea populi sp. nov.
Four subspecies of Lonsdalea quercina ( L. quercina subsp. quercina , L. quercina subsp. britannica , L. quercina subsp. iberica and L. quercina subsp. populi ) were studied by genome sequence-derived average nucleotide identity (ANI), phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis (MLSA) and phenotypic characteristics. In phylogenetic trees, based on 16S rRNA gene sequences, and in MLSA data, the four subspecies were divided into four subclusters in the Lonsdalea clade with high boot strap support. The ANI values between the four subspecies were 88.71–93.38 %, respectively, lower than the proposed species boundary ANI cut-off (95–96 %) that is considered the most important criterion to reclassify these subspecies at the species level. It is proposed that three subspecies be elevated to the species level as Lonsdalea britannica sp. nov. (type strain R-43280T=LMG 26267T=NCPPB 4481T=CFCC 10822T), Lonsdalea iberica sp. nov. (type strain R-44166T=LMG 26264T=NCPPB 4490T=CFCC 10824T) and Lonsdalea populi sp. nov. (type strain NY060T=DSM 25466T=NCAIM B 02483T=LMG 27349T=CFCC 13125T).
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Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment
More LessTwo facultative chemolithotrophic, nitrate-reducing thiosulfate-oxidizing strains, F43bT and F21, were isolated from the sulfide-rich anoxic sediment of an urban creek in Pearl River Delta, China. Both strains were Gram-negative, facultatively anaerobic, non-spore-forming and rod-shaped with a flagellum. Phylogenetic analyses of 16S rRNA genes and the thrC, recA, glnII and atpD housekeeping genes revealed that the type strain shared high sequence similarities to Ciceribacter lividus MSSRFBL1T, with 98.8, 90.9, 94.8, 95.4 and 96.1 % identity, respectively. In addition, the major isoprenoid quinone (ubiquinone Q-10) and the DNA G+C content (66.0 mol%) of the type strain were similar to those of Ciceribacter lividus MSSRFBL1T. These results strongly support the classification of strains F43bT and F21 into the genus Ciceribacter . However, these strains diverged markedly from strain MSSRFBL1T with respect to several physiological and biochemical properties such as their semi-translucent colonies and nitrate-reducing and simultaneous thiosulfate-oxidizing respiration. Furthermore, the predominant fatty acids of strain F43bT were summed feature 2 (C18 : 1ω9t and/or C18 : 1ω9c and/or C18 : 1ω11t), C14 : 0 3-OH, C18 : 0 and C16 : 0, and its polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidymonomethylethanolamine and an unidentified glycolipid, which represented another two significant differences from strain MSSRFBL1T. Importantly, the DNA–DNA relatedness between strain F43bT and MSSRFBL1T was only 47.7 %. Based on the aforementioned polyphasic taxonomic results, the two isolates are suggested to represent a novel species of the genus Ciceribacter , for which the name Ciceribacter thiooxidans sp. nov. is proposed; the type strain is F43bT (=CCTCC AB 2016062T=KCTC 52231T).
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Caldovatus sediminis gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a hot spring
A Gram-stain-negative, ovoid-shaped, aerobic, non-motile, catalase- and oxidase-positive, and moderately thermophilic bacterial strain, designated strain YIM 72346T, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth occurred at 37–50 °C (optimum, 45 °C), at pH 6.0–9.0 (optimum, pH 6.5–7.0) and in the presence of 0.5–1.0 % (w/v) NaCl (optimum, 0.5 %). The major cellular fatty acids were C18 : 1ω7c, C16 : 0, C19 : 0cyclo ω8c,and C18 : 1 2-OH. The genomic DNA G+C content was determined to be 69.8 mol%. The predominant ubiquinone was Q-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified phospholipids. Bacteriochlorophyll α and carotenoic acids were not detected. Strain YIM 72346T was not observed for the accumulation of poly-β-hydroxybutyrate. The strain shared highest 16S rRNA gene sequence identities with Crenalkalicoccus roseus YIM 78023T (93.3 %) and Craurococcus roseus NS130T (92.7 %), but formed a distinct lineage within the family Acetobacteraceae in the phylogenetic trees. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 72346T is considered to represent a novel genus and species of the family Acetobacteraceae , for which the name Caldovatus sediminis gen. nov., sp. nov. is proposed. The type strain of Caldovatus sediminis is YIM 72346T (=KCTC 52714T=CGMCC 1.16330T).
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Phenylobacterium deserti sp. nov., isolated from desert soil
A novel bacterial strain, designated YIM 73061T, was isolated from the Cholistan desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Phenylobacterium conjunctum FWC21T (97.6 %), Phenylobacterium lituiforme FaiI3T (97.4 %), Phenylobacterium composti 4T-6T (97.0 %) and Phenylobacterium aquaticum W2-3-4T (96.8 %). Cells were Gram-stain-negative, aerobic and motile rods that formed orange colonies. The strain was oxidase- and catalase-positive. Growth occurred at 20–40 °C (optimum, 30–37 °C) at pH 5.0–8.0 (optimum, pH 7.0) and with 0–1 % (w/v) NaCl (optimum, 0–0.5 %). The major cellular fatty acids (>10 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol and four unidentified glycolipids. The major isoprenoid quinone was ubiquinone-10 (Q-10). The G+C content of the genomic DNA was 66.8 mol%. Strain YIM 73061T showed low levels of DNA–DNA relatedness to P. conjunctum FWC21T (27.2±2.6 %), P. lituiforme FaiI3T (24.6±1.1 %) and P. composti 4T-6T (18.4±3.1 %). On the basis of phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain YIM 73061T should be classified as representing a novel species, for which the name Phenylobacterium deserti sp. nov. is proposed. The type strain is YIM 73061T (=DSM 103871T=CCTCC AB 2016297T).
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Quisquiliibacterium transsilvanicum gen. nov., sp. nov., a novel betaproteobacterium isolated from a waste-treating bioreactor
A new betaproteobacterium, CGI-09T, was isolated from an activated sludge bioreactor which treated landfill leachate. Based on 16S rRNA gene sequence analysis, the new strain shared the highest pairwise similarity values with members of the order Burkholderiales : Derxia gummosa IAM 13946T (family Alcaligenaceae ), 93.7 % and Lautropia mirabilis DSM 11362T (family Burkholderiaceae ), 93.6 %. Cells of strain CGI-09T were rod-shaped and non-motile. The new strain was oxidase and catalase positive and capable of reducing nitrate to nitrite. The predominant fatty acids were C16 : 1 ω7c, C16 : 0, cycloC17 : 0 and C18 : 1 ω7c, the major respiratory quinone was Q-8, and the detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. The G+C content of the genomic DNA of strain CGI-09T was 70.2 mol%. The new bacterium can be distinguished from the members of genera Derxia and Lautropia based on its non-motile cells, arginine dihydrolase activity, its high cyclo C17 : 0 fatty acid content and the lack of hydroxy fatty acids. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGI-09T is considered to represent a new genus and species within the family Burkholderiaceae , for which the name Quisquiliibacterium transsilvanicum gen. nov., sp. nov. is proposed. The type strain is CGI-09T (=DSM 29781T=JCM 31785T).
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Salsuginimonas clara gen. nov., sp. nov., a member of the family Pseudoalteromonadaceae isolated from a brackish river
More LessA bacterial strain designated LSN-49T was isolated from a brackish river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain LSN-49T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate accumulating, motile by means of a monopolar flagellum, non-spore forming, straight rods and formed shiny and translucent colonies. Growth occurred at 20–40 °C (optimum, 25–30 °C), at pH 6–10 (optimum, pH 7–8) and with 0–3 % (w/v) NaCl [optimum, 0–1 % (w/v)]. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω8c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine, (PC), two uncharacterized aminophospholipids (APL1 and APL2), one uncharacterized glycolipid (GL1), four uncharacterized phospholipids (PL1–PL4) and four uncharacterized lipids (L1–L4). The major polyamine was putrescine. The major isoprenoid quinone was Q-8 and the DNA G+C content was 51.0 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that LSN-49T formed a distinct lineage with respect to closely related genera in the family Pseudoalteromonadaceae . LSN-49T was most closely related to Pseudoalteromonas , Algicola and Psychrosphaera and showed 89.3–92.1 % sequence similarity with members of the family Pseudoalteromonadaceae with validly published names. On the basis of the genotypic and phenotypic data, LSN-49T represents a novel genus and species of the family Pseudoalteromonadaceae , for which the name Salsuginimonas clara gen. nov., sp. nov. is proposed. The type strain is LSN-49T (=BCRC 81005T=LMG 29726T=KCTC 52439T).
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Paraglaciecola aestuariivivens sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, singly flagellated, aerobic and coccoid, ovoid or rod-shaped bacterium, designated strain JDTF-33T, was isolated from a tidal flat in Jindo, an island of South Korea. Strain JDTF-33T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, demonstrated that strain JDTF-33T belonged to the genus Paraglaciecola , joining the type strain of the species Paraglaciecola aquimarina with 97.9 % sequence similarity. Strain JDTF-33T exhibited 16S rRNA gene sequence similarities of 97.1 and 97.0 % to the type strains of Paraglaciecola arctica and Paraglaciecola psychrophila , respectively, and of 96.1–96.6 % to the type strains of the other species of the genus Paraglaciecola . Strain JDTF-33T showed DNA–DNA relatedness values of 11–24 % to the type strains of the species P. aquimarina , P. arctica and Paraglaciecola psychrophila . Strain JDTF-33T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain JDTF-33T were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain JDTF-33T was 41.7 mol%. Differential phenotypic properties, together with phylogenetic and genetic data, demonstrate that strain JDTF-33T is separate from species of the genus Paraglaciecola with validly published names . On the basis of the data presented, strain JDTF-33T represents a novel species of the genus Paraglaciecola , for which the name Paraglaciecola aestuariivivens sp. nov. is proposed. The type strain is JDTF-33T (=KCTC 52838T=NBRC 112782T).
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Paracoccus litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-spore-forming, non-motile and coccoid, ovoid or short rod-shaped bacterial strain, designated GHD-05T, was isolated from a tidal flat on the Yellow Sea in South Korea. Strain GHD-05T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain GHD-05T belonged to the genus P aracoccus , clustering with the type strain of P aracoccus aestuariivivens. Strain GHD-05T exhibited 16S rRNA gene sequence similarity values of 97.0–99.1 % to the type strains of P aracoccus aestuariivivens, P aracoccus limosus, P aracoccus laeviglucosivorans and P aracoccus marinus, and of 94.2–96.9 % to the type strains of the other Paracoccus species. Strain GHD-05T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain GHD-05T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content of strain GHD-05T was 64.1 mol% and its DNA–DNA relatedness values with the type strains of P. aestuariivivens , P aracoccus limosus, P. laeviglucosivorans and P. marinus were 13–32 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain GHD-05T is separated from recognized Paracoccus species. On the basis of the data presented here, strain GHD-05T is considered to represent a novel species of the genus Paracoccus , for which the name Paracoccus litorisediminis sp. nov. is proposed. The type strain is GHD-05T (=KCTC 52978T=NBRC 112902T).
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Acidocella aquatica sp. nov., a novel acidophilic heterotrophic bacterium isolated from a freshwater lake
More LessA novel acidophilic heterotrophic bacterium, strain Ok2GT, was isolated from a freshwater lake in Japan. Cells of the isolate were Gram-stain-negative and non-motile rods (0.6–0.8×1.0–2.8 µm). Growth was observed at 4–35 °C with an optimum growth temperature of 28 °C. The pH range for growth was 3.0–6.2 with an optimum pH of 4.5. The strain utilized fructose, glucose, sucrose, mannitol, sorbitol, ethanol, benzyl alcohol, pyruvate, yeast extract and tryptone as carbon and energy sources for aerobic growth. DNA G+C content was 62.6 mol%. The major cellular fatty acid and the isoprenoid quinone were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and Q-10, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain Ok2GT belongs to the genus Acidocella but is distinct from existing species with sequence similarities lower than 97 %. On the basis of these results, strain Ok2GT (=NBRC 112502T=DSM 104037T) is proposed as the type strain of a novel species, Acidocella aquatica sp. nov.
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Characterization of Marinomonas algicida sp. nov., a novel algicidal marine bacterium isolated from seawater
More LessA novel Marinomonas -like, aerobic, Gram-reaction-negative, moderately halophilic, acidophilic, motile by a single polar flagellum, non-spore-forming, rod-shaped bacterium that showed algalytic activity, designated strain Yeongu 1-4T, was isolated from surface seawater of Geoje Island in the South Sea, Republic of Korea. The strain was oxidase-negative and weakly positive for catalase. Growth of this bacterium was observed at temperatures from 4 to 42 °C, at salinities from 0 to 12 % and at pH from 4.5 to 9.0, and it was not able to degrade starch, gelatin, casein or Tween 80. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Yeongu 1-4T was related most closely to Marinomonas spartinae SMJ19T with similarity of 99.3 %. However, levels of DNA–DNA relatedness between strain Yeongu 1-4T and the most closely related species were lower than 70 %, confirming that they represent distinct genomic species. The genomic DNA G+C content of strain Yeongu 1-4T was 44.2 mol%. The organism used Q-8 as the predominant respiratory quinone, and C16 : 1ω7c, C18 : 1ω7c and C16 : 0 as major cellular fatty acids. Based on data from this polyphasic taxonomic study, strain Yeongu 1-4T belongs to a novel species of the genus Marinomonas , within the family Oceanospirillaceae , for which the name Marinomonas algicida is proposed. The type strain is Yeongu 1-4T (=KEMB 9005-327T=MCCC 1K00609T).
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Planktotalea lamellibrachiae sp. nov., isolated from a marine organism in Kagoshima Bay, Japan
More LessA novel marine bacterial strain, designated JAM 119T, was isolated from a tubeworm trophosome in Kagoshima Bay, Japan. Cells were Gram-negative, rod-shaped, non-spore-forming aerobic chemoorganotrophs and motile by means of a single polar flagellum. The isolate grew optimally at 25–27 °C and in the presence of 3 % NaCl. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. Phosphatidylcholine, phosphatidylglycerol and an unidentified aminolipid were the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Planktotalea in the class Alphaproteobacteria , and the 16S rRNA gene sequence similarity of the new isolates with the closest related species, Planktotalea frisia SH6-1T, was 97.3 %. The DNA G+C content of the novel strain was 57.0 mol%. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Planktotalea , for which the name Planktotalea lamellibrachiae sp. nov. (type strain JAM 119T; JCM 31859T=DSMZ 104669T) is proposed.
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Psychrosphaera aquimarina sp. nov., a marine bacterium isolated from seawater collected from Asan Bay, Republic of Korea
More LessCells of strain SW33T, isolated from the seawater of Asan Bay, Republic of Korea, were characterized as Gram-stain-negative, aerobic, rod-shaped, motile and non-spore-forming. Phylogenetic analysis revealed that strain SW33T belonged to the genus Psychrosphaera and clustered distantly with the other genera in the family Pseudoalteromonadaceae in the phylogenetic tree. The 16S rRNA sequences of strain SW33T revealed high similarities to Psychrosphaera saromensis SA4-48T (98.7 %), Psychrosphaera haliotis KDW4T (97.4 %) and Psychrosphaera aestuarii PSC101T (97.3 %). The major fatty acids were C16 : 0 (27.9 %), summed feature 3 (32.2 %) and summed feature 8 (17.2 %). The predominant quinone was Q-8, and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. The DNA G+C content was 38.3 mol%. The DNA–DNA relatedness values with the three species of Psychrosphaera saromensis KCTC 23240T, Psychrosphaera haliotis KCTC 22500T and Psychrosphaera aestuarii KCTC 32274T were 22, 23 and 18 %, respectively. Based on the phenotypic characteristics and taxonomic analyses, we propose that strain SW33T represents a novel species within the genus Psychrosphaera , for which the name Psychrosphaera aquimarina sp. nov. with the type strain SW33T (=KCTC 52743T=CICC 24249T) is proposed.
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Roseomonas terricola sp. nov., isolated from agricultural soil
More LessA novel strain, designated EM302T, was isolated from a soil sample collected from farmland located in Yesan-gun in the Republic of Korea. The cells were Gram-stain-negative, aerobic, non-motile without flagella and coccobacilli-shaped. Colonies were circular with entire edges, convex, opaque and pink. The strain grew at 15–40 ˚C (optimum, 35 ˚C) and pH 6.0–9.0 (optimum, 7.0). The strain grew in R2A medium without the addition of NaCl. Based on 16S rRNA gene sequences analysis, strain EM302T was found to be phylogenetically related to Roseomonas wooponensis WW53T (96.5 % 16S rRNA gene sequence similarity), Roseomonas arcticisoli MC 3624T (95.2 %), Roseomonas aerilata 5420-30T (94.5 %), Roseomonas pecuniae N75T (94.4 %) and Roseomonas vinacea CPCC 100056T (94.4 %). The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of the type strain was 65.7 mol%. On the basis of data presented here, strain EM302T is considered to represent a novel species of the genus Roseomonas , for which the name Roseomonas terricola sp. nov. is proposed. The type strain is EM302T (=KACC 13942T=KCTC 42906T=NBRC 111477T).
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Oceanibaculum nanhaiense sp. nov., isolated from surface seawater
More LessA taxonomic study was carried out on strain L54-1-50T, which was isolated from surface seawater of the South China Sea. Cells of strain L54-1-50T were Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth was observed at salinities from 0 to 9 % (optimum 2 %, w/v), at pH 6.0–10.0 (optimum 8.0–9.0) and at temperatures from 10 to 45 °C (optimum 25–37 °C), but not at 4 or 50 °C. The 16S rRNA gene sequence analysis indicated that strain L54-1-50T was a member of the genus Oceanibaculum , related to Oceanibaculum indicum P24T (98.8 %) and Oceanibaculum pacificum MC2UP-L3T (97.7 %). The digital DNA–DNA hybridization values between strain L54-1-50T and the two type strains O. indicum P24T and O. pacificum MC2UP-L3T were 35.4±2.5 and 23.7±2.5 %, respectively. The average nucleotide identity values between strain L54-1-50T and two type strains were 79.7 and 88.3 %, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 1 2-OH. The respiratory quinone was Q-10. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, two unidentified phospholipids and three unidentified lipids. The G+C content of the chromosomal DNA was 65.1 mol%. The combined genotypic and phenotypic data showed that strain L54-1-50T represents a novel species of the genus Oceanibaculum , for which the name Oceanibaculum nanhaiense sp. nov. is proposed, with the type strain L54-1-50T (=KCTC 52312T=MCCC 1A05150T).
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Altererythrobacter mangrovi sp. nov., isolated from mangrove sediment
More LessA Gram-stain-negative, facultative anaerobic, yellow-pigmented, rod-shaped, non-flagellum and non-motile bacterial strain, designed C9-11T, was isolated from mangrove sediment in Zhangzhou, Fujian Province, China. Growth was observed at temperatures from 15 to 37 °C (optimum 30 °C), at salinities from 0 to 4 % (optimum 0.5–2 %) and at pH from 6 to 8 (optimum 7). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain C9-11T was a member of the genus Altererythrobacter . Strain C9-11T was related most closely to Altererythrobacter oceanensis Y2T (96.8 % 16S rRNA gene sequence similarity), followed by Altererythrobacter marinus H32T (96.5 %). The G+C content of the genomic DNA was 63.5 mol%. The dominant fatty acids were C18 : 1ω7c (41.6 %), C17 : 1ω6c (15.4 %), 11-methyl C18 : 1ω7c (8.1 %), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c 7.4 %) and C16 : 0 (6.2 %). The predominant respiratory quinone was ubiquinone-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence analysis, strain C9-11Tbelongs to genus Altererythrobacte r, but can readily be distinguished from recognized species. Strain C9-11T is proposed as the type strain of a novel species of the genus Altererythrobacte r, for which the name Altererythrobacter mangrovi sp. nov (=MCCC 1K03311T=JCM 32056T) is proposed.
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Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample
Strain SYSU D8009T was isolated from a desert sample collected from Saudi Arabia. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, non-motile, aerobic and non-spore-forming. It was able to grow at 4–45 °C and pH 4.0–8.0, and exhibited NaCl tolerance of up to 1.5 % (w/v). Strain SYSU D8009T shared the closest 16S rRNA gene sequence similarities with members of the family Acetobacteraceae , with a value of less than 96.0 %. In the phylogenetic dendrograms, the strain clustered with the genera Paracraurococcus , Craurococcus and Crenalkalicoccus within the family Acetobacteraceae but with a distinct lineage, thereby demonstrating that the strain should be classified within the family Acetobacteraceae . The respiratory ubiquinone was found to be Q-10. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminolipids. The predominant cellular fatty acids were summed feature 8 (C1 8 : 1ω7c and/or C1 8 : 1ω6c) and C16 : 0. The genomic DNA G+C content of strain SYSU D8009T was determined to be 71.6 mol%. Based on the results of the phylogenetic analyses and differences in the physiological and biochemical characteristics, strain SYSU D8009T merits representation of a novel species of a new genus within the family Acetobacteraceae , for which the name Siccirubricoccus deserti gen. nov., sp. nov. is proposed. The type strain of Siccirubricoccus deserti sp. nov. is SYSU D8009T (=CGMCC 1.15936T=KCTC 62088T).
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- Eukaryotic Micro-organisms
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Description of Dioszegia patagonica sp. nov., a novel carotenogenic yeast isolated from cold environments
During a survey of carotenogenic yeasts from cold and oligotrophic environments in Patagonia, several yeasts of the genus Dioszegia (Tremellales, Agaricomycotina) were detected, including three strains that could not be assigned to any known taxa. Analyses of internal transcribed spacer and D1/D2 regions of the large subunit rRNA gene showed these strains are conspecific with several other strains found in the Italian Alps and in Antarctica soil. Phylogenetic analyses showed that 19 of these strains represent a novel yeast species of the genus Dioszegia. The name Dioszegia patagonica sp. nov. is proposed to accommodate these strains and CRUB 1147T (UFMG 195T=CBMAI 1564T=DBVPG 10618T=CBS 14901T; MycoBank MB 819782) was designated as the type strain. This Dioszegia species accumulates biotechnologically valuable compounds such as carotenoid pigments and mycosporines.
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Jaminaea pallidilutea sp. nov. (Microstromatales), a basidiomycetous yeast isolated from plant material of mangrove forests in Iran
In the course of an ongoing study aiming to catalogue the natural yeast biodiversity of Iran, a number of yeasts were isolated from plant material collected from mangrove forests on the shoreline of Qeshm Island. Two strains were identified as members of order Microstromatales. Standard phenotypic, biochemical, physiological characterization and a phylogenetic analyses of the combined 26S rRNA gene (D1/D2 domains) and ITS region sequences showed the conspecificity of these isolates and suggest their placement in the genus Jaminaea, close to Jaminaea lanaiensis and Jaminaea angkoriensis. Here, we describe this species as Jaminiaea pallidilutea sp. nov. with IBRC-M 30284T=DSM 104392T=CBS 14684T as the type strain. The Mycobank accession number is MB 819618.
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Heitmania gen. nov., a new yeast genus in Microbotryomycetes, and description of three novel species: Heitmania litseae sp. nov., Heitmania castanopsis sp. nov. and Heitmania elacocarpi sp. nov.
More LessNine anamorphic yeast strains isolated from various plant leaves collected in southern China were phylogenetically characterized based on sequences of the internal transcribed spacer (ITS) region, the D1/D2 domains of the large subunit (LSU) rRNA gene, the small subunit (SSU) rRNA gene, the two subunits of the RNA polymerase II gene (RPB1 and RPB2) and the translation elongation factor 1-α (TEF1). Phylogenetic analysis of the combined sequences of the six genes showed that the new strains formed a distinct clade in the class Microbotryomycetes but could not be assigned to any of the existing genera, families or orders of the class. Three separate groups were consistently resolved from the nine new strains based on the combined sequences of the six genes and single gene sequences of ITS, RPB1, RPB2 and TEF1. The results suggest that the nine yeast strains compared represent three novel species in a novel genus. The names Heitmania gen. nov. (MycoBank registration number MB819987), Heitmania litseae sp. nov. (MB820112, type strain CGMCC 2.5697T=CBS 14756T), Heitmania castanopsis sp. nov. (MB819988, CGMCC 2.5698T=CBS 14750T) and Heitmania elacocarpi sp. nov. (MB820113, CGMCC 2.5695T=CBS 14752T) are proposed for the new taxa.
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Kuraishia mediterranea sp. nov., a methanol-assimilating yeast species from olive oil and its sediment
More LessSix yeast strains isolated from olive oil sediments and spoiled olive oils originating from Slovenia and Portugal, respectively, proved to represent an undescribed yeast species based on DNA sequence comparisons. The analysis of gene sequences for internal transcribed spacer regions and the large subunit rRNA gene D1/D2 domain placed the novel species in the genus Kuraishia in a subclade containing Kuraishia capsulata, the type species of the genus. Although the novel species is well separated genetically from the recognized species of the genus, only a minor phenotypic difference differentiating it from Kuraishia capsulata and K. molischiana was observed. Relevant to its isolation source, no lipolytic activity was detected in the strains of the novel species. To accommodate the above-noted strains, Kuraishia mediterranea sp. nov. (holotype: ZIM 2473T; isotype: CBS 15107T; MycoBank no.: MB 822817) is proposed.
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- Erratum
Volumes and issues
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