- Volume 69, Issue 4, 2019
Volume 69, Issue 4, 2019
- Notification List
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- Review
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Techniques and tools for species identification in ciliates: a review
More LessCiliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
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The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation
Linhuan Wu and Juncai MaThe World Federation of Culture Collections and the World Data Center for Microorganisms (wdcm) initiated an international community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims to cooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology and contribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the wdcm and participant culture collections to submit a type strain sequencing proposal.
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- New Taxa
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- Actinobacteria
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Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.
A polyphasic study was designed to establish the taxonomic status of a Streptomyces strain isolated from soil from the QinLing Mountains, Shaanxi Province, China, and found to be the source of known and new specialized metabolites. Strain MBT76T was found to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces . The strain formed a distinct branch in the Streptomyces16S rRNA gene tree and was closely related to the type strains of Streptomyces hiroshimensis and Streptomyces mobaraerensis. Multi-locus sequence analyses based on five conserved house-keeping gene alleles showed that strain MBT76T is closely related to the type strain of S. hiroshimensis, as was the case in analysis of a family of conserved proteins. The organism was also distinguished from S. hiroshimensis using cultural and phenotypic features. Average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain MBT76T and S. hiroshimensis DSM 40037T were 88.96 and 28.4±2.3%, respectively, which is in line with their assignment to different species. On the basis of this wealth of data it is proposed that strain MBT76T (=DSM 106196T=NCCB 100637T), be classified as a new species, Streptomyces roseifaciens sp. nov.
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Collinsella vaginalis sp. nov. strain Marseille-P2666T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis
A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acids were C18:1ω9 (38 %), C16 : 0 (24 %) and C18 : 0 (19 %). The G+C content of the genome sequence of strain Marseille-P2666T is 64.6 mol%. On the basis of its phenotypic, phylogenetic and genomic features, strain Marseille-P2666T (=CSUR 2666T=DSM103342T) was classified as type strain of a novel species within the genus Collinsella for which the name Collinsella vaginalis sp. nov. is proposed.
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Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil
A novel actinomycete, designated strain NEAU-TCZ24T, was isolated from soil and characterized using a polyphasic approach. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Cellulomonas and formed a stable clade with its closest relatives Cellulomonas terrae JCM 14899T (98.4 % 16S rRNA gene sequence similarity), Cellulomonas xylanilytica JCM 14281T (97.9 %) and Cellulomonas humilata JCM 11945T (97.7 %). The major menaquinones were identified as MK-9(H4) and MK-8(H4). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositolmannoside, a ninhydrin-positiveglycolipid, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15 : 0, C18 : 1ω9c, C16 : 0 and anteiso-C17 : 0. Moreover, morphological and chemotaxonomic properties of NEAU-TCZ24T also confirmed the affiliation of the isolate to the genus Cellulomonas . However, multilocus sequence analysis based on five other house-keeping genes (gyrB, rpoB, recA, relA and atpD), DNA–DNA relatedness, physiological and biochemical data indicated that NEAU-TCZ24T could be distinguished from its closest relatives. Therefore, it is proposed that NEAU-TCZ24T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas rhizosphaerae sp. nov. is proposed. The type strain is NEAU-TCZ24T (=CCTCC AA 2018042T=JCM 32383T).
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Streptomyces cadmiisoli sp. nov., a novel actinomycete isolated from cadmium-contaminated soil
More LessA novel Streptomyces strain, ZFG47T, isolated from a cadmium-contaminated soil sample, was taxonomically studied in detail. Strain ZFG47T formed long, flexuous spiral spore chains consisting of elliptoid spores with spiny surfaces. The cell-wall hydrolysates contained ll-diaminopimelic acid as the diagnostic diamino acid. The major menaquinones consisted of MK-9(H2), MK-9(H4) and MK-9(H8). The major polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannosides. The predominant cellular fatty acids were iso-C16 : 0, C16 : 0 and anteiso-C15 : 0. The 16S rRNA gene sequence-based phylogenetic analysis indicated that this strain belongs to the genus Streptomyces , showing the highest sequence similarity to Streptomyces koyangensis VK-A60T (98.7 %). However, the digital DNA–DNA hybridization value, the average nucleotide identity value and the MLSA evolutionary distance between this strain and S. koyangensis VK-A60T showed that it belonged to a distinct species. Furthermore, the novel isolate could be distinctly differentiated from S. koyangensis VK-A60T by morphological, physiological and biochemical characteristics. On the basis of the evidence from this polyphasic study, it is concluded that strain ZFG47T represents a novel species of the genus Streptomyces , for which the name Streptomyces cadmiisoli sp. nov. is proposed, with strain ZFG47T (CICC 11050T=JCM 32897T) as the type strain.
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Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus
The taxonomic position of strain 15-057AT, an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057AT and its closest phylogenetic neighbours, Streptomyces griseoplanus NBRC 12779T and Streptacidiphilus oryzae TH49T, were 99.7 and 97.6 %, respectively. The G+C content of isolate 15-057AT was determined to be 72.6 mol%. DNA–DNA relatedness and average nucleotide identity between isolate 15-057AT and Streptomyces griseoplanus DSM 40009T were 29.2±2.5 % and 85.97 %, respectively. Chemotaxonomic features of isolate 15-057AT were consistent with its assignment within the genus Streptacidiphilus : the whole-cell hydrolysate contained ll-diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and ribose as cell-wall sugars; the major menaquinone was MK9(H8); the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophospholipid, aminoglycophospholipid and an unknown lipid; the major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phenotypic and morphological traits distinguished isolate 15-057AT from its closest phylogenetic neighbours. The results of our taxonomic analyses showed that strain 15-057AT represents a novel species within the evolutionary radiation of the genus Streptacidiphilus , for which the name Streptacidiphilus bronchialis sp. nov. is proposed. The type strain is 15-057AT (=DSM 106435T=ATCC BAA-2934T).
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Reclassification of Arthrobacter endophyticus (Wang et al. 2015) as Glutamicibacter endophyticus comb. nov.
More LessThe species Arthrobacter endophyticus is phylogenetically placed within the Glutamicibacter clade and shares 97.3–98.4 % 16S rRNA gene sequence similarities with the species of this genus. The quinone system with the major menaquinone MK-9 and the peptidoglycan amino acids alanine, glutamic acid and lysine are consistent with the characteristics of the members of the genus Glutamicibacter but the polar lipid profile with phosphatidylinositol distinguishes A. endophyticus from species of the genus Glutamicibacter . Re-analysis of both peptidoglycan structure and polar lipid profile revealed peptidoglycan type l-Lys–l-Ala–l-Glu (A11.35) and a polar lipid profile lacking phosphatidylinositol. These traits are consistent with those of representatives of the genus Glutamicibacter and distinguish A. endophyticus from members of the genus Arthrobacter sensu stricto. Due to its phylogenetic position and congruence with the key characteristics of members of the genus Glutamicibacter we here propose the reclassification of Arthrobacter endophyticus as a species of the genus Glutamicibacter , Glutamicibacter endophyticus comb. nov. (EGI 6500322T=DSM 28750T=KCTC 29490T=JCM 30091T).
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Proposal of new combination, Cutibacterium acnes subsp. elongatum comb. nov., and emended descriptions of the genus Cutibacterium, Cutibacterium acnes subsp. acnes and Cutibacterium acnes subsp. defendens
More LessIn 2016, division of the genus Propionibacterium into four distinct genera was proposed. As a consequence, the species Propionibacterium acnes was transferred to Cutibacterium gen. nov. as Cutibacterium acnes comb. nov. The three recently proposed subspecies of P. acnes were not, however, accommodated in this proposal. Following a very recent validation of a new combination for C. acnes subsp. defendens and an automatically created C. acnes subsp. acnes , we now propose the new combination, C. acnes subsp. elongatum comb. nov. The type strain of Cutibacterium acnes subsp. elongatum is JCM 18919T (=NCTC 13655T). On the basis of further genomic and phenotypic (haemolysis and MALDI-TOF mass spectrometry) analyses of these subspecies, we also provide emended descriptions of the genus Cutibacterium Scholz and Kilian 2016, C. acnes subsp. acnes (Gilchrist 1900) Nouioui et al. 2018, and C. acnes subsp. defendens (McDowell et al. 2016) Nouioui et al. 2018.
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Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai–Tibet Plateau
Two novel aerobic, Gram-staining-positive and non-spore-forming bacterial strains, 194T and S1194, were isolated from faeces of Tibetan antelopes sampled at the Qinghai–Tibet Plateau of China. The strains were able to grow in medium up to 10 % NaCl, similar to the NaCl-resistant property of the genus Salinibacterium members. The 16S rRNA gene sequences of the strains showed the highest similarity to Salinibacterium xinjiangense(98.1–98.2 %), and phylogenetic analysis based on 16S rRNA gene sequences indicated that strains 194T and S1194 represent a new lineage. The DNA G+C contents of strain 194T and S1194 are 64.1 and 64.2 mol%. Their genomes exhibit less than 96 % average nucleotide identity and 70 % DNA–DNA relatedness to known species of Salinibacterium . Strains 194T and S1194 are unable to utilize d-mannose or produce naphthol-AS-BI-phosphohydrolase. The two strains had anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids, and their cell walls contained lysine, alanine, glycine and glutamic acid. The predominant menaquinones identified were MK-11 and MK-10, with diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. Overall, the major cellular content profiles of 194T agreed with those of Salinibacterium xinjiangense and Salinibacterium amurskyense, though the proportions were distinct. Based on genotypic, phenotypic and biochemical analyses, the novel species Salinibacterium hongtaonis sp. nov. is proposed. The type strain is 194T (=CGMCC 1.16371T=DSM 106171T).
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Mycetocola zhujimingii sp. nov., isolated from faeces of Tibetan antelopes (Pantholops hodgsonii)
Strains 449T and 622 are both aerobic, Gram-stain-positive, short, rod-shaped bacilli that were recently isolated from the faeces of Tibetan antelopes on the Qinghai–Tibet Plateau in China. Their 16S rRNA gene sequences were most similar to those of Mycetocola zhadangensis ZD1-4T(97.9–98.0 %) and Mycetocola miduiensis CGMCC 1.11101T(97.3–97.4 %). Phylogenetic analysis of the 16S rRNA gene sequences further suggested that strains 449T and 622 represent a new lineage within the genus Mycetocola . The G+C content of strain 449T is 64.9 mol%. Optimal growth was achieved at pH 7.0 and 28 °C. Cells contained anteiso-C15 : 0 as the major cellular fatty acid, MK-10 and MK-11 as predominant menaquinones, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids, and lysine as the diagnostic diamino acid. The DNA–DNA hybridization values of strains 449T and 622 were below the 70 % cut-off with respect to known strains of the genus Mycetocola . Based on these genotypic, phenotypic and biochemical characteristics, it seems rational to conclude that strains 449T and 622 belong to the genus Mycetocola and thus represent a novel species, for which the name Mycetocola zhujimingii sp. nov. is proposed. The type strain is 449T (=CGMCC 1.16372T=DSM 106173T).
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Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov.
More LessPrevious analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related Olsenella species. To clarify the relationship of these two species, we determined the genome sequence of P. catena JCM 31932T and compared it with that already sequenced for L. massiliensis Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between P. catena JCM 31932T and L. massiliensis Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that P. catena JCM 31932T and L. massiliensis Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between L. massiliensis Marseille-P3237T and other closely related species. In addition, the genome of P. catena JCM 31932T had a high degree of synteny conservation with that of L. massiliensis Marseille-P3237T. On the basis of these findings, we propose that L. massiliensis should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).
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Litorihabitans aurantiacus gen. nov., sp. nov., an actinobacterium of the family Beutenbergiaceae isolated from beach sand
More LessA novel actinobacterium, designated HIsM16-52T, was isolated from beach sand collected from Ishigaki Island in Japan and its taxonomic position was investigated by a polyphasic approach. Strain HIsM16-52T contained both lysine and ornithine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and C14 : 0. The detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was determined to be 73.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIsM16-52T fell within the cluster of the family Beutenbergiaceae and formed a reliable cluster with the members of the genus Serinibacter . The highest 16S rRNA gene sequence similarities were obtained to species of the genus Serinibacter (97.8–97.9 %), followed by the genera Miniimonas (97.0 %), Beutenbergia (96.4 %) and Salana (95.9 %). However, strain HIsM16-52T differed from the members of the genus Serinibacter and the other genera within the family Beutenbergiaceae in terms of chemotaxonomic characteristics. Therefore, strain HIsM16-52T is concluded to represent a novel genus and species of the family Beutenbergiaceae , for which the name Litorihabitans aurantiacus gen. nov., sp. nov. is proposed. The type strain of L. aurantiacus is HIsM16-52T (=NBRC 112290T=TBRC 7759T).
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Actinomadura craniellae sp. nov., isolated from a marine sponge in the South China Sea
More LessA novel marine actinomycete, designated LHW63021T, was isolated from a marine sponge, genus Craniella, collected in the South China Sea. A polyphasic approach was applied to characterize the taxonomic position of this strain. The strain was found to have scarce aerial mycelia that differentiated into spore chains. The cell-wall hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid. Glucose, galactose, mannose and madurose were found in the whole-cell hydrolysates. The dominant polar lipids were phosphatidylinositol and diphosphatidylglycerol. MK-9(H6) and MK-9(H8) were the predominant menaquinones. The major fatty acids were iso-C16 : 0, iso-C18 : 0, 10-methyl C17 : 0 and C18 : 1 ω9c. The DNA G+C content based on the draft genome sequence was 72.0 mol%. 16S rRNA gene sequence analysis indicated that strain LHW63021T was a member of the genus Actinomadura and had the highest similarity to Actinomadura echinospora DSM 43163T (97.3 %). Phylogenetic trees supported their close relationship. The average nucleotide identity and digital DNA–DNA hybridization values between the whole genome sequences of strain LHW63021T and A. echinospora DSM 43163T were 79.13 and 23.20 %, respectively. The evidence from the polyphasic study shows that strain LHW63021T represents a novel species of the genus Actinomadura , for which the name Actinomadura craniellae sp. nov. is proposed. The type strain is LHW63021T (=DSM 106125T=CCTCC AA 2018015T).
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- Archaea
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Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea
A novel hydrogenotrophic methanogen, strain HHBT, was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60–80 °C, pH 5.0–7.4 and with 1–4 % of NaCl (w/v). The isolate utilized H2/CO2 as the only substrates for growth and methane production. The results of phylogenetic analyses of both 16S rRNA and mcrA gene sequences and comparative genome analysis indicated that HHBT represented a member of the order Methanococcales , and was closely related to the members of the genera Methanothermococcus and Methanotorris . The most closely related species were Methanothermococcus okinawensis IH1T and Methanotorris igneus Kol 5T in comparison of 16S rRNA gene sequences (each with 93 % identity), and Methanotorris formicicus Mc-S-70T in the case of deduced amino acid sequence similarity of mcrA genes (92 % similarity). The ANI and AAI values between HHBT and the members of the genera Methanothermococcus and Methanotorris were 69–72 % and 66–70 %, respectively. Although many of the morphological and physiological characteristics were quite similar between HHBT and the species of the genera Methanothermococcus and Methanotorris , they were distinguishable by the differences in susceptibility to antibiotics, formate utilization, growth temperature and NaCl ranges. On the basis of these phenotypic, phylogenetic and genomic properties, we propose that strain HHBT represents a novel species, of a novel genus, Methanofervidicoccus abyssi gen. nov., sp. nov. The type strain is HHBT (=JCM 32161T=DSM 105918T).
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- Bacteroidetes
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Chitinophaga silvisoli sp. nov., isolated from forest soil
More LessA Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901T, was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10′ 24′′ N; 112° 32′ 10′′ E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901T belongs to the genus Chitinophaga , and showed the highest similarities to Chitinophaga sancti NBRC 15057T (98.6 %) and Chitinophaga oryziterrae JCM 16595T (96.9 %). The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901T was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain K20C18050901T and C. sancti NBRC 15057T were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga silvisoli sp. nov. is proposed. The type strain is K20C18050901T (=GDMCC 1.1411T=KCTC 62860T).
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Marinilabilia rubra sp. nov., isolated from a marine solar saltern
More LessA novel cherry-red-pigmented, Gram-stain-negative, gliding, facultatively anaerobic and rod-shaped bacterium, designated strain WTE16T, was isolated from a sediment sample taken from a marine solar saltern of Wendeng, China (36° 59′ 56.49′′ N 122° 1′ 38.84′′ E). The novel isolate was able to grow at 20–40 °C (optimum 33 °C), at pH 6.0–9.0 (optimum pH 7.0) and with 1.0–12.0 % (w/v) NaCl (optimum 3.0–5.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species is Marinilabilia salmonicolor JCM 21150T (96.0 % similarity). Average nucleotide identity, average amino acid identity, percentage of conserved proteins and digital DNA–DNA hybridization values between strain WTE16T and Marinilabilia salmonicolor JCM 21150T were 73.8 %, 73.5 %, 63.4 % and 19.5–24.2 %, respectively. The genomic DNA G+C content of strain WTE16T was 40.8 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acids included iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain WTE16T included phosphatidylethanolamine, three unidentified phospholipids and three unidentified lipids. On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics, strain WTE16T is suggested to represent a novel species of the genus Marinilabilia , for which the name Marinilabilia rubra sp. nov. is proposed. The type strain is WTE16T (=KCTC 62599T=MCCC 1H00311T).
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Sinomicrobium soli sp. nov., isolated from arctic soil
More LessA bacterial strain, designated N-1-3-6T, was isolated from a soil sample collected from the arctic regions. The cells were short rods, Gram-stain-negative, catalase- and oxidase-positive. Growth was observed with 0–12 % (w/v) NaCl, with optimal growth at 0.5–2 %, and at pH 6.0–9.0, with optimum of pH 7.0, and a growth temperature of 10–45 °C, with an optimum of 28–37 °C. Phylogenetic analysis based on the 16S rRNA gene placed N-1-3-6T in the genus Sinomicrobium with the closest relative being Sinomicrobium pectinilyticum 5DNS001T, exhibiting 95.3 % 16S rRNA pairwise similarity. A polyphasic taxonomic study, including phenotypic, chemotaxonomic and molecular analyses, was performed to clarify its taxonomic position. N-1-3-6T contained MK-6 as the predominant menaquinone. Polar lipids consisted of phosphatidylethanolamine and several unidentified aminolipids, phospholipids and lipids. The principal fatty acids (>10 %) were iso-C15 : 0 (26.9 %), summed feature 3 [C16 : ω7c/ω6c (17.2 %)] and iso-C17 : 0 3-OH (14.7 %). The DNA G+C content of N-1-3-6T was 47.7 mol%. On the basis of its phenotypic and genotypic properties, strain N-1-3-6T should be classified as representing a novel species of the genus Sinomicrobium , for which the name Sinomicrobium soli sp. nov. is proposed, with the type strain N-1-3-6T (=MCCC 1A06047T=KCTC 52339T).
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Taibaiella helva sp. nov., isolated from farmland soil in China
More LessA yellow-coloured bacterial strain, designated F-4T, was isolated from a farmland soil sample from Qianshan, Anhui province, China. Strain F-4T was Gram-stain-negative, strictly aerobic, oval-shaped, motile (by gliding) and non-spore-forming. Growth occurred at 20–35 °C (optimum, 30 °C), at pH 6.0–8.0 (pH 7.0) and with 0–1.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F-4T belonged to the genus Taibaiella . 16S rRNA gene sequence similarity values between strain F-4T and the type strains of the three recognized species of the genus Taibaiella , Taibaiella koreensis KACC 17171T, Taibaiella soli KCTC 42277T and Taibaiella chishuiensis JCM 19637T, were 98.1, 96.4 and 95.9 %, respectively. The predominant respiratory quinone was MK-7, with MK-8 as a minor component. The major polar lipids of strain F-4T were three unidentified lipids, two unidentified aminolipids, three unidentified phospholipids, an unidentified aminophospholipid and phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0. The G+C content of the genomic DNA based on total genome calculations was 51.3 mol%. The major polyamine of strain F-4T was homospermidine. The average nucleotide identity and the digital DNA–DNA hybridization values for draft genomes between strain F-4T and strain THG-DT86T were 79.8 and 22.6 %, respectively. On the basis of the genotypic and phenotypic data presented here, strain F-4T represents a novel species of the genus Taibaiella , for which the name Taibaiella helva sp. nov. is proposed. The type strain is F-4T (=KCTC 62442T=CGMCC 1.13562T).
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Chitinophaga alhagiae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia
More LessA Gram-stain-negative, non-flagellated, rod-shaped bacterium, designated strain T22T, was isolated from rhizosphere soil of Alhagi sparsifolia, collected from Xinjiang, China. Its major fatty acids (>5 %) were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0-3OH, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H) and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). The predominant respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, two aminolipids and four unidentified lipids. The DNA G+C content of the type strain was 53.4 mol%. According to phylogenetic analysis based on 16S rRNA gene sequences, strain T22T was related most closely to Chitinophaga barathri YLT18T (=CCTCC AB 2015054T) with similarity of 97.7 %. However, strain T22T was clearly distinguished from Chitinophaga barathri YLT18T using genome-to-genome distance and average nucleotide identity value calculation, as well as a range of physiological and biochemical characteristics comparisons. It is obvious from the genotypic and phenotypic data that strain T22T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga alhagiae sp. nov., is proposed. The type strain is T22T (=ACCC 60125T=KCTC 62518T).
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- Firmicutes and Related Organisms
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Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates
A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of Lactobacillus acidipiscis (sequence similarity, 97.6 %) and Lactobacillus pobuzihii (97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and L. acidipiscis DSM 15836T and 74.0 % between YK43T and L. pobuzihii E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).
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Bacillus acidinfaciens sp. nov., isolated from farmland soil
More LessA Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).
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Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member
A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella , Finegoldia , Gallicola and Parvimonas . The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).
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Paenibacillus zeisoli sp. nov., isolated from maize-cultivated soil artificially contaminated with cadmium
More LessA Gram-stain-negative, rod-shaped, motile bacterial strain, designated 3-5-3T, was isolated from maize-cultivated soil artificially contaminated with cadmium, in Nanyang, Henan Province, China. Strain 3-5-3T was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-5-3T was affiliated with the genus Paenibacillus and most closely related to Paenibacillus anaericanus MH2T (96.5 % similarity). The average nucleotide identity and digital DNA–DNA hybridization values between 3-5-3T and the closely related species ranged 69.4–84.5 % and 18.1–18.4 %. The genomic G+C content was 53.8 mol%. Anteiso-C15 : 0 was the major fatty acid and MK-7 was the only menaquinone. The diamino acid in the cell-wall peptidoglycan contains meso-diaminopimelic acid. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, two unidentified glycolipids, two unidentified aminolipids, one unidentified phospholipid, one unidentified phosphoaminolipid and six unidentified lipids. On the basis of the results obtained in this study, strain 3-5-3T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus zei soli sp. nov. is proposed. The type strain is 3-5-3T (=CGMCC 1.13686T=KCTC 33998T).
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Bacillus aciditolerans sp. nov., isolated from paddy soil
A Gram-stain-positive, motile, rod-shaped bacterial strain, YN-1T, was isolated from a rice field in the town of Jietou, Yunnan Province, PR China. Colonies were circular, 1–2 mm in diameter, creamy white, with slightly irregular margins. The isolate grew optimally at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence similarity comparisons, YN-1T clustered together with other species of the genus Bacillus and showed highest similarities with Bacillus onubensis 0911MAR22V3T (98.0 %), Bacillus humi LMG22167T (97.5 %), ' Bacillus timonensis ' 10403023 (97.4 %) and ' Bacillus sinesaloumensis' P3516 (97.1 %). However, the DNA–DNA hybridization values between YN-1T and closely related strains of species of the genus Bacillus were well below 47 %, indicating that they represent different taxa. The average nucleotide identity and the Genome-to-Genome Distance Calculator also revealed low relatedness (below 95 and 70 %, respectively) between YN-1T and type strains of closely related species of the genus Bacillus . The DNA G+C content of the strain was 40 mol%. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids and two other unidentified lipids. Physiological and biochemical test results were also different from those of the most closely related species. On the basis of the phenotypic, genetic and chemotaxonomic data, strain YN-1T is considered to represent a novel species of the genus Bacillus , for which the name Bacillus aciditolerans sp. nov. is proposed, with strain YN-1T (=CCTCC AB 2017280T=JCM 32973T) as the type strain.
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Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi)
More LessA Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4T grew at pH 6.0–9.0 (optimum, 7.5), at 20–40 °C (37 °C) and in 0–15 % (w/v) NaCl (1–3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124T, Bacillus marisflavi JCM 11544T, Bacillus aquimaris JCM 11545T and B acillus oryzaecorticis JCM 19602T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4T were 70.0 and 84.3 %, respectively, and the digital DNA–DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4T (=JCM 33205T=KCTC 43014T=TISTR 2596T).
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Streptococcus chenjunshii sp. nov. isolated from feces of Tibetan antelopes
Three Gram-stain-positive, catalase-negative, α-haemolytic, chain-forming and coccus-shaped microorganisms (strains Z15T, Z1 and Z2) were isolated from feces of Tibetan antelopes collected from the Qinghai–Tibet plateau, PR China. The results of 16S rRNA gene sequence studies indicated that Z15T shared 94.5, 93.1 and 92.2 % similarity with Streptococcus pantholopis DSM 102135T, Streptococcus ursoris NUM 1615T and Streptococcus dentapri NUM 1529T, respectively. rpoB and groEL-based sequence analysis of our three novel isolates revealed interspecies divergence of 16.7 and 14.3 % from Streptococcus pantholopis DSM 102135T. The genomic DNA G+C content of Z15T is 42.48 mol%. Z15T has an average nucleotide identity (ANI) value of 81.19 % with S. pantholopis DSM 102135T and a DNA–DNA relatedness value of less than 70 % in the in-silico DNA–DNA hybridization (isDDH) with other species of genus Streptococcus deposited in the GenBank database. A whole-genome phylogenetic tree based on 246 core genes of 78 genomes of members of the genus Streptococcus indicated that Z15T represents a member of genus Streptococcus but one well separated from the currently recognized species. Z15T contains C18 : 1ω7c (25.5 %), C18 : 1ω9c (19.6 %), C16 : 0 (17.5 %) and C16 : 1ω9c (13.3 %) as its major cellular fatty acids. According to the morphological, biochemical and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus , and Streptococcus chenjunshii sp. nov. is thus proposed. The type strain is Z15T (=CGMCC 1.16529=DSM 106182).
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- Other Bacteria
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Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus
Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermus with validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus . The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov.
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Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi
A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5–0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20–37 °C (optimum, 30 °C), pH 5.5–8.0 (pH 6.5–7.0), and 0–30 g l−1 NaCl (5 g l−1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~105 cells ml−1, respectively. Strain MO-CFX2T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1T and Thermomarinilinea lacunifontana SW7T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2T (=KCTC 15625T, =JCM 32065T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.
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Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia
An isolate of strictly aerobic, pale-pink pigmented bacteria, strain AF10T, was obtained from an organic soil layer in forested tundra, Nadym region, West Siberia. Cells of strain AF10T were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance and formed large cell aggregates in old cultures. These bacteria were chemoorganotrophic, mildly acidophilic and psychrotolerant, and grew between pH 3.5 and 7.0 (optimum, pH 4.5–5.0) and at temperatures between 2 and 30 °C. The preferred growth substrates were sugars and some polysaccharides. The major fatty acids were iso-C15 : 0, C16 : 0, C16 : 1∆9 c and 13,16-dimethyl octacosanedioic acid. The genome of strain AF10T was 6.14 Mbp in size and encoded a wide repertoire of carbohydrate active enzymes. The genomic DNA G+C content was 59.8 mol%. Phylogenetic analysis indicated that strain AF10T is a member of the genus Granulicella, family Acidobacteriaceae , but displays 94.4–98.0 % 16S rRNA gene sequence similarity to currently described members of this genus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analyses, we propose to classify this bacterium as representing a novel species of the genus Granulicella, Granulicella sibirica sp. nov. Strain AF10T (=DSM 104461T=VKM B-3276T) is the type strain.
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Roseithermus sacchariphilus gen. nov., sp. nov. and proposal of Salisaetaceae fam. nov., representing new family in the order Rhodothermales
More LessA novel bacterium with cells that were pinkish-cream-coloured, aerobic, rod-shaped, 0.62–1.00 µm wide and 2.3–3.3 µm long, designated as strain MEBiC09517T, was isolated from Buksung-Po, a small port in Incheon, Republic of Korea. Strain MEBiC09517T had low 16S rRNA gene sequence similarity to validly reported strains; among them, Rubrivirga profundi SAORIC-476T displayed highest sequence similarity (89.9 %). Nevertheless, the novel strain shared a phylogenetic line with members of the genus Rhodothermus , not the genus Rubrivirga . Optimum growth conditions of strain MEBiC09517T were at 50–55 °C, pH 7 and in 2.0–4.0 % salt concentration. Strain MEBiC09517T was found to be an obligate marine bacterium that requires KCl, MgCl2 and CaCl2 as well as NaCl for growth. A phosphatidylethanolamine, a diphosphatidylglycerol, three glycolipids and four unidentified lipids were the strain's predominant polar lipid components. The fatty acid of the cell wall mainly consisted of carbons with 16 or 18 chain lengths such as C16 : 0, C18 : 0, C18 : 1 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant menaquinone was MK-7. The DNA G+C content is 68.65 mol%. Strain MEBiC09517T differs from genera of the order Rhodothermales in terms of fatty acid composition, growth conditions, and range of carbon source utilization. Based on phylogenetic analysis using the strain's 16S rRNA gene sequence and results of physiological tests, strain MEBiC09517T (KCCM=43267T, JCM=32374T) is proposed as Roseithermus sacchariphilus gen. nov., sp. nov. Additionally, the novel family Salisaetaceae fam. nov. based on phylogenetic analysis and physiological characteristics is suggested.
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- Proteobacteria
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Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov.
More LessComparative 16S rRNA gene sequence analysis and major physiological differences indicate two distinct sublineages within the genus Azoarcus : the Azoarcus evansii lineage, comprising Azoarcus evansii (type strain KB740T=DSM 6898T=CIP 109473T=NBRC 107771T), Azoarcus buckelii (type strain U120T=DSM 14744T=LMG 26916T), Azoarcus anaerobius (type strain LuFRes1T=DSM 12081T=LMG 30943T), Azoarcus tolulyticus (type strain Tol-4T=ATCC 51758T=CIP 109470T), Azoarcus toluvorans (type strain Td21T=ATCC 700604T=DSM 15124T) and Azoarcus toluclasticus (type strain MF63T=ATCC 700605T), and the Azoarcus indigens lineage, comprising Azoarcus indigens (type strain VB32T=ATCC 51398T=LMG 9092T), Azoarcus communis (type strain SWub3T=ATCC 51397T=LMG 9095T) and Azoarcus olearius (type strain DQS-4T=BCRC 80407T=KCTC 23918T=LMG 26893T). Az. evansii lineage members have remarkable anaerobic degradation capacities encompassing a multitude of alkylbenzenes, aromatic compounds and monoterpenes, often involving novel biochemical reactions. In contrast, Az. indigens lineage members are diazotrophic endophytes lacking these catabolic capacities. It is proposed that species of the Az. evansii lineage should be classified in a novel genus, Aromatoleum gen. nov. Finally, based on the literature and new growth, DNA–DNA hybridization and proteomic data, the following five new species are proposed: Aromatoleum aromaticum sp. nov. (type strain EbN1T=DSM 19018T=LMG 30748T and strain pCyN1=DSM 19016=LMG 31004), Aromatoleum petrolei sp. nov. (type strain ToN1T=DSM 19019T=LMG 30746T), Aromatoleumbremense sp. nov. (type strain PbN1T=DSM 19017T=LMG 31005T), Aromatoleum toluolicum sp. nov. (type strain TT=DSM 19020T=LMG 30751T) and Aromatoleum diolicum sp. nov. (type strain 22LinT=DSM 15408T=LMG 30750T).
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Thalassococcus profundi sp. nov., a marine bacterium isolated from deep seawater of the Okinawa Trough
More LessA novel Gram-stain-negative, strictly aerobic, rod-shaped motile bacterium with a single flagellum, designated strain WRAS1T, was isolated from deep seawater of the Okinawa Trough. Growth occurred in the presence of 0.0–9.0 % NaCl (w/v; optimum, 3.0–4.0 %), at 4–45 °C (optimum, 28–37 °C) and pH 7.0–10.0 (optimum, pH 7.0–8.0). The major fatty acid (>10 % of total fatty acids) was summed feature 8, comprising C18:1 ω6c and/or C18:1 ω7c. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WRAS1T was in the genus Thalassococcus and showed the highest 16S rRNA gene sequence similarity of 97.5 % to Thalassococcus halodurans JCM13833T. Genome relatedness between strain WRAS1T and T. halodurans JCM13833T was computed using both average nucleotide identity and DNA–DNA hybridization with values of 74.11 % and 22.70±2.3 %, respectively. The genomic DNA G+C content calculated from the genome sequence of strain WRAS1T was 65.6 %. On the basis of polyphasic analyses, strain WRAS1T is considered to represent a novel species in the genus Thalassococcus , for which the name Thalassococcus profundi sp. nov. is proposed. The type strain is WRAS1T (=CGMCC 1.16123T=MCCC 1K03253T =KCTC 52696T).
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Lysobacter psychrotolerans sp. nov., isolated from soil in the Tianshan Mountains, Xinjiang, China
A novel aerobic bacterial strain, designated ZS60T, with long, rod-shaped, Gram-staining-negative, aerobic cells was isolated from the soil in the Tianshan Mountains, Xinjiang, China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain ZS60T was affiliated with the genus Lysobacter , and was most closely related to Lysobacter daejeonensis GH1-9T (96.9 %), Lysobacter caeni BUT-8T (96.8 %) and Lysobacter ruishenii CTN-1T (96.7 %). The average nucleotide identity values between strain ZS60T, L. daejeonensis GH1-9T and L. ruishenii CTN-1T were 78.14 and 78.39 %, respectively. The DNA–DNA relatedness between strain ZS60T, L. daejeonensis GH1-9T and L. caeni BUT-8T were 44.8 and 39.1 %, respectively. The genomic DNA G+C content of the strain ZS60T was 67.7 mol% (draft genome sequence), and Q-8 was the predominant ubiquinone. The major cellular fatty acids of strain ZS60T were iso-C15 : 0 (23.4 %), iso-C17 : 0 (17.2 %) and iso-C17 : 1 ω9c (12.6 %). On the basis of genotypic, phenotypic and biochemical data, strain ZS60T is considered to represent a novel species of the genus Lysobacter , for which the name Lysobacter psychrotolerans sp. nov. is proposed. The type strain is ZS60T (=CGMCC 1.15509T=NBRC 112614T).
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Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean
More LessA taxonomic study was carried out on strain CIC4N-9T, which was isolated from deep-sea water of the Indian Ocean. The bacterium was Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0–9% and at temperatures of 4–41 °C. The isolate was able to degrade gelatin but not aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CIC4N-9T belonged to the genus Pararhodobacter , with the highest sequence similarity to the only recognized species, Pararhodobacter aggregans D1-19T (96.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain CIC4N-9T and P. aggregans D1-19T were 80.4 and 23.0 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C18 : 1ω7c 11-methyl, C18 : 0 and C17 : 0. The G+C content of the chromosomal DNA was 66.8 mol%. The sole respiratory quinone was determined to be Q-10. Phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unknown phospholipids, four unknown aminolipids and one unknown polar lipid were present. The combined genotypic and phenotypic data show that strain CIC4N-9T represents a novel species within the genus Pararhodobacter , for which the name Pararhodobacter marinus sp. nov. is proposed. The type strain is CIC4N-9T (=MCCC 1A01225T=KCTC 52336T).
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Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil
More LessA Gram-stain-negative, aerobic, motile, yellow-pigmented, rod-shaped with a single polar flagellum bacterial strain, designated strain DHG54T, was isolated from a forest soil sample of Dinghushan Biosphere Reserve, Guangdong Province, China. Strain DHG54T grew at 12–37 °C (optimum, 28 °C), pH 4.5–8.0 (optimum, pH 6.0–7.0) and in the presence of 0–3.0 % (w/v) NaCl (optimum, 0–1.5 %, w/v). Based on 16S rRNA gene sequence analysis, strain DHG54T formed a clade with the members of the genus Dyella and showed highest sequence similarities of 98.2 % to Dyella japonica DSM 16301T and Dyella terrae KACC 12748T. This was also supported by phylogenetic analysis based on the concatenated partial gyrB, lepA and recA housekeeping gene sequences. DNA–DNA hybridization results between strain DHG54T and closely related Dyella species were all lower than 70 %. Ubiquinone-8 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c were major fatty acids. The DNA G+C content of strain DHG54T was 65.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of the polyphasic characterization results presented here, strain DHG54T represents a novel species of the genus Dyella , for which the name Dyella solisilvae sp. nov. (type strain DHG54T=GDMCC 1.1187T = LMG 30091T) is proposed.
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Glaciecola amylolytica sp. nov., an amylase-producing bacterium isolated from seawater
A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium (THG-3.7T) was isolated from seawater. Growth occurred at 10–30 °C (optimum 25 °C), at pH 6–8 (optimum 7) and in the presence of 1–8 % (w/v) NaCl (optimum 4 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-3.7T were identified as Paraglaciecola mesophila DSM 15026T (95.3 % similarity), Glaciecola pallidula DSM 14239T (95.2 %), Paraglaciecola aquimarina KCTC 32108T (95.1 %), Paraglaciecola arctica KACC 14537T (94.9 %), Glaciecola nitratireducens KCTC 12276T (94.7 %) and Paraglaciecola psychrophila CGMCC 1.6130T (94.7 %). 16S rRNA gene sequence similarities among strain THG-3.7T and other species were lower than 94.7 %. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The quinone system was composed of Q-8. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain THG-3.7T was 47.9 mol%. On the basis of the data presented, strain THG-3.7T represents a novel species of the genus Glaciecola , for which the name Glaciecola amylolytica sp. nov. is proposed. The type strain is THG-3.7T (=KACC 19478T=CCTCC AB 2017258T).
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Paracoccus suum sp. nov., isolated from a pig farm dust collector
More LessA Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, coccoid- or short rod-shaped bacterial strain, designated SC2-6T, was isolated from a dust collector of a pig farm located in Wanju-gun, Jeollabuk-do, Republic of Korea. Strain SC2-6T grew within the ranges of 10–37 °C (28–30 °C, optimally), pH 6.0–10.0 (pH 7.0–8.0, optimally) and 0–3% NaCl (w/v). The 16S rRNA gene sequence similarity of strain SC2-6T showed the highest values to Paracoccus kondratievae GBT (96.3%), Paracoccus denitrificans DSM 413T (96.3%) and Paracoccus sanguinis 5503T (96.1%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain SC2-6T belonged to the genus Paracoccus and clustered with Paracoccus pacificus F14T. The phylogenetic tree based on the rpoD gene sequences also demonstrated that strain SC2-6T fell into the clade of the genus Paracoccus . The DNA G+C content was 66.9 mol%. The major respiratory quinone was ubiquinone-10 and the major fatty acids (> 10% of the total fatty acids) were summed feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c). The polar lipids were composed of diphosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, two unidentified aminolipids and two unidentified lipids. On the basis of phenotypic, phylogenetic and genomic data, strain SC2-6T was classified in the genus Paracoccus as a member of a novel species, for which the name Paracoccus suum sp. nov. is proposed. The type strain is SC2-6T (=KACC 19328T=NBRC 113110T).
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Profundibacter amoris gen. nov., sp. nov., a new member of the Roseobacter clade isolated from Loki’s Castle Vent Field on the Arctic Mid-Ocean Ridge.
A bacterial strain, designated BAR1T, was isolated from a microbial mat growing on the surface of a barite chimney at the Loki’s Castle Vent Field, at a depth of 2216 m. Cells of strain BAR1T were rod-shaped, Gram-reaction-negative and grew on marine broth 2216 at 10–37 °C (optimum 27–35 °C), pH 5.5–8.0 (optimum pH 6.5–7.5) and 0.5–5.0 % NaCl (optimum 2 %). The DNA G+C content was 57.38 mol%. The membrane-associated major ubiquinone was Q-10, the fatty acid profile was dominated by C18 : 1ω7c (91 %), and the polar lipids detected were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified lipid and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BAR1T clustered together with Rhodobacterales bacterium PRT1, as well as the genera Halocynthiibacter and Pseudohalocynthiibacter in a polyphyletic clade within the Roseobacter clade. Several characteristics differentiate strain BAR1T from the aforementioned genera, including its motility, its piezophilic behaviour and its ability to grow at 35 °C and under anaerobic conditions. Accordingly, strain BAR1T is considered to represent a novel genus and species within the Roseobacter clade, for which the name Profundibacter amoris gen. nov., sp. nov. is proposed. The type strain is Profundibacter amoris BAR1T (=JCM 31874T=DSM 104147T).
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Genome analysis-based reclassification of Lelliottia aquatilis as a later heterotypic synonym of Lelliottia jeotgali
More LessThe aim of this study was to further clarify the taxonomic relationship between the two recently described bacterial species, Lelliottia jeotgali sp. nov. and Lelliottia aquatilis sp. nov. Whole genome sequences of types strains of the two species are available for analysis. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the two type strains were determined. The ANI and isDDH values between type strains of the two species are 98.7 and 91.0 %, respectively, which are higher than cut-offs to define a bacterial species. It is therefore clear that the two species actually belong to the same species. The name of L.aquatilis was published at an earlier date than that of L. aquatilis . We therefore propose that L. aquatilis is a later heterotypic synonym of L. jeotgali .
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Altererythrobacter insulae sp. nov., a lipolytic bacterium isolated from a tidal flat
More LessA lipolytic, Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated BPTF-M16T, was isolated from tidal flat sediment on the Yellow Sea in the Republic of Korea. Strain BPTF-M16T grew optimally at 30 °C and in the presence of 2.0–3.0 % (w/v) NaCl. A phylogenetic tree of 16S rRNA gene sequences showed that strain BPTF-M16T fell within the clade comprising the type strains of Altererythrobacter species. Strain BPTF-M16T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.1 % to the type strains of Altererythrobacter ishigakiensis and A ltererythrobacter marinus , respectively, and of less than 97.0 % to the type strains of the other recognized species. Strain BPTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain BPTF-M16T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unidentified glycolipid. Mean DNA–DNA relatedness values of strain BPTF-M16T with the type strains of A. ishigakiensis and A. marinus were 22 and 13 %, respectively. The average nucleotide identity value between strain BPTF-M16T and the type strain of A. ishigakiensis was 76.80 %. Differential phenotypic properties, together with the phylogenetic and genetic data, revealed that strain BPTF-M16T is separated from recognized Altererythrobacter species. On the basis of the data presented here, strain BPTF-M16T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter insulae sp. nov. is proposed. The type strain is BPTF-M16T (=KCTC 62421T=KACC 19609T=NBRC 113190T).
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Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China
More LessCells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.
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Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume
A Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001T, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001T represents a member of the genus Sphingomonas , with the highest sequence similarity (97.7 %) to the type strain of Sphingomonas ginsengisoli . SYSUP0001T grew at 14–37 °C and pH 6–8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001T and closely related members of the genus Sphingomonas were below the cut-off level (95–96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001T represents a novel species of the genus Sphingomonas , for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001T (=KCTC 62179 T=CGMCC 1.16462T).
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Paracoccus sediminilitoris sp. nov., isolated from a tidal flat sediment
More LessA novel marine Gram-stain-negative, non-spore-forming, motile, aerobic, coccoid or ovoid bacterium, designated as strain DSL-16T, was isolated from a tidal flat sediment on the East China Sea and characterized phylogenetically and phenotypically. Optimal growth of the strain occurred at 35 °C (range 4–40 °C), at pH 6 (range 5–11) and with 4 % (w/v) NaCl (range 1–14 %). The nearest phylogenetic neighbour was Paracoccus seriniphilus DSM 14827T (98.2 % 16S rRNA gene sequence similarity). The digital DNA–DNA hybridization value between strain DSL-16T and P. seriniphilus DSM 14827T was 19.5±2.2 %. The average nucleotide identity value between strain DSL-16T and P. seriniphilus DSM 14827T was 83.6 %. The sole respiratory ubiquinone was Q-10. The major polar lipids were phosphatidylmonomethylethanolamine (PME), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidyglycerol (DPG) and glycolipid (GL). The predominant cellular fatty acids of strain DSL-16T were C18 : 1ω7c, C18 : 0 and 11-methyl C18 : 1ω7c. The G+C content of the genomic DNA was 64.5 mol%. The combined genotypic and phenotypic data indicated that strain DSL-16T represents a novel species of the genus Paracoccus , for which the name Paracoccus sediminilitoris sp. nov. is proposed. The type strain is DSL-16T (=KCTC 62644T=MCCC 1K03534T).
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Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge
More LessA Gram-stain-negative, motile bacterium, designated strain YE3T, was isolated from activated sludge obtained from a municipal wastewater treatment plant in Daejeon Metropolitan City, Republic of Korea. The cells were oxidase- and catalase-positive, and grew under aerobic conditions at 10–40 °C (optimum, 30 °C), with 1.0–8.0 % (w/v) NaCl (1.0 %) and at pH 5.5–9.0 (pH 7.0). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YE3T was most closely related to Pusillimonas harenae KACC 14927T (98.2 % sequence similarity) and Pusillimonas ginsengisoli KCTC 22046T (98.0 %). DNA–DNA relatedness values for strain YE3T and P. harenae KACC 14927T, P. ginsengisoli KCTC 22046T and P. soli KCTC 22455T were 28.7±2.27 %, 21.3±1.16 %, and 14.0±0.67 %, respectively. The genomic G+C content of the type strain YE3T was 59.3 mol%, as determined by whole-genome sequencing. The dominant fatty acids were C16 : 0 (39.2 %) and C17 : 0cyclo (37.5 %). The major polar lipids of strain YE3T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Two aminophospholipids and four unidentified lipids were also detected. Furthermore, strain YE3T was able to oxidize thiosulfate under heterotrophic conditions. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain YE3T represents a novel species of the genus Pusillimonas , for which the name Pusillimonas thiosulfatoxidans sp. nov. is proposed. The type strain is YE3T (=KCTC 62737T=NBRC 113113T).
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Desulfovibrio gilichinskyi sp. nov., a cold-adapted sulfate-reducing bacterium from a Yamal Peninsula cryopeg
More LessA psychrotolerant non-spore-forming sulfate-reducing bacterium, strain K3ST, was isolated from a Yamal Peninsula cryopeg within permafrost. Strain K3ST grew at subzero temperatures and required Na+ for growth. The new bacterium was able to use lactate, formate, pyruvate, fumarate, alanine, ethanol and molecular hydrogen as electron donors in the presence of sulfate, and used sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors in the presence of lactate. Fe(III)-citrate and Fe(III)-EDTA were reduced without visible growth. Major polar lipids were рhosphatidylserine, рhosphatidylethanolamine, phospholipids, cardiolipin and aminolipid; major cellular fatty acids were C16 : 1ω7, C16 : 0 and C18 : 1ω7; and the predominant isoprenoid quinone was MK-6 (H2). The genomic DNA G+C content was found to be 42.33 mol%. Phylogenetic analysis showed that the closest relative of the new isolate was Desulfovibrio ferrireducens strain 61T with 97.1 % 16S rRNA gene similarity. In addition, the ANI value between strain K3ST and D. ferrireducens 61T was 82.1 %. On the basis of the genomic and polyphasic taxonomy data of strain K3ST, we conclude that the strain is a representative of a novel species Desulfovibrio gilichinskyi sp. nov. (=VKM B-2877T=DSM 100341T).
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Erythrobacter spongiae sp. nov., isolated from marine sponge
More LessA taxonomic study was carried out on strain HN-E23T, which was isolated from sponge collected from Yangpu Bay, Hainan, China. Cells of strain HN-E23T were Gram-stain-negative, non-motile, orange-yellow-pigmented, short rods, that could grow at 10–40 °C (optimum, 28 °C), at pH 5–11 (optimun, pH 7) and in 0.5–12 % (w/v) NaCl (optimum, 3 %). This isolate was positive for oxidase, catalase, and the hydrolysis of aesculin, but negative for indole production and the reduction of nitrate. The phylogenetic tree based on 16S rRNA gene sequences revealed that strain HN-E23T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Strain HN-E23T shared the highest 16S rRNA gene sequence similarity to Erythrobacter aquimixticola JSSK-14T (97.2 %), followed by Erythrobacter atlanticus s21-N3T (96.6 %), Erythrobacter luteus KA37T (96.5 %) and Erythrobacter citreus RE35F/1T (96.4 %). The digital DNA–DNA hybridization (dDDH) and the average nucleotide identity (ANI) values between strain HN-E23T and JSSK-14T were 18.8 and 74.9 %, respectively. The dDDH and ANI values are below the standard cut-off criteria for delineation of bacterial species. The dominant fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and summed feature 3 (C16 : 1ω7c/ω6c). The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, an unidentified glycolipid and six unidentified lipids. The respiratory lipoquinone was identified as Q-10. The G+C content of the genomic DNA was 65.5 mol%. Based on the phenotypic and phylogenetic data, strain HN-E23T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter spongiae sp. nov. is proposed, with the type strain HN-E23T (=MCCC 1K03331T=LMG 30457T).
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Microbulbifer flavimaris sp. nov., a halophilic Gammaproteobacteria isolated from marine sediment of the Yellow Sea, China
A Gram-stain-negative, aerobic, non-flagellated, non-motile bacterium, designated strain WRN-8T, was isolated from marine sediment of the Yellow Sea, China (36° 5′ 33′′ N, 121° 20′ 37′′ E). Colonies of strain WRN-8T were 0.2–0.3 µm wide, 2.1–2.8 µm long, catalase-positive and oxidase-positive. Colonies on marine agar solid media were circular, wet, smooth, light yellow and approximately 1.3 mm in diameter. Growth occurred optimally at 33–37 °C, pH 7.0–7.5 and in the presence of 2–4 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicated that strain WRN-8T is a member of the genus Microbulbifer within the family Microbulbiferaceae , and the closest described neighbour in terms of 16S rRNA gene sequence identity is Microbulbifer aestuariivivens KCTC 52569T (98.1 %). The major respiratory quinone of strain WRN-8T is Q-8, its predominant fatty acids are iso-C15 : 0, iso-C17 : 0, C16 : 0, iso-C11 : 03-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, glycolipid, an unidentified phospholipid and an unidentified lipid. The draft genome obtained in this study was 3 643 020 bp, and the G+C content was 59.2 mol%. DNA–DNA hybridization (<46.3 %) and average nucleotide identity (<86.7 %) values between strain WRN-8T and the closest-related recognized Microbulbifer species confirmed the novelty of this new species. Therefore, we propose a novel species in the genus Microbulbifer to accommodate the novel isolate: Microbulbifer flavimaris sp. nov. (type strain WRN-8T=KCTC 42989T=ACCC 19926T).
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Phenylobacterium parvum sp. nov., isolated from lake water
More LessA Gram-stain-negative, rod-shaped and aerobic bacterium, designated HYN0004T, was isolated from lake water. The strain grew at 15–35 °C and pH 7.0–9.0 on R2A. The isoprenoid quinone was Q10 and major polar lipids were phosphatidylglycerol and one unidentified glycolipid. The genome was 2.83 Mb with a DNA G+C content of 69.9 mol%. 16S rRNA gene sequence analyses revealed that HYN0004T represented a member of the genus Phenylobacterium and shared sequence similarities with Phenylobacterium conjunctum (97.8 %), Phenylobacterium koreense (97.5 %), Phenylobacterium aquaticum (97.2 %), and Phenylobacterium heamatophilum (97.0 %). In addition to the low sequence similarities, the phylogenetic tree shapes indicated that HYN0004Trepresents an independent species of this genus. The genomic and phenotypic properties, including small genome size, inability to carry out numerous enzymatic reactions and high ratio of C18 : 1ω6c and/or C18 : 1ω7c in fatty acids, verified the differentiation between HYN0004T and related species. Thus, we propose a novel species of the genus Phenylobacterium , named as Phenylobacterium parvum sp. nov. The type strain is HYN0004T (=KACC 19185T=NBRC 112736T).
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