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Volume 70,
Issue 1,
2020
Volume 70, Issue 1, 2020
- New Taxa
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- Firmicutes and Related Organisms
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A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.
More LessThe genus Bacillus , harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA–GyrB–RpoB–RpoC proteins, and UvrD–PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5–23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct ‘ Bacillus ’ clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus .
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Bacillus taxi sp. nov., a novel endophytic bacterium isolated from root of Taxus chinensis (Pilger) Rehd
Li Tuo, Fang Liu, Xiao-Rui Yan and Yun LiuA Gram-staining-positive, aerobic, rod-shaped, endospore-forming bacterium, designated strain M5HDSG1-1T, was originally isolated from a surface-sterilized root of Taxus chinensis (Pilger) Rehd. in Guizhou, PR China. This bacterium was tested by a polyphasic approach to determine its taxonomic position. A 16S rRNA gene-based phylogenetic analysis revealed that M5HDSG1-1T had the greatest similarity to the type strain of Bacillus nealsonii DSM 15077T (99.1 %). The average nucleotide identity values between M5HDSG1-1T and Bacillus nealsonii DSM 15077T and Bacillus circulans NBRC 13626T were 73.3 and 72.8 %, respectively. The digital DNA–DNA hybridization values between M5HDSG1-1T and Bacillus nealsonii DSM 15077T and Bacillus circulans NBRC 13626T were 20.1 and 20.6 %, respectively, which were below the recommended thresholds. M5HDSG1-1T grew at a pH range of 6.0–12.0 (optimum, 7.0–8.0), at temperatures between 10 and 45 °C (optimum, 30 °C) and at 0–2 % (w/v) NaCl (optimum, 1 %). Neither substrate nor aerial mycelia was formed, and no diffusible pigments were observed on the media tested. The predominant isoprenoid quinone was menaquinone-7 (MK-7). The major fatty acids were anteiso-C15 : 0, and iso-C15 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified phospholipid. The DNA G+C content was 37.5 mol%. According to the phylogeneic, phenotypic and chemotaxonomic data, M5HDSG1-1T was clearly distinguishable from other species with validly published names in the genus Bacillus and should therefore be classified as representing a novel species, and we suggest the name Bacillus taxi sp. nov. The type strain is M5HDSG1-1T (=JCM 33117T=CGMCC 1.13668T).
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Lactococcus kimchii sp. nov., a new lactic acid bacterium isolated from kimchi
More LessA coccus strain designated S-13T was isolated from commercial baechu-kimchi in Korea. Comparison of the 16S rRNA gene sequence indicated that strain S-13T had the highest similarity to Lactococcus taiwanensis 0905C15T (97.9 %), Lactococcus lactis subsp. tructae L105T (97.6 %), Lactococcus lactis subsp. cremoris NCDO 607T (97.5 %), Lactococcus lactis subsp. hordniae NBRC 100931T (97.2 %), and Lactococcus lactis subsp. lactis JCM 5805T (97.2 %). The detailed phylogenetic analyses based on the 16S rRNA, rpoB and recA genes indicated that S-13T was separated from the other species and subspecies in the genus Lactococcus . The DNA–DNA relatedness between S-13T and closely related type strains, such as L. taiwanensis 0905C15T, L. lactis subsp. tructae L105T, L. lactis subsp. cremoris NCDO 607T, L. lactis subsp. hordniae NBRC 100931T, and L. lactis subsp. lactis JCM 5805T was 25.6, 20.4, 25.1, 20.2 and 21.7 %, respectively. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and C 14 : 0. The DNA G+C content of S-13T was 39.4 mol%. From the results of the phenotypic characteristics and chemotaxonomic analysis, it was concluded that strain S-13T represents a novel species in the genus Lactococcus for which the name Lactococcus kimchii sp. nov. (=KCTC 21096T=NBRC 113348T) is proposed.
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Bacillus natronophilus sp. nov., an alkaliphilic bacterium isolated from a soda lake
More LessAn alkaliphilic, moderately halophilic, heterotrophic, rod-shaped, spore-forming bacterium (M30T) was isolated from a sediment sample collected from a soda lake (Lake Magadi, Tanzania). Strain M30T was strictly aerobic, catalase-positive, oxidase-negative and non-motile. Growth occurred at 12–43 °C (optimum, 25–30 °C), at pH 8.0–12 (optimum, pH 9.5–10) and at salinities of 0.5–15 % (w/v) NaCl (optimum 5 %). It utilized various sugars and organic acids as sole carbon sources and was positive for amylase, cellulase, gelatinase, protease and xylanase activities. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified lipid and one unidentified phospholipid. The DNA G+C content was 48.9 mol%. The predominant menaquinone was MK-7 and the major fatty acids (>10 %) comprised anteiso-C15 : 0, iso-C15 : 0, and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence affiliated M30T to the genus Bacillus and showed the highest similarities to Bacillus populi FJAT-45347T (96.4 %) and Bacillus aurantiacus K1-5T (96.2 %). Based on the data from the current polyphasic study, M30T represents a novel species of the genus Bacillus , for which the name Bacillus natronophilus sp. nov. is proposed. The type strain is M30T (=JCM 32118T=CGMCC 1.16739T=MCC 3010T).
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Dialister hominis sp. nov., isolated from human faeces
An obligately anaerobic, Gram-stain-negative, rod or coccobacilli organism was isolated from a faecal sample of a healthy Japanese woman. In the 16S rRNA gene sequence analysis, strain 5BBH33T showed the highest 16S rRNA gene sequence similarity to Dialister succinatiphilus YIT 11850T (95.9 %), Dialister propionicifaciens ADV 1053.03T (94.3 %), Dialister micraerophilus DSM 19965T (93.1 %), Dialister invisus DSM 15470T (92.5 %) and Dialister pneumosintes ATCC 33048T (91.4 %). The hsp60 gene sequence analysis also revealed strain 5BBH33T had relatively low hsp60 gene sequence similarities (74.4–85.3 %) to other Dialister species. Strain 5BBH33T showed 21.8–23.9 % in silico DNA–DNA hybridization values with other Dialister species. In addition, the average nucleotide identity values between strain 5BBH33T and other Dialister species ranged from 68.7–74.2 %, indicating that this strain should be considered as new species based on whole-genome relatedness. Strain 5BBH33T was asaccharolytic and largely unreactive for commercial kit. However, its growth was enhanced by adding 1 % (w/v) succinate to the medium; strain 5BBH33T was able to decarboxylate succinate to propionate. The strain 5BBH33T genome contained the enzymes involved in succinate utilization. These results improve our understanding of succinate-utilizing bacteria. On the basis of the collected data, strain 5BBH33T represents a novel species in the genus Dialister , for which the name Dialister hominis sp. nov. is proposed. The type strain of D. hominis is 5BBH33T (=JCM 33369T=DSM 109768T).
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Paenibacillus piri sp. nov., isolated from urban soil
More LessA rod-shaped, Gram-stain-positive bacterial strain, MS74T, was isolated from soil beside Itaewon road, Seoul, Republic of Korea. The strain could grow well on R2A, nutrient agar and tryptone soya agar, but not in LB agar. MS74T tolerated 3.0 % NaCl (w/v), pH 9.0 and a temperature range from 10 to 35 °C (optimal temperature, 28 °C). From the comparison of 16S rRNA gene sequence, the strain is most closely related to Paenibacillus vulneris CCUG 53270T , Paenibacillus esterisolvens CFH S0170T, Paenibacillus rigui JCM 16352T and Paenibacillus yunnanensis YN2T with similarity percentages of 96.6 %, 96.4 %, 95.9 % and 95.8 % respectively. Major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The major menaquinone was MK-7. The fatty acids profile mainly consisted of C15 : 0 anteiso, C15 : 0 iso, C16 : 0 iso, and C16 : 0. The DNA G+C content of the isolated strain determined from the whole-genome sequence was 51 mol%. MS74T had an average nucleotide identity (ANI) value of 73.9 % and a digital DNA–DNA hybridization (dDDH) value of 20.6 % with most closely related strain, Paenibacillus vulneris CCUG 53270T. On the basis of phenotypic, chemotypic and genotypic evidence, the isolate was identified as representing a novel species of the genus Paenibacillus , for which the name Paenibacillus piri sp. nov. is proposed. The type strain is MS74T (=KACC 19385T =DSM 105496T)
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- Proteobacteria
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Lampropedia aestuarii sp. nov., isolated from the estuary of a freshwater river
More LessA Gram-stain-negative, strictly aerobic, catalase-positive and oxidase-positive bacterium, designated strain YIM MLB12T, was isolated from estuary sediment sampled at Maliao River where it flows into a plateau lake (Dianchi) in Yunnan, south-west PR China. Cells were non-motile and rod-shaped. Growth was observed at 15–35 °C (optimum, 25–30 °C), pH 6.0–10.0 (optimum, pH 7.0–8.0) and in the presence of 0–7 % (w/v) NaCl (optimum, 0.5–2 %). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM MLB12T formed a tight phylogenic lineage with members of the genus Lampropedia and was closely related to ‘ Lampropedia puyangensis ’ 2-bin with 98.3 % sequence similarity and had low similarities to the type strains of Lampropediahyalina ATCC 11041T (96 %) and Lampropedia cohaerens CT6T (95.5 %). Average nucleotide identity and in silico DNA–DNA hybridization values between strain YIM MLB12T and ‘ L. puyangensis ’ KCTC 32235 were 76.5 and 22.6 %, respectively. Strain YIM MLB12T contained ubiquinone-8 as the major quinone. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C10 : 0 3-OH, summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C12 : 0 3-OH and C14 : 0. The polar lipid profile of strain YIM MLB12T was composed predominantly of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The major polyamine was spermidine. The genomic DNA G+C content of strain YIM MLB12T was 56.8 mol%. Based on its genotypic and chemotaxonomic features and results of phenotypic analyses, strain YIM MLB12T represents a novel species of the genus Lampropedia , for which the name Lampropedia aestuarii sp. nov. is proposed. The type strain is YIM MLB12T (=KCTC 42886T=CGMCC 1.17071T).
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Marinomonas agarivorans sp. nov., an agar-degrading marine bacterium isolated from red algae
More LessA Gram-stain-negative, aerobic and curved-rod-shaped bacterium, designated QM202T, was isolated from red algae (Gracilaria blodgettii). Cells of strain QM202T were 0.2–0.3 µm wide and 1.0–2.5 µm long, catalase-negative and oxidase-positive. The strain exhibited an agar-degrading activity. It was motile by means of a single polar flagellum. Optimal growth occurred at 28–30 °C, pH 7.0–7.5 and in the presence of 2.0–3.0 % (w/v) NaCl. The DNA G+C content was 41.4 mol%. The isoprenoid quinone was identified as Q-8. Phophatidylethanolamine and phosphatidylglycerol were the predominant phospholipids. The dominant fatty acids were C18:1ω7c, C16:0 and C16:1ω7c and/or iso-C15:0 2-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QM202T belonged to the genus Marinomonas. The closest described neighbour in terms of 16S rRNA gene sequence identity was Marinomonas blandensis MED121T (95.5 %). The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness indicated that strain QM202T can be considered to represent a novel species, Marinomonas agarivorans sp. nov. The type strain is QM202T (=KCTC 52475T=MCCC 1H00145T).
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Fluviibacterium aquatile gen. nov., sp. nov., isolated from estuary sediment
A Gram-negative, aerobic, non-flagellated and ovoid- or rod-shaped bacterium, designated strain SM1902T, was isolated from the sediment sampled at the Jia River estuary, Yantai, PR China. The strain grew at 10–37 °C (optimum, 25–30 °C), pH 6.0–10.0 (pH 7.0) and with 0.5–13.0 % (w/v) NaCl (2.5%). It reduced nitrate to nitrite, but did not produce bacteriochlorophyll a. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1902T constituted a separated lineage within the family Rhodobacteraceae and was closely related to Meridianimarinicoccus roseus TG-679T and Phycocomes zhengii LMIT002T with 96.1 and 94.3 % 16S rRNA gene sequence similarities, respectively. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid. The sole respiratory quinone was ubiquinone-10. The in silico DNA–DNA hybridization values between strain SM1902T and Meridianimarinicoccus roseus TG-679T and Phycocomes zhengii LMIT002T were 19.6 and 19.5 %, respectively; and the average nucleotide identity values between them were 76.1 and 74.2 %, respectively. The genomic DNA G+C content of strain SM1902T was 58.2 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1902T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Fluviibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is SM1902T (=KCTC 72045T=MCCC 1K03596T=CCTCC AB 2018346T).
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Entomomonas moraniae gen. nov., sp. nov., a member of the family Pseudomonadaceae isolated from Asian honey bee gut, possesses a highly reduced genome
More LessThe honey bee gut microbiota contains many bacterial lineages that are specific to this ecosystem. Apis cerana, raised across the Asian continent, is of great significance to the maintenance and development of ecology and agriculture in Asia. Here, we report the isolation and characterization of strain QZS01T from the gut of Apis cerana from Pingwu County, Sichuan Province, PR China. The results of phylogenetic analysis based on 16S rRNA sequences showed that strain QZS01T forms a monophyletic group together with clone sequences derived from variable insect hosts, and it shows 92% sequence similarity to its closest relative, Pseudomonas knackmussii. Strain QZS01T possesses a reduced genome (3.3 Mbp; G+C content, 38.05 mol%) compared to all other Pseudomonas species, and the whole-genome based phylogenetic reconstruction showed that strain QZS01T represents a novel genus within the family Pseudomonadaceae. Strain QZS01T is a Gram-stain-negative facultative anaerobe. It grows on brain heart infusion agar and the energy sources utilized for growth are very limited. Based on the results of genotypic and phenotypic analyses, we propose a novel genus and species, Entomomonas moraniae gen. nov., sp. nov., with the type strain QZS01T (=CGMCC 1.13498T=KCTC 62495T).
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Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea
Two Gram-stain-negative, catalase- and oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains BEI176T and BEI207T, were isolated from seawater collected in the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains BEI176T and BEI207T belonged to the genus Vibrio and were closely related to each other with 98.18 % similarity. The closest phylogenetic relatives of strain BEI176T were Vibrio alginolyticus LMG 4409T (98.85 %) and Vibrio campbellii LMG 11216T (98.81 %), whereas the closest relative of strain BEI207T was Vibrio hepatarius LMG 20362T (98.64 %). The two strains showed growth at different conditions; while strain BEI176T grew at 16–37 °C, pH 5.0–9.5 and 0–7.0 % (w/v) NaCl, the growth of strain BEI207T occurred at 10–37 °C, pH 6.0–9.5 and 1.0–7.0 % (w/v) NaCl. Both strains shared the same major fatty acid components of summed feature 3 (C16 : 1ω7c or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω6c or C18 : 1ω7c). The DNA G+C contents of the assembled genomic sequences were 44.73 and 45.06 mol% for strains BEI176T and BEI207T, respectively. Average nucleotide identity values between the two strains and their reference species were lower than the threshold for species delineation (95–96 %); in silico DNA–DNA hybridization further showed that the two strains had less than 70 % similarity to their relatives. Therefore, two novel Vibrio species are proposed to accommodate them: Vibrio ouci sp. nov. (type strain, BEI176T=MCCC 1K03515T=JCM 32690T= KCTC 62616T) and Vibrio aquaticus sp. nov. (type strain, BEI207T=MCCC 1K03516T=JCM 32691T=KCTC 62617T).
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Phylogenomic analysis of Haemophilus parasuis and proposed reclassification to Glaesserella parasuis, gen. nov., comb. nov.
More LessThe Gram-negative bacterium Haemophilus parasuis is the etiologic agent of Glässer’s disease in pigs, and causes significant economic losses to the swine industry. This bacterium has been classified as a member of the family Pasteurellaceae in the genus Haemophilus , but phylogenetic relatedness has not been adequately examined to support this genus classification. Phenotypically, all 38 strains of H. parasuis tested were positive for catalase activity, oxidase activity, V-factor requirement, and acid formation from maltose and d-galactose without gas. All strains were negative for X-factor requirement, formation of indole from tryptophan, urease, l-arabinose, and α-glucosidase activity. To determine whether H. parasuis belongs to one of the current Pasteurellaceae genera 40 H . parasuis genomes, plus those of representative Pasteurellaceae , were subjected to phylogenetic analysis of concatenated, multi-protein alignments. Sequence variation at 16S rRNA and rpoB loci allowed the 15 reference serovars of H. parasuis to be integrated into the whole-genome tree. The phylogenetic analysis showed H. parasuis to be a distinct and tight clade whose sister taxon is the genus Bibersteinia . Within H. parasuis two clades were identified with individual serovars distributed between the two. As a result, H. parasuis was confirmed as a member of the family Pasteurellaceae , but was distinct from other genera in this family. Therefore, we propose the name Glaesserella parasuis, gen. nov., comb. nov. for bacterial strains currently classified as H. parasuis . The reference strain of this species is ATCC 19417 (1374)T, NCTC 4557T, DSM 21448T, CCUG 3712T.
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Brevundimonas fluminis sp. nov., isolated from a river
More LessA Gram-stain-negative, rod-shaped, motile, facultatively aerobic and ivory-pigmented bacterium (designated strain LA-55T) was isolated from a river in the Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-55T clustered with species of the genus Brevundimonas and was closely related to B revundimonas kwangchunensis KSL-102T (97.3 %), B revundimonas aurantiaca DSM 4731T (97.1 %), B revundimonas albigilva NHI-13T (97.0 %), B revundimonas balnearis FDRGB2bT (97.0 %) and Brevundimonas aveniformis DSM 17977T (97.0 %). The average nucleotide identity value between strain LA-55T and its closest-related strain was 74.1 %, indicating that strain LA-55T represents a novel species of the genus Brevundimonas . Growth occurred at 15–40 °C on Reasoner's 2A medium in the presence of 0–2 % NaCl (w/v) and at pH 6.0–8.0. The genomic DNA G+C content was 70.5 mol% and ubiquinone 10 (Q-10) was the major respiratory quinone. The major cellular fatty acids (>5 %) were C1 8 :1 ω6c and/or C1 8 :1 ω7c (summed feature 8), C16 : 0, C1 6 :1 ω6c and/or C1 6 :1 ω7c (summed feature 3) and C18 : 1 ω7c 11-methyl. The polar lipids consisted of phosphatidylglycerol, 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol, 1,2-di-O-acyl-3-O-α-d-glucopyranuronosyl glycerol, unidentified aminolipid, unidentified phosphoglycolipid and unidentified lipids. Physiological and biochemical characteristics indicated that strain LA-55T represents a novel species of the genus Brevundimonas , for which the name Brevundimonas fluminis sp. nov. is proposed. The type strain is LA-55T (=KACC 19639T=LMG 30850T).
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Psychrobacter pygoscelis sp. nov. isolated from the penguin Pygoscelis papua
One slightly beige-white pigmented, Gram-stain-negative, rod-shaped bacterium, strain I-STPP5bT, was isolated from the trachea of a Gentoo penguin chick individual (Pygoscelin papua) investigated in Fildes Bay, Chilean Antarctic (62° 12′ S, 58° 57′ W). I-STPP5bT consists of a 3.4 Mb chromosome with a DNA G+C content of 44.4 mol%. Of the 3056 predicted genes, 1206 were annotated as hypothetical proteins and 51 were tRNAs. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared a 16S rRNA gene sequence identity to the type strains of Psychrobacter phenylpyruvicus (98.8 %), Psychrobacter arenosus and Psychrobacter pasteurii (both 98.3 %), Psychrobacter piechaudii (98.2 %) and Psychrobacter sanguinis (98.1 %), but 16S rRNA gene sequence similarities to all other Psychrobacter species were ≤98.0 %. Partial gyrB nucleotide and amino acid sequence similarities among strain STPP5bT and the next related type strains were all below 81.8 and 92.9%, respectively. DNA–DNA hybridisation (DDH) with P. phenylpyruvicus LMG 5372T, P. arenosus DSM 15389T and P. sanguinis DSM 23635T also showed low values (all below 30 %). The main cellular fatty acids of the strain were C18 : 1ω9c and C16 : 1ω7c and/or C16 : 1ω6c. Based on phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a new species of the genus Psychrobacter, with the name Psychrobacter pygoscelis sp. nov. and strain I-STPP5bT (=CIP 111410T= CCM 8799T=LMG 30301T) as type strain.
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Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes(Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans
Strain EAR18T was isolated as an endophyte from the roots of a halophyte plant, Arthrocnemum macrostachyum, growing in the Odiel marshes (Huelva, Spain). Cells of strain EAR18T were Gram- stain-negative, motile, non-spore-forming aerobic rods. It grew optimally on tryptic soy agar supplemented with 2.5 % NaCl (w/v), at pH 7 and 30 °C for 48 h. It tolerated NaCl from 0 to 25 % (w/v). It presented Q9 as the major quinone and C19 : 0 cyclo ω8c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified phospholipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EAR18T formed a well-supported clade with species Halomonas zincidurans B6T and Halomonas xinjiangensis TRM 0175T (similarities of 98.3 and 96.1 % respectively). Furthermore, digital DNA–DNA hybridization analysis resulted in values of 20.4 % with H. xinjiangensis TRM 0175T and 35.50 % with H. zincidurans B6T, and ANIb/ANIm results in values of 73.8 %/84.2 % with H. xinjiangensis TRM 0175T and 86.8 %/89.4 % with H. zincidurans B6T. Based on phylogeny and differential phenotypic properties in comparison with its closest related species, strain EAR18T is suggested to represent a new species in the genus Halomonas , for which the name Halomonas radicis sp. nov. is proposed. The type strain is EAR18T (=CECT 9077T=LMG 29859T). The whole genome was sequenced, and it had a total length of 4.6 Mbp and a G+C content of 64.9 mol%.
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Thiomicrorhabdus indica sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a deep-sea hydrothermal vent environment
More LessA new mesophilic bacterium, designated strain 13-15AT, was isolated from the deep-sea water from the Carlsberg Ridge, northwestern Indian Ocean. Cells were short rods and motile with a single polar flagellum. Growth was observed in the presence of 85–1700 mM NaCl (optimum 680 mM), at 10–45 °C (optimum, 28 °C) and pH 5.0–9.0 (optimum, pH 7.0). The isolate was an obligate chemolithoautotroph capable of growth using thiosulfate, sulfide, elemental sulfur or tetrathionate as the sole energy source, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The major fatty acids were C16 : 1 (45.0 %), C18 : 1 (22.5 %) and C16 : 0 (20.1 %). The G+C content of the genomic DNA was 41.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate belonged to the genus Thiomicrorhabdus and was most closely related to Thiomicrorhabdus hydrogeniphila MAS2T (94.8 % sequence similarity). On the basis of the taxonomic data obtained in this study, strain 13-15AT represents a novel species of the genus Thiomicrorhabdus , for which the name Thiomicrorhabdus indica sp. nov. is proposed, with the type strain 13-15AT (=MCCC 1A13986T=KCTC 15750T).
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Komagataeibacter diospyri sp. nov., a novel species of thermotolerant bacterial nanocellulose-producing bacterium
Thermotolerant bacterial nanocellulose-producing strains, designated MSKU 9T and MSKU 15, were isolated from persimmon and sapodilla fruits, respectively. These strains were aerobic, Gram-stain-negative, had rod-shaped cells, were non-motile and formed white–cream colonies. Phylogeny based on the 16S rRNA gene sequences revealed that MSKU 9T and MSKU 15 represented members of the genus Komagataeibacter and formed a monophyletic branch with K. swingsii JCM 17123T and K. europaeus DSM 6160T. The genomic analysis revealed that overall genomic relatedness index values of MSKU 9T with K. swingsii JCM 17123T and K. europaeus DSM 6160T were ~90 % average nucleotide identity (ANI) and ≤58.2 % digital DNA–DNA hybridization (dDDH), respectively. MSKU 9T and MSKU 15 can be differentiated from the closely related K. swingsii JCM 17123T by their growth on 30 % d-glucose and ability to utilize and to form acid from raffinose and sucrose as carbon sources, and from K. europaeus DSM 6160T by their ability to grow without acetic acid. The genomic DNA G+C contents of MSKU 9T and MSKU 15 were 60.4 and 60.2 mol%, respectively. The major fatty acids of MSKU 9T and MSKU 15 were summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c). The respiratory quinone was determined to be Q10. On the basis of the results of the polyphasic taxonomic analysis, MSKU 9T (=TBRC 9844T=NBRC 113802T) represents a novel species of the genus Komagataeibacter , for which the name Komagataeibacter diospyri sp. nov. is proposed.
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Marimonas lutisalis sp. nov., isolated from a tidal mudflat and emended description of the genus Marimonas
More LessA Gram-reaction-negative bacterial strain, designated GH1-19T, was isolated from a tidal mudflat sample collected in Gangwha Island, Republic of Korea. Cells of the novel micro-organism were strictly aerobic, non-sporulating, motile and rod-shaped. Growth occurred at 10–40 °C (optimum, 30 °C), pH 6–9 (pH 8) and in the presence of 1–9 % NaCl (3 %). Comparative analysis of complete or nearly complete 16S rRNA gene sequences exhibited that strain GH1-19T formed a distinct cluster between Marimonas arenosa CAU 1311T (97.42 % sequence similarity) and Aquicoccus porphyridii L1 8-17T (97.35 %). Similarity levels of 16S rRNA gene sequences between the novel strain and other members of the family Rhodobacteraceae were below 96.6 %. The isoprenoid quinone was Q-10. The major fatty acids were C18 : 1ω7c, C16 : 0, summed feature 3 (C16 : 0 ω7c and/or C16 : 0 ω6c) and C12 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the DNA was 63.2 mol% (draft genome). DNA–DNA relatedness value between the novel strain and the type strain of Marimonas arenosa was 12.7±9.0 %. On the basis of data from phenotypic, chemotaxonomic and DNA–DNA hybridization studies together with phylogenetic analyses, strain GH1-19T (=KCTC 62376T=DSM 106292T) represents a novel species of the genus Marimonas , for which the name Marimonas lutisalis sp. nov. is proposed, with the emended description of the genus Marimonas .
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Saliniradius amylolyticus gen. nov., sp. nov., isolated from solar saltern sediment
More LessA novel non-pigmented, Gram-stain-negative, motile by means of a polar flagellum, aerobic and rod-shaped bacterium, designated HMF8227T, was isolated from solar saltern sediment sampled at Shinan, Republic of Korea. The isolate was able to grow at 15–42 °C (optimum, 37 °C), at pH 6–8 (pH 7) and with 0.5–12 % NaCl (2–5 %). Strain HMF8227T was positive for hydrolysis of starch and dextrin. 16S rRNA gene sequence analysis revealed that strain HMF8227T was affiliated with the family Alteromonadaceae , sharing the highest sequence similarities to the genera Salinimonas (93.0–94.4 %), Aestuariibacter (92.0–94.2 %), Alteromonas (92.0–93.6 %) and Lacimicrobium (93.6 %). In the phylogenetic trees, strain HMF8227T formed an independent clade with Lacimicrobium alkaliphilum X13M-12T. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids are phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and two unidentified glycolipids. The DNA G+C content of the genomic DNA was 52.1 mol%. On the basis of the polyphasic characterizations, strain HMF8227T represents a novel species and genus within the family Alteromonadaceae , for which the name Saliniradius amylolyticus gen. nov., sp. nov. is proposed, with the type strain being HMF8227T (=KCTC 62462T =NBRC 113230T).
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Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge
More LessA taxonomic study was carried out on strain HN-E21T, which was isolated from sponge collected from Yangpu Bay, Hainan, PR China. Cells of strain HN-E21T were Gram-stain-negative, non-spore-forming, tumbling-motile, ovoid- to rod-shaped and pale-yellow-pigmented that could grow at 15–42 °C (optimum, 37 °C), at pH 6–11 (pH 7) and in 0–14 % (w/v) NaCl (2–3 %). This isolate was positive for oxidase and catalase, but negative for hydrolysis of aesculin and gelatin. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HN-E21T formed a clade with Pelagivirga sediminicola BH-SD19T, Pontibaca methylaminivorans GRP21T, Roseovarius antarcticus M-S13-148T, Roseovarius aquimarinus CAU1059T and Roseovarius nanhaiticus NH52JT within the family Rhodobacteraceae . Strain HN-E21T shared the highest similarity to Pelagivirga sediminicola BH-SD19T (95.5 %), followed by Roseovarius lutimaris 112T (95.3 %), Pelagicola litorisediminis D1-W8T (95.2 %), Roseovarius gaetbuli YM-20T (95.0 %) and Roseovarius marisflavi H50T (95.0 %). The dominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16:0. The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, three unidentified lipids and one unidentified phospholipid. The respiratory quinone was identified as Q-10. The G+C content of the genomic DNA was 66.4 mol%. Based on the phenotypic and phylogenetic data, strain HN-E21T represents a novel species of the genus Roseovarius , for which the name Roseovarius spongiae sp. nov. is proposed, with the type strain HN-E21T (=MCCC 1K03333T=LMG 30456T).
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