- Volume 69, Issue 7, 2019
Volume 69, Issue 7, 2019
- Editorial
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- Validation List
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- Notification List
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- List of Changes in Taxonomic Opinion
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- Insight Review
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Minimal standards for the description of new genera and species of rhizobia and agrobacteria
Philippe M. de Lajudie, Mitchell Andrews, Julie Ardley, Bertrand Eardly, Estelle Jumas-Bilak, Nemanja Kuzmanović, Florent Lassalle, Kristina Lindström, Ridha Mhamdi, Esperanza Martínez-Romero, Lionel Moulin, Seyed Abdollah Mousavi, Xavier Nesme, Alvaro Peix, Joanna Puławska, Emma Steenkamp, Tomasz Stępkowski, Chang-Fu Tian, Pablo Vinuesa, Gehong Wei, Anne Willems, Jerri Zilli and Peter YoungHerein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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- New taxa
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- Actinobacteria
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Bailinhaonella thermotolerans gen. nov., sp. nov., a new member of the order Streptosporangiales
A Gram-positive, aerobic, non-motile actinobacterium, designated YIM 75507T, that was isolated from a soil sample collected from a dry-hot valley, was subjected to a polyphasic taxonomic study. The isolate formed branched hyphae and no fragmentation was found. Clustered spore chains were borne from aerial mycelium. The cell-wall peptidoglycan contained glutamic acid, alanine and meso-diaminopimelic acid. Whole-cell sugars were galactose, mannose, glucosamine, glucose and ribose. The major menaquinones were MK-9(H6), MK-9(H8) and MK-10(H6). The polar phospholipids contained phosphatidylmethylethanolamine, phosphatidylethanolamine and ninhydrin-positive phosphoglycolipid. Major fatty acids were iso-C16 : 0 and 10-methyl-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 75507T formed a stable and distinct lineage clustered with the genus Sinosporangium in the family Streptosporangiaceae . The draft genome sequence of strain YIM 75507T exhibited low average nucleotide identity to the closest related strain, Sinosporangium album CPCC 201354T (83.97 %), well below the 95–96 % species circumscription threshold. The G+C content of the genomic DNA was 73.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic evidence, strain YIM 75507T is assigned to a novel species of a new genus, for which the name Bailinhaonella thermotolerans gen. nov., sp. nov. is proposed. The type strain of Bailinhaonella thermotolerans is YIM 75507T (=KCTC 49229T=CGMCC 4.7547T).
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Nesterenkonia natronophila sp. nov., an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia
A Gram-stain-positive, alkaliphilic, moderately halophilic, cocci-shaped actinobacterium (strain M8T) was isolated from a sample of soda lake sediment (Lake Magadi, Tanzania). The isolate was heterotrophic, strictly aerobic, catalase-positive, oxidase-negative and formed orange-pigmented colonies in solid media. It utilized various sugars and organic acids as sole carbon sources. The organism grew at 10–38 °C, at pH 7.5–12.0 and in the presence of 1–12 % (w/v) NaCl, with optimal growth occurring at 30 °C, at pH 10 and in the presence of 5 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain M8T belonged to the genus Nesterenkonia , sharing the closest similarities to Nesterenkoniahalobia DSM 20541T, Nesterenkoniahalophila YIM 70179T and Nesterenkoniaaethiopica DSM 17733T (97.5, 97.5 and 97.1 %, respectively). The characteristic diamino acid of strain M8T was found to be lysine and the polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. The DNA G+C content was 61.8 mol% (genome). The strain contained MK-7, MK-9 and MK-10 as the respiratory quinones, and the major fatty acids (>10 %) comprised anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of phylogenetic analyses and phenotypic data, strain M8T is considered to represent a novel species, for which the name Nesterenkonia natronophila sp. nov. is proposed. The type strain is M8T (=JCM 32100T=CGMCC 1.16706T=MCC 3367T).
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Serinicoccus sediminis sp. nov., isolated from tidal flat sediment
A novel Gram-strain-positive, non-spore-forming bacterial strain, designated GP-T3-3T, was isolated from sediment sampled at a tidal flat in Gopado, Republic of Korea. Cells were aerobic, catalase-negative, oxidase-positive, non-motile cocci that occurred singly, in pairs or in clusters. Strain GP-T3-3T grew at 4–45 °C (optimum, 28–37 °C), at pH 4.0–12.0 (pH 8.0–9.0) and in the presence of 0–15 % (w/v) NaCl (3–5 %). Colonies of strain GP-T3-3T were deep-yellow, circular, smooth and pulvinate. The results of the phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GP-T3-3T was closely related to Serinicoccus profundi MCCC 1A05965T (99.1 %), Serinicoccus chungangensis CAU 9536T (99.0 %) and Serinicoccus marinus JC1078T (98.0 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-8(H4) and the major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of diphosphadidylglycerol, phosphadidylglycerol, phosphatidylcholine, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was 72.9 mol%. DNA–DNA relatedness values between strain GP-T3-3T and type strains of the genus Serinicoccus ranged from 28.9 to 50.5 %. On the basis of the phenotypic differences and DNA–DNA relatedness data, the isolate represents a new species of the genus Serinicoccus , for which the name Serinicoccus sediminis sp. nov. is proposed. The type strain is GP-T3-3T (=KCTC 49173T=JCM 32825T=KCCM 43309T=KACC 19850T).
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Kocuria soli sp. nov., an actinobacterium isolated from soil
More LessA Gram-stain-positive, aerobic, coccoid-shaped, non-spore-forming actinobacterial strain, designated M5W7-7T, was isolated from a hot spring soil sample collected from Anshan, Liaoning province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M5W7-7T clustered closely with species of the genus Kocuria , and showed the highest sequence similarity of 97.1 % to Kocuria subflava YIM 13062T. Strain M5W7-7T grew at 10–37 °C (optimum, 37 °C), pH6.0–11.0 (pH 6.0–7.0) and in the presence of 0–7 % (w/v) NaCl (0 %). Substrate mycelia and aerial mycelia were not formed, and diffusible pigments were not observed on any media tested. Strain M5W7-7T contained MK-6(H2) and MK-7(H2) as the dominant menaquinones. The polar lipid profile of strain M5W7-7T contained diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The predominant whole-cell sugars were galactose and glucose. The predominant fatty acid was anteiso-C15 : 0. The DNA G+C content of strain M5W7-7T was 67.0 mol%. On the basis of phylogenetic relationships, phenotypic characterization and chemotaxonomic analyses, strain M5W7-7T represents a novel species of the genus Kocuria , for which the name Kocuria soli sp. nov. is proposed. The type strain is M5W7-7T (=KCTC 49195T =CGMCC 1.13744T).
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Descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.
More LessTo complete the valid publication of the new species names resulting from reclassification of the genus Clavibacter , we here provide descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.
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Leucobacter muris sp. nov., isolated from the nose of a laboratory mouse
A Gram-stain-positive, rod-shaped, aerobic, non-motile, white, opaque bacterial isolate, designated 924/12T, was isolated from the nose of a laboratory mouse in Düsseldorf, Germany. The 16S rRNA gene sequence analyses indicated the phylogenetic position of the strain within the genus Leucobacter . Similarity levels over 97 % were recorded between the 16S rRNA gene sequence of strain 924/12T and the type strains of the species Leucobacter chironomi DSM 19883T (99.5 %), followed by Leucobacter celer subsp. astrifaciens CBX151T (97.6 %), Leucobacter celer subsp. celer NAL101T (97.5 %), ‘ Leucobacter kyeonggiensis ’ F3-P9 (97.5 %), Leucobacter zeae CC-MF41T (97.3 %), Leucobacter chromiiresistens JG31T (97.1 %), Leucobacter triazinivorans JW-1T (97.1 %), Leucobacter corticis 2 C-7T (97.0 %) and Leucobacter aridicolis CIP108388T (97.0 %). DNA–DNA hybridization and whole genomic comparison, mandatory to taxonomically separate strain 924/12T from the type strain of L. chironomi , revealed similarity values of 40.4 and 30.8 %, respectively, thus below the threshold of 70 % recommended differentiating between species. The cell-wall amino acids of the novel isolate were diaminobutyric acid, alanine, glycine, threonine and glutamic acid. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unknown lipid, whereas the predominant menaquinones were MK-11 and MK-10. The genomic DNA G+C content of strain 924/12T was 70.6 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences and the phenotypical differences between strain 924/12T and the other closely related type strains of the genus Leucobacter indicated that strain 924/12T represents a novel species within the genus Leucobacter , family Microbacteriaceae , for which the name Leucobacter muris sp. nov. is proposed. The type strain is 924/12T (=DSM 101948T=CCM 8761T).
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Protaetiibacter intestinalis gen. nov., of the family Microbacteriaceae, isolated from gut of Protaetia brevitarsis seulensis, reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. and emended description of the genus Lysinimonas Jang et al. 2013
A Gram-stain-positive, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, designated strain 2DFWR-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis, in the Republic of Korea. Strain 2DFWR-13T showed high sequence similarities to Lysinimonas kribbensis MSL-13T (97.7 %), Homoserinibacter gongjuensis 5GH26-15T (97.2 %), Microbacterium deminutum KV-483T (97.1 %) and Herbiconiux ginsengi CGMCC 4.3491T (97.1 %). The predominant fatty acids (>10 % of the total fatty acids) were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major menaquinones were MK-13 and MK-12. The peptidoglycan type was type B2 with the diagnostic amino acid d-DAB. The N-acyl type of the murein was glycolyl. The polar lipids consisted of diphosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The DNA G+C content was 71.5 mol%. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics, we conclude that strain 2DFWR-13T represents a novel genus and species of the family Microbacteriaceae , for which the name Protaetiibacter intestinalis gen. nov., sp. nov. is proposed. The type strain of Protaetiibacter intestinalis is 2DFWR-13T (=KACC 19321T=NBRC 113050T). In addition, an emended description of the genus Lysinimonas Jang et al. 2013 and the reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. are proposed.
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- Archaea
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Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria
More LessTwo mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5T and D3CT, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20–0.25 µm wide and 0.49–2.00 µm long. Strain NF5T possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2 -) and used bicarbonate as a carbon source. Strain D3CT was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5T and D3CT have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria , sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5T (=JCM 32270T =NCIMB 15114T) and D3CT (=JCM 32271T =DSM 106147T =NCIMB 15115T) are type strains of the species Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., respectively.
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- Bacteroidetes
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Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana
More LessOne Gram-stain negative, aerobic, non-motile bacterial strain, 2c-3T, was isolated from symptomatic canker bark tissue of Populus × euramericana. It was studied by the genome sequence-derived average nucleotide identity (ANI), phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics. 16S rRNA gene data revealed that the novel isolate shares the greatest sequence similarity to Sphingobacterium populi 7Y-4T (97.0 %). The ANI values between the novel isolate and S. populi 7Y-4T was 81.19 %, lower than the proposed species boundary ANI cut-off (95–96 %). The major fatty acids are iso-C15 : 0, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipids of the novel isolate included phosphatidylethanolamine, phospholipid, aminophospholipid and unknown lipids (L1–10). The menaquinone of the novel isolate was MK-7. The DNA G+C content was 41.96 mol %. Based on phenotypic and genotypic characteristics, the isolate represents a novel species within the genus Sphingobacterium , for which the name Sphingobacterium corticibacter is proposed. The type strain is 2c-3T (=CFCC 11898T=KCTC 52798T).
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Pedobacter chinensis sp. nov., a cellulose-decomposing bacterium from Arctic tundra soil
More LessA novel bacterial strain, JDX94T, was isolated from tundra soil sampled north of the Yellow River station, Arctic. Cells were Gram-stain-negative, non-spore-forming, short rod-shaped and aerobic. The strain displayed growth at 4–37 °C with an optimum at 28 °C, with 0–1.0 % (w/v) NaCl (optimum, 0%) and at pH 6.0–9.0 (optimum, pH 7.0–7.5). Cells contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as its major cellular fatty acids and menaquinone-7 as the only respiratory quinone. The polar lipid profile of strain JDX94T consisted of phosphatidylethanolamine, two unidentified aminolipids and four unknown polar lipids. The DNA G+C content was 37.5 mol%. On the basis 16S rRNA gene sequence comparison, strain JDX94T showed the highest sequence similarity (96.7 %) to Pedobacteragri JCM 15120T, followed by Pedobacteralluvionis DSM 19624T (96.3 %). Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain JDX94T and related species of the genus Pedobacter were 74.6–79.2 % and 18.9–24.5 %, respectively. Based on the presented results, we propose a novel species for which the name Pedobacter chinensis sp. nov. is suggested, with the type strain JDX94T (=MCCC 1H00335T= KCTC 62850T).
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Aquiflexum aquatile sp. nov., isolated from lake water
More LessA Gram-stain-negative, facultative anaerobic, red-coloured, rod-shaped, non-flagellated, non-motile and non-gliding bacterium, designated strain Z0201T, was isolated from lake water in Yunnan, China (26° 16′ N, 99° 94′ E). Cells of strain Z0201T were 0.2–0.4 µm wide and 1.4–2.5 µm long, catalase-positive and oxidase-negative. Strain Z0201T was found to grow at 4–37 °C (optimum, 30 °C) and pH 6.5–8.5 (pH 7.5) in the presence of 0–2.0 % (w/v) NaCl (0–0.5 %). The sole respiratory quinone of strain Z0201T was MK-7 and the DNA G+C content was 41.2 mol%. The major fatty acid was iso-C15 : 0 (49.4 %). The polar lipid profile of strain Z0201T consisted of aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, two unidentified phospholipids and five unidentified lipids. Based on the 16S rRNA gene sequence analysis, strain Z0201T was a member of the genus Aquiflexum , appearing to be closely related to Aquiflexum balticum (95.4 %). On the basis of phenotypic distinctiveness and phylogenetic divergence, strain Z0201T is considered to represent a novel species of the genus Aquiflexum , for which the name Aquiflexum aquatile sp. nov. is proposed. The type strain is Z0201T (=KCTC 62450T=MCCC 1H00328T).
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Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae
More LessThree Gram-stain-negative, aerobic, non-motile, oxidase- and catalase positive, rod-shaped, pink-coloured bacterial strains, DMA-K-7aT, DMA-K-1 and DMG-N-1, were isolated from water sampled at Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Cytophagaceae of the phylum Bacteroidetes , and their closest relatives are Rhabdobacter roseus R49T (95.66 %) and Dyadobacter sediminis Z12T (95.38 %). The assembled genome of strain DMA-K-7aT had a total length of 5.8 Mb and a DNA G+C content of 45.7 mol%. The major isoprenoid quinone was menaquinone-7 (MK-7). The major cellular fatty acids were C16 : 1 ω7c, iso-C15 : 0, C16 : 1 ω5c, C16 : 0 and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylserine, an unknown aminolipid, an unknown glycolipid and five unknown lipids. Flexirubin-type pigments were absent. Strain DMA-K-7aT (=DSM 106737T=NCAIM B.02641T) is proposed as the type strain of a new genus and species in the family Cytophagaceae , for which the name Arundinibacter roseus gen. nov., sp. nov. is proposed.
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Flavisolibacter nicotianae sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.
A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated strain X7XT, was isolated from a rhizosphere soil sample of Nicotiana tabacum L. collected from a tobacco factory located in Kunming, south-western China. The cells showed oxidase-positive and catalase-positive reactions. Growth occurred at 20–40 °C and pH 6.0–8.0, with optimal growth at 30 °C and pH 7.0. The predominant respiratory quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The cellular polar lipids contained phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, four unidentified aminolipids and four unidentified lipids. The genomic DNA G+C content was 49.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain X7XT should be affiliated to the genus Flavisolibacter . Results from further analysis showed that strain X7XT had highest 16S rRNA gene sequence similarity to Flavisolibacter metallilatus TX0661T (96.4 %) and ‘ Flavisolibacter swuensis ’ SR2-4-2T (96.4 %), followed by other species of the genus Flavisolibacter . The polyphasic taxonomic characteristics indicated that strain X7XT represents a novel species of the genus Flavisolibacter , for which the name Flavisolibacter nicotianae sp. nov. (type strain X7XT=KCTC 62326T=CGMCC 16451T) is proposed.
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Muricauda nanhaiensis sp. nov., isolated from seawater of the South China Sea
A Gram-stain-negative, aerobic, oxidase- and catalase-positive, non-flagellated, non-gliding, yellow-pigmented, and rod-shaped bacterium with appendages, designated strain SM1704T, was isolated from surface seawater collected from the South China Sea. The strain grew at 15–42 °C and with 1–10 % NaCl. It hydrolysed aesculin, but did not hydrolyse gelatin and Tween 80 nor reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SM1704T was affiliated with the genus Muricauda , sharing 94.1–95.9 % sequence similarities with type strains of recognized Muricauda species. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH and the main polar lipids were phosphatidylethanolamine, three unidentified lipids and three unidentified aminolipids. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content of strain SM1704T was 40.7 mol%. On the basis of results from polyphasic analysis of strain SM1704T, it is considered to represent a novel species within the genus Muricauda , for which the name Muricauda nanhaiensis sp. nov. is proposed. The type strain is SM1704T (=KCTC 62797T=MCCC 1K03557T).
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Algoriphagus sanaruensis sp. nov., a member of the family Cyclobacteriaceae, isolated from a brackish lake in Hamamatsu, Japan
More LessStrain M8-2T, which was isolated from brackish lake water (Lake Sanaru) in Japan, was characterized for representation of a novel species in the genus Algoriphagus . Cells of strain M8-2T were aerobic, Gram-stain-negative and curved-rod-shaped (0.2–0.5 µm wide and 0.7–1.9 µm long). Strain M8-2T grew optimally at 30 °C, pH 6.5–7.5 and in the presence of 0.5–1.0 % (w/v) NaCl. MK-7 was the sole isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid and an unidentified polar lipid. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain M8-2T belonged to the genus Algoriphagus and was closely related to Algoriphagus aquatilis A8-7T, Algoriphagus boseongensis BS-R1T, Algoriphagus aquaeductus T4T, Algoriphagus olei CC-Hsuan-617T, Algoriphagus shivajiensis NIO-S3T and Algoriphagus mannitolivorans DSM 15301T with sequence similarities of 96.6–97.4 %. Results of average nucleotide identity (<75 %) and digital DNA–DNA hybridization (<19 %) studies showed that M8-2T was distinct from its phylogenetic relatives. Based on the results of tests for acid production, the predominant cellular fatty acid composition, the DNA G+C content and phylogenetic position, a novel species in the genus Algoriphagus , with the name Algoriphagus sanaruensis sp. nov., is proposed for strain M8-2T (=JCM 31446T=LMG 29969T).
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Chitinophaga lutea sp. nov., isolated from arsenic-contaminated soil
More LessA yellow-coloured bacterial strain, designated ZY74T, was isolated from arsenic contaminated soil (34 mg kg−1) sample collected in Longkou, Hubei Province, PR China. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. Strain ZY74T produced round, yellow-pigmented, smooth and opaque colonies. Based on the results of 16S rRNA gene sequence analysis, strain ZY74T was found to be affiliated with members of the genus Chitinophaga . Its closest members were Chitinophagabarathri YLT18T (97.72 %) and Chitinophaganiabensis JS13-10T (97.17 %). The genome size of strain ZY74T was 6.61 Mb, containing 5351 predicted protein-coding genes, with a DNA G+C content of 55.0 mol%. The average nucleotide identity values of strain ZY74T with C. barathri YLT18T and C. niabensis DSM 24787T were 76.12 and 73.32 %, respectively. The digital DNA–DNA hybridization values of strain ZY74T with C. barathri YLT18T and C. niabensis JS13-10T were 20.60 and 19.40 %, respectively. The major respiratory quinone was menaquinone 7 and the predominant fatty acids (>5 %) were iso-C15:0, C16 : 1ω5c and iso-C17 : 03-OH. On the basis of phylogenetic, genotypic, phenotypic and chemotaxonomic characterization, strain ZY74T represents a novel species in the genus Chitinophaga , for which the name Chitinophaga lutea sp. nov. is proposed. The type strain is ZY74T (=CCTCC AB2018369T=KCTC 72039T).
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Hymenobacter metallilatus sp. nov., isolated from abandoned lead–zinc ore
An aerobic, non-motile, Gram-stain-negative, red-to-pinkish and rod-shaped bacterium, designated 9PBR-2T, was isolated from an abandoned lead–zinc ore sample collected from Meizhou, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 9PBR-2T belongs to the genus Hymenobacte r and was most closely related to Hymenobacter rigui KCTC 12533T (98.0 %), Hymenobacter swuensis KCTC 32018T (97.8 %) and Hymenobacter perfusus LMG 26000T (97.6 %). The calculated average nucleotide identity values based on whole genome sequences between strain 9PBR-2T and closely related type strains ranged from 81.3 to 84.1 %. Correspondingly, the digital DNA-DNA hybridization values ranged from 25.5 to 28.1 %. The major fatty acids of strain 9PBR-2T were iso-C15:0, anteiso-C15:0, C16:1 ω5c, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). It contained menaquinone 7 (MK-7) as the major isoprenoid quinone and phosphatidylethanolamine as the major polar lipid. The genomic DNA G+C content based on whole genome sequence was 59.8 mol%. Characterization based on phylogenetic, chemotaxonomic and phenotypic analyses clearly indicated that strain 9PBR-2T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter metallilatus sp. nov. is proposed. The type strain is 9PBR-2T (=GDMCC 1.1492T=JCM 32699T).
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- Firmicutes and Related Organisms
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Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field
More LessA Gram-stain-negative oval-rod-shaped, spore-forming anaerobic bacterium, designated as strain MCWD5T, was isolated from sediment of a salt pond in the Republic of Korea (35° 7′ 18″ N 126° 19′ 4″ E). The 16S rRNA gene sequence analysis revealed that strain MCWD5T had low similarity values to members in the family Lachnospiraceae , such as Robinsoniella peoriensis PPC31T (94.8 %), Ruminococcus gauvreauii CCRI-16110T (94.2 %) and Lachnotalea glycerini DLD10T (94.0 %), and its phylogenetic position is unstable. The strain could grow at 20–42 °C (optimum, 38–42 °C), pH 5.5–10.0 (pH 7.0) and with 0–6 % (2.0 %) NaCl. Strain MCWD5T could not use nitrate, nitrite, sulfate or sulfite as electron acceptors. The strain could utilize various carbohydrates, such as arabinose, cellobiose, glucose, etc., and polymers such as pectin and starch. The major fatty acids of strain MCWD5T were C14 : 0, C16 : 0, C16 : 1 ω7c, C18 : 1 ω7c DMA and summed feature 8 (C17 : 1 ω8c and/or C17 : 2), which was clearly different from those of related genera. The major polar lipids were diphosphatidyglycerol, phosphatidyglycerol and an unknown phospholipid. Based on the results of phylogenetic, physiologic and chemotaxonomic studies, Anaerosacchariphilus polymeriproducens gen. nov., sp. nov. with the type strain MCWD5T (=KCTC 15595T=DSM 105757T) is proposed in the family Lachnospiraceae .
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Phascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces
More LessTwo strictly anaerobic strains (MB11T and MB56) were isolated from common marmoset (Callithrixjacchus) faeces. Cells of the two strains were Gram-stain-negative, pleomorphic short (strain MB11T) or long (strain MB56) rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates were related to the genus Phascolarctobacterium . They had 16S rRNA gene sequences similarities lower than 93 % to previously described species, Phascolarctobacterium faecium ACM 3679T and Phascolarctobacterium succinatutens YIT 12067T, and 98.7 % between themselves. DNA–DNA hybridization values showed that strains MB11T and MB56 were the same species. The genomic DNA G+C content of strains MB11T and MB56 were 47.3–47.4 mol% and 47.7–48.0 mol%. The isolates had different enzymatic activities compared with P. succinatutens JCM 16074T and different major cellular fatty acids compared with P. faecium ACM 3679T. Substrate availability revealed that they utilized not only succinate, but also pyruvate. With pyruvate supplementation, they produced both propionate and acetate, while only propionate production occured with succinate. As suggested by the phylogenic and physiological properties of strains MB11T and MB56, we propose the name Phascolarctobacterium wakonense sp. nov. with the type strain MB11T (=JCM 32899T=DSM 107697T).
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Cohnella endophytica sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia apetala
More LessA Gram-stain-positive, aerobic, rod-shaped, endospore-forming bacterium, designated strain M2MS4P-1T, was isolated from surface-sterilized bark of Sonneratiaapetala sampled in Guangxi, China. The bacterium was characterized by a polyphasic approach to determine its taxonomic position. 16S rRNA gene sequence comparisons revealed that strain M2MS4P-1T belonged to the genus Cohnella and was most closely to Cohnella luojiensis HY-22RT (98.4 % similarity). The average nucleotide identity value and estimated DDH value between strain M2MS4P-1T and the type strain of C. luojiensis HY-22RT were 79.2 and 20.1 %, respectively. Neither substrate nor aerial mycelia were formed, and no diffusible pigments were observed on the media tested. Strain M2MS4P-1T grew in the pH range 6.0–9.0 (optimum, pH 7.0–8.0), at temperatures between 10–37 °C (30 °C) and in 0–1 % (w/v) NaCl (0 %). The predominant isoprenoid quinone in strain M2MS4P-1T was menaquinone-7. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, four unidentified aminophospholipids and two unidentified phospholipids. The DNA G+C content was 51.5 mol%. According to the phylogenetic, phenotypic and chemotaxonomic evidence, strain M2MS4P-1T was clearly distinguishable from other species with validly published names in the genus Cohnella and should therefore be classified as a novel species, for which we suggest the name Cohnella endophytica sp. nov. The type strain is M2MS4P-1T (=KCTC 43011T=CGMCC 1.13745T).
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Genome-based taxonomic classification within the family Thermoactinomycetaceae
More LessThe family Thermoactinomycetaceae comprises 43 validly published species, which were identified by a polyphasic taxonomic study based on molecular phylogenetics, physiological and biochemical characteristics. However, phylogenetic analysis merely based on 16S rRNA gene sequences cannot infer a robust and reliable phylogeny. For disentangling the phylogenetic relationships among members of this family, we used a large collection of genome data and the approach of phylogenomics, to re-examine their taxonomy. The topologies of phylogenomic trees are different from those of the 16S rRNA gene sequences. In addition, based on the average nucleotide identity, digital DNA–DNA hybridization, phenotypic and biochemical characteristics, we found that Laceyella sediminis should be reclassified as a later heterotypic synonym of Laceyella tengchongensis ; and reclassified Thermoactinomyces guangxiensis as Paenactinomyces guangxiensis gen. nov., comb. nov.; and establish Novibacillaceae fam. nov. to accommodate the genus Novibacillus as the type genus. In addition, compared to values calculated directly from genome sequences, the genomic DNA G+C contents mentioned in some species descriptions are too imprecise; and the corrected G+C content values have a significantly better fit to the phylogeny. Thus, the corresponding emendations of species descriptions are also proposed. In this paper, phylogenomics has been used to resolve the classification of the family Thermoactinomycetaceae .
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Faecalibacillus intestinalis gen. nov., sp. nov. and Faecalibacillus faecis sp. nov., isolated from human faeces
More LessTwo long-rod-shaped, Gram-stain-positive, obligately anaerobic and non-spore-forming strains, SNUG30099T and SNUG30370T, were isolated from faecal samples of healthy Korean subjects. The strains formed circular ivory-coloured colonies on Brain-heart infusion medium supplemented with 0.5% Difco yeast extract (YBHI) agar and cells were approximately 3.5–4.5×0.3–0.4 µm in size. Taxonomic analyses based on 16S rRNA gene sequences distinguished the strains from other species within the family Erysipelotrichaceae . The closest relative of strains SNUG30099T and SNUG30370T was Longibaculum muris (92.9 % and 93.6 % similarity, respectively), followed by Clostridium saccharogumia (92.3 % and 92.2 %). Phylogenetic inference also divided the strains into a unique branch that differed from other related strains that belong to the family Erysipelotrichaceae . DNA G+C contents based on the whole genome sequences of strains SNUG30099T and SNUG30370T were 29.2 and 30.2 mol%, respectively. Both novel strains possessed meso-diaminopimelic acid as the peptidoglycan, and phosphatidylethanolamine was observed as one of the major polar lipids. The major cellular fatty acid composition was different from those of other related taxa. In addition, the profile of biochemical activities advocated that the strains have distinct characteristics in comparison to other strains. Taken together, a novel genus, named Faecalibacillus gen. nov., is proposed, which includes the type species Faecalibacillus intestinalis sp. nov. for strain SNUG30099T and Faecalibacillus faecis sp. nov. for strain SNUG30370T. The type strains of these novel species are SNUG30099T (=KCTC 15631T=JCM 32256T) and SNUG30370T (=KCTC 15632T=JCM 32257T).
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Lactobacillus hulanensis sp. nov., isolated from suancai, a traditional Chinese pickle
Wei Zhao and Chun Tao GuA Gram-stain-positive bacterial strain, ZW163T, isolated from suancai, a traditional pickle of Heilongjiang province in China, was characterized by a polyphasic approach, including phenotypic characterization, sequence analyses of the 16S rRNA gene and two housekeeping genes (pheS and rpoA), whole genome sequencing and cellular fatty acid composition. Strain ZW163T was phylogenetically related to Lactobacillus sharpeae , Lactobacillus songhuajiangensis , Lactobacillus pantheris and Lactobacillus thailandensis , having 93.8–98.7 % 16S rRNA gene sequence similarities, 76.5–87.1 % pheS gene sequence similarities and 74.3–95.7 % rpoA gene sequence similarities to the type strains of L. sharpeae , L. songhuajiangensis , L. pantheris and L. thailandensis , respectively. Average nucleotide identity and in silico DNA–DNA hybridization values between strain ZW163T and the type strains of L. sharpeae , L. songhuajiangensis , L. pantheris and L. thailandensis were less than 77.7 % and 23.6 % respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus hulanensis sp. nov., is proposed and the type strain is ZW163T (=NCIMB 15193T=CCM 8926T=CCTCC AB 2019015T).
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- Other Bacteria
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Tengunoibacter tsumagoiensis gen. nov., sp. nov., Dictyobacter kobayashii sp. nov., Dictyobacter alpinus sp. nov., and description of Dictyobacteraceae fam. nov. within the order Ktedonobacterales isolated from Tengu-no-mugimeshi, a soil-like granular mass of micro-organisms, and emended descriptions of the genera Ktedonobacter and Dictyobacter
Three mesophilic, Gram-stain-positive, aerobic bacterial strains, designated Uno3T, Uno11T and Uno16T, were isolated from a soil-like granular micro-organism mass (termed Tengu-no-mugimeshi) collected from Tsumagoi, Gunma, Japan. They grow at 11–37 °C and pH 4.0–8.0, form branched mycelia, and have a G+C content between 49.4–50.3 mol%. The major menaquinone and fatty acid of Uno3T are MK-9 and iso-C16 : 0, respectively, whereas Uno11T and Uno16T share MK-9 (H2) and C16 : 1-2OH. The major cell-wall sugars are mannose (Uno3T and Uno11T) and glucose (Uno16T). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these three strains belong to the order Ktedonobacterales and are most closely related to Dictyobacter aurantiacus S-27T (sequence similarity of 91.3, 96.4 and 95.5 %). Average nucleotide identity values were <79.9 % among Uno11T, Uno16T and D. aurantiacus S-27T, well below the 95–96 % species circumscription threshold. Based on phenotypic features and phylogenetic positions, we propose that Uno3T represents a novel genus and species, Tengunoibacter tsumagoiensis gen. nov., sp. nov. (type strain Uno3T=NBRC 113152T=LMG 30471T=BCRC 81113T) within the new family Dictyobacteraceae fam. nov. Strains Uno11T and Uno16T are also considered to represent novel species: Dictyobacter kobayashii sp. nov. (type strain Uno11T=NBRC 113153T=LMG 30472T=BCRC 81114T) and Dictyobacter alpinus sp. nov. (type strain Uno16T=NBRC 113154T=BCRC 81115T). We also propose an emended description of the genus Dictyobacter , classifying it within family Dictyobacteraceae, and provide emended descriptions of the genera Dictyobacter and Ktedonobacter .
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- Proteobacteria
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Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector
More LessAn aerobic, Gram-stain-negative, polar-flagellated, rod-shaped bacterium, designated as SC2-7T, was isolated from the dust collector at a pig farm located in Wanju-gun, Jeollabuk-do, Republic of Korea. Growth occurred at 10–37 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum, 7.0–8.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 %) on Reasoner’s 2A medium. The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain SC2-7T was a member of the family Comamonadaceae , forming a robust cluster with the genera Alicycliphilus , Oryzisolibacter and Melaminivora . The 16S rRNA gene sequences of strain SC2-7T showed the highest sequence similarities to Alicycliphilus denitrificans K601T (97.2 %), Oryzisolibacter propanilivorax EPL6T (97.0 %), Melaminivora alkalimesophila CY1T (96.9 %), Diaphorobacter polyhydroxybutyrativorans SL-205T (96.6 %), Diaphorobacter nitroreducens NA10BT (96.6 %) and Melaminivora jejuensis KBB12T (96.5 %). The tree based on the gyrA gene sequences also showed that strain SC2-7T fell into a phylogenetic position similar to that based on the 16S rRNA gene sequences. The polar lipids present were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminolipid and an unidentified phospholipid. The predominant quinone was ubiquione-8. The major fatty acids were summed feature 3 (including C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (including C18 : 1ω6c and/or C18 : 1 ω7c). The genomic DNA G+C content was 69.1 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented here, strain SC2-7T represents a novel species of a new genus, for which the name Pulveribacter suum gen. nov., sp. nov., is proposed. The type strain of Pulveribacter suum is SC2-7T (=KACC 19309T=NBRC 113102T).
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Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.
A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain C8-1T, was isolated from the rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10–40 °C, at pH 6.0–8.0 and in the presence of up to 1 % (w/v) NaCl, with optimal growth at 30 °C and pH 7.0. The predominant isoprenoid quinone was Q-8. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. The genomic DNA G+C content was 70.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C8-1T should be assigned to the genus Lysobacter . 16S rRNA gene sequence similarity analysis showed that strain C8-1T was closely related to Lysobacter cavernae YIM C01544T (98.6 %), Lysobacter soli DCY21T (97.6 %), Lysobacter panacisoli CJ29T (97.3 %), Lysobacter firmicutimachus PB-6250T (97.3 %), Lysobacter niastensis GH41-7T (97.3 %) and Lysobacter gummosus KCTC 12132T (97.1 %). DNA–DNA hybridization data indicated that the isolate may represent a novel genomic species belonging to the genus Lysobacter . Polyphasic taxonomic characteristics indicated that strain C8-1T represents a novel species of the genus Lysobacter , for which the name Lysobacter tabacisoli sp. nov. is proposed. The type strain is C8-1T (=KCTC 62034T=CGMCC 1.16271T) .
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On the nomenclatural types of Methylothermus thermalis Tsubota et al. 2005, Methylothermus Tsubota et al. 2005 and Methylothermaceae Hirayama et al. 2014, their status under the International Code of Nomenclature of Prokaryotes and valid publication of the names Methylothermus gen. nov., Methylothermus subterraneus Hirayama et al. and Methylothermaceae Hirayama et al.
More LessThe nomenclatural type of Methylothermus thermalis Tsubota et al. 2005 is based on MYHT=IPOD FERM P-19714=VKM B-2345. IPOD FERM P-19714 is a collection accession number issued solely for patent purposes and under Rule 30(4) cannot serve as the nomenclatural type of the species. Since the deposit of the type strain in at least two publicly accessible culture collections in different countries from which subcultures must be available after 1 January 2001 is a prerequisite of the valid publication of a name at the rank of species, the name Methylothermus thermalis Tsubota et al. 2005 is not validly published. If the name Methylothermus thermalis Tsubota et al. 2005 is not validly published it has no status under the Code and cannot serve as the nomenclatural type of the genus Methylothermus Tsubota et al. 2005. Since it is a prerequisite of valid publication of a name that a nomenclatural type must be designated, the name Methylothermus Tsubota et al. 2005 is not validly published. If the name Methylothermus Tsubota et al. 2005 is not validly published, then the name at the rank of family Methylothermaceae Hirayama et al. 2014 is not based on a validly published name and it also has no type. Consequently, the name Methylothermaceae Hirayama et al. 2014 is not validly published
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Magnetospirillum kuznetsovii sp. nov., a novel magnetotactic bacterium isolated from a lake in the Moscow region
Strain LBB-42T was isolated from sediment sampled at Lake Beloe Bordukovskoe, located in the Moscow region (Russia). Phylogenetic analyses based on 16S rRNA gene sequencing results assigned the strain to the genus Magnetospirillum . Major fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1 ω9/C18 : 1 ω7. Genome sequencing revealed a genome size of 4.40 Mbp and a G+C content of 63.4 mol%. The average nucleotide identity and digital DNA–DNA hybridization values suggested that strain LBB-42T represents a new species, for which we propose the name Magnetospirillum kuznetsovii sp. nov., with the type strain LBB-42T (=VKM B-3270T=KCTC 15749T).
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Vibrio albus sp. nov., isolated from marine sediment
More LessA Gram-stain-negative, facultative anaerobic, motile, slightly bent rod-shaped bacterium, designated strain E4404T, was isolated from coastal sediment sampled Weihai, China. According to phylogenetic analysis based on its 16S rRNA gene sequence, strain E4404T shared the highest similarity with the type strain of Vibrio variabilis (97.0 %), followed by the type strains of Vibrio maritimus (96.1 %) and Vibrio europaeus (96.0 %). Multilocus sequence analysis based on the 16S rRNA gene and eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) showed that strain E4404T formed a unique clade in the genus Vibrio . The average nucleotide identity and digital DNA–DNA hybridization values between strain E4404T and some other species in the genus Vibrio were 71.0–72.7 % and 20.4–22.4 %, respectively. Cells grew at 15–37 °C and pH 6.0–8.5 in the presence of 1.0–6.0 % (w/v) NaCl, with optimal growth at 33 °C and pH 7.0–7.5 in the presence of 3.0–3.5 % (w/v) NaCl. No growth was observed on thiosulfate citrate bile salts sucrose medium. The major fatty acids of strain E4404T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The genomic DNA G+C content of strain E4404T was 46.1 mol%. Based on the phylogenetic, genotypic, phenotypic, biochemical and chemotaxonomic characteristics, strain E4404T represented a novel species of the genus Vibrio , for which the name Vibrio albus sp. nov. is proposed. The type strain is E4404T (=MCCC 1H00197T=KCTC 52890T).
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Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment
More LessA Gram-stain-negative bacterium, designated CM5-1T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain CM5-1T belongs to the genus Devosia , with closely related type strains Devosia submarina KMM 9415T (98.6 %), Devosia psychrophila Cr7-05T (98.6 %) and Devosia psychrophila E84T (98.2 %). Up-to-date bacterial core gene set analysis revealed that strain CM5-1T represents one independent lineage with D. submarina KMM 9415T. The average nucleotide identity values of CM5-1T with D. submarina KMM 9415T and D. psychrophila Cr7-05T are 80.1 and 77.9 %, respectively. In silico DNA–DNA hybridization values between strain CM5-1T and D. submarina KMM 9415T and D. psychrophila Cr7-05T are 23.8 and 21.9 %, respectively. Strain CM5-1T contains diphosphatidylglycerol, phosphatidylglycerol and glycolipid as major polar lipids. The sole isoprenoid quinone is ubiquinone-10, and C18 : 1ω7c and 11-methyl C18 : 1ω7c are the dominant cellular fatty acids. The G+C content of the genomic DNA is 61.4 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain CM5-1T could be differentiated from closely related species. Therefore, we propose strain CM5-1T as a novel species of the genus Devosia , for which the name Devosia naphthalenivorans sp. nov. is suggested. The type strain is CM5-1T (=JCM32509T=CGMCC 1.13553T).
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Oceaniradius stylonematis gen. nov., sp. nov., isolated from a red alga, Stylonema cornu-cervi
A Gram-stain-negative, strictly aerobic bacterium, designated StC1T, was isolated from a marine alga, Stylonema cornu-cervi, in the Republic of Korea. Cells were oxidase- and catalase-positive rods that were motile by a single lateral flagellum. Growth of strain StC1T was observed at 30–45 °C(optimum, 37 °C), pH 6.0–11.0 (pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (2 %). Strain StC1T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1 ω6c) and 11-methyl-C18 : 1ω7c as the major fatty acids. Sulfoquinovosyl diacylglycerol, phosphatidylethanolamine and phosphatidylglycerol and ubiquinone-10 were identified as the major polar lipids and the sole isoprenoid quinone, respectively. The G+C content of the genomic DNA was 64.7 mol%. Strain StC1T was most closely related to Oricola cellulosilytica CC-AMH-OT, Nitratireductor basaltis J3T, Aquamicrobium ahrensii 905/1T and Mesorhizobium tamadayense Ala-3T with 97.3 , 96.9 , 96.8 and 96.6 % 16S rRNA gene sequence similarities, respectively, but it formed a distinct phylogenic lineage within the family Phyllobacteriaceae . On the basis of phenotypic, chemotaxonomic and molecular properties, strain StC1T represents a novel genus of the family Phyllobacteriaceae , for which the name Oceaniradius stylonematis gen. nov., sp. nov. is proposed. The type strain is StC1T (=KACC 19231T=JCM 32050T).
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Altererythrobacter lutipelagi sp. nov., isolated from a tidal mudflat, and emended description of the genus Altererythrobacter
More LessA marine proteobacterium, designated strain GH1-16T, was isolated from a sample of tidal mudflat collected at the seashore of Gangwha Island, Republic of Korea and the taxonomic status was examined by a polyphasic approach. The isolate was Gram-reaction-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short-rod-shaped and produced yellow-coloured colonies. An absolute requirement for Na+ was observed. The major respiratory quinone was ubiquinone-10. The major polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The dominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c. The DNA G+C content was 60.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GH1-16T was closely related to members of the genus Altererythrobacter . The closest relative was Altererythrobacter marensis MSW-14T (97.3 % sequence similarity) followed by Altererythrobacter aquaemixtae JSSK-8T (96.8 %) and Altererythrobacter epoxidivorans JCS350T (96.7 %). The DNA relatedness of strain GH1-16T against its closest relative was 21.8–25.0 %. On the basis of data obtained by a polyphasic taxonomic approach, strain GH1-16T (=KCTC 52845T=NBRC 113275T) is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter lutipelagi sp. nov. is proposed.
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Azotobacter bryophylli sp. nov., isolated from the succulent plant Bryophyllum pinnatum
More LessA Gram-stain-negative, aerobic, nitrogen-fixing bacterium, designated strain L461T, was isolated from leaves of Bryophyllum pinnatum growing at the South China Agricultural University. Phylogenetic analysis of the 16S rRNA gene sequence indicated it as a member of the genus Azotobacter closely related to Azotobacter beijerinckii JCM 20725T (97.82 % similarity) and Azotobacter chroococcum ATCC 9043T (97.34 %). Its major fatty acid components were C16 : 1 ω9c and C16 : 0. Its predominant isoprenoid quinone was Q-9. Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, phospholipid and one unknown lipid. Its DNA G+C content was 64.9 mol% (Tm). DNA–DNA relatedness values between strain L461T and the reference strains of A. beijerinckii and A. chroococcum were 46.43 and 28.23 %, respectively. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, and comparison of cellular fatty acids distinguished strain L461T from the closely related Azotobacter species. Based on these data, the novel species Azotobacter bryophylli sp. nov. is proposed, with the type strain L461T (=KCTC 62195T=GDMCC 1.1250T).
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Sneathiella limimaris sp. nov., a marine alphaproteobacterium isolated from a tidal mudflat and emended description of the genus Sneathiella
More LessA novel marine bacterium, designated strain GH1-24T, was isolated from a tidal mudflat sample collected at Gangwha Island, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence comparison exhibited that the novel isolate was most closely related to Sneathiella and formed a tight cluster with Sneathiella glossodoripedis JCM 23214T with 98.1 % sequence similarity. The 16S rRNA gene sequence similarities to other Sneathiella species were low: Sneathiella chinensis LMG 23452T (96.1 %) and Sneathiellachungangensis CAU 1294T (95.8 %). Cells of the organism were Gram-reaction-negative, strictly aerobic, catalase- and oxidase-positive, motile rods and showed growth at 0.5–6 % NaCl, 20–42 °C and pH 6.0–8.0. The G+C content of the DNA was 54.9 mol%. The major isoprenoid quinone was Q-10. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and C19 : 0cyclo ω8c. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The results of phenotypic and phylogenetic analyses and DNA–DNA relatedness studies suggest that the isolate can be a member of a novel species of the genus Sneathiella , for which the name Sneathiella limimaris sp. nov. is proposed. The type strain is GH1-24T (=KCTC 52846T=NBRC 113276T)
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Altererythrobacter spongiae sp. nov., a novel member of the genus Altererythrobacter isolated from marine sponge
More LessA taxonomic study was carried out on strain HN-Y73T, which was isolated from sponge collected from Yangpu Bay, Hainan, PR China. Strain HN-Y73T was Gram-stain-negative, non-motile, ovoid- to rod-shaped, yellow-pigmented and could grow at 10–42 °C (optimum, 28 °C), at pH 5.0–9.0 (pH 8.0) and in 0.5–16 % (w/v) NaCl (3–4 %). This isolate was positive for oxidase, catalase and the hydrolysis of aesculin and xylan, but negative for the hydrolysis of casein and gelatin. Strain HN-Y73T shared the highest 16S rRNA gene sequence similarity with Altererythrobacter endophyticus BR75T (96.9 %), followed by Altererythrobacter estronivorus MH-B5T (96.0 %), Altererythrobacter indicus MSSRF26T (95.9 %) and Altererythrobacter mangrovi C9-11T (95.7 %). The phylogenetic tree showed that strain HN-Y73T forms a clade with A. endophyticus BR75T, A. indicus MSSRF26T and A. estronivorus MH-B5T within the genus Altererythrobacter . The dominant fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0cyclo ω8c. The major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, sphingoglycolipid phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, one unidentified glycolipid, two unidentified phospholipids and four unidentified lipids. The respiratory lipoquinone was identified as Q-10. The G+C content of the genomic DNA was 57.6 mol%. Based on the phenotypic and phylogenetic data, strain HN-Y73T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter spongiae sp. nov. is proposed. The type strain is HN-Y73T (=MCCC 1K03324T=LMG 30461T).
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Rhizobium chutanense sp. nov., isolated from root nodules of Phaseolus vulgaris in China
Two Gram-stain-negative, rod-shaped bacterial strains (C5T and C16), isolated from root nodules of Phaseolus vulgaris L. in Jiangxi Province, PR China, were characterized by using a polyphasic taxonomical approach. The phylogenetic analysis of the 16S rRNA gene and three concatenated housekeeping genes (recA–glnII–atpD) revealed that C5T and C16 were members of the genus Rhizobium , yet were distinct from known species. The case for strain C5T representing a novel species was supported by genomic results. Pairwise digital DNA–DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. The genome-based phylogenetic tree reconstructed by using the up-to-date bacterial core gene set consisting of 92 genes showed that the strains formed a monophyletic branch, further supporting this result. The symbiotic genes of nodC and nifH were identified in both strains; each could nodulate Phaseolus vulgaris and Glycine max but not Leucaena leucocephala, Pisum sativum or Medicago sativa plants. Major cellular fatty acids of C5T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 58.8 %), C18 : 1 ω7c 11-methyl (14.2 %) and C18 : 0 (8.1 %). The DNA G+C content of C5T was 61.4 mol%. Based on these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Rhizobium chutanense sp. nov. The type strain is C5T (=CCTCC AB 2018143T=LMG 30777T).
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Xinfangfangia humi sp. nov., isolated from soil amended with humic acid
Two slightly beige-pigmented, Gram-stain-negative, rod-shaped bacterial strains, IMT-291T and IMT-297, were isolated from soil in a field located in Malvern, Alabama, USA. The source soil had been amended with humic acid and continuously used for the cultivation of worms used for fish bait. It is still conceivable that the source of the strains is from the humic acid amendment, although all attempts to isolate the novel phenotypes from the humic acid source have failed. The two strains were identical based on morphology, growth rate and subsequently by 16S rRNA gene sequences, but showed differences in genomic fingerprint patterns generated by rep-PCR. Phylogenetic analysis based on the 16S rRNA gene revealed a placement of the strain in a distinct cluster with Xinfangfangia soli (97.2 % 16S rRNA gene sequence similarity) and in close proximity to the genus Falsirhodobacter with highest 16S rRNA gene sequence similarity of 95.3 % to the type strain of Falsirhodobacter deserti . Sequence similarities to all other type strains were below 95.0 %. The chemotaxonomic analysis showed a clear similarity to the genus Xinfangfangia . The main cellular fatty acids of the strain were C18 : 1 ω7c, 11-methly-C18 : 1 ω7c and C16 : 0. The major quinone was ubiquinone Q-10. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine were predominant in the polar lipid profile. The polyamine pattern contained the major compound spermidine and moderate amounts of putrescine and cadaverine. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses we propose a new species of the genus Xinfangfangia , with the name Xinfangfangia humi sp. nov. and strain IMT-291T (=LMG 30636T=CIP 111625T=CCM 8858T) as type strain.
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Legionella qingyii sp. nov., isolated from water samples in China
Three Legionella -like strains, designed km488T, km489 and km521, were isolated from freshwater samples in China. Cells were Gram-stain-negative, rod-shaped and non-spore-forming. Growth was observed on BCYEα agar, but not on BCYEα agar without l-cysteine, chocolate agar with PolyViteX or Columbia blood agar. The major fatty acids (>5 %) of strains km488T, km489 and km521 were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The mip gene sequences (574 nt) showed the isolates were almost identical with more than 99.7 % sequence similarities, and closely matched to L. gormanii ATCC 33297T with 95.4–95.6 % sequence similarities. Phylogenetic analyses based on concatenated gene (16S rRNA, mip, rpoB and rnpB) sequences indicated that the isolates formed a distinct cluster along with L. gormanii within the genus Legionella . Matrix-assisted laser desorption ionization time-of-flight analyses also demonstrated a clear separation between the isolates and other closely and distantly related Legionella species. DNA–DNA hybridization studies demonstrated that the isolates were closely related (92.0 –95.0 % DNA-DNA relatedness) but differentiated from their phylogenetic neighbours (<70 % DNA–DNA relatedness). The whole genome of km488T was sequenced, and showed a G+C content of 37.8 mol%. Based on the findings from this polyphasic taxonomic study, the isolates are considered to represent a single novel species, for which the name Legionella qingyii sp. nov. is proposed. The type strain is km488T (KCTC 15636T=CCTCC AB 2018025T=NRBC 113223T).
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Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies
More LessIn the last 4 years, most of the species previously classified as members of the genus Burkholderia have been transferred to the novel genera Paraburkholderia , Caballeronia , Robbsia , Mycetohabitans and Trinickia . However, there have been objections to splitting the genus Burkholderia sensu lato, and based on this taxonomic opinion, strain RPE64T, which has the 16S rRNA gene sequence identical to that of Caballeronia peredens LMG 29314T, has recently been proposed as the type strain of Burkholderia insecticola sp. nov. The arguments against the split were analysed in this study and found to be not convincing enough to revise the taxonomic positions of members of the novel genera. Therefore, based on the results of phylogenetic analyses, including comparisons of 16S rRNA gene sequences and those of concatenated proteins, as well as on the fact that strain RPE64T had all molecular signatures included as Caballeronia -specific markers in the genus description, we propose to reclassify B. insecticola as Caballeronia insecticola comb. nov. The results of this study also showed that ‘ Burkholderia novacaledonica ’ and ‘ Burkholderia ultramafica ’ should be transferred to the genera Caballeronia and Paraburkholderia , respectively.
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Jannaschia formosa sp. nov., isolated from marine saltern sediment
More LessA novel blush-red-pigmented, Gram-stain-negative, gliding, aerobic and rod- or oval-shaped bacterium, designated strain 12N15T, was isolated from sediment sampled at a marine saltern located in Wendeng, China (36° 59′ 56.49″ N, 122° 1′ 38.84″ E). Growth was observed at 10–40 °C (optimum, 28 °C), in 1.0–12.0 % NaCl (2.0–5.0 %, w/v) and at pH 6.0–9.5 (pH 7.0). The respiratory quinones were determined to be Q-10 and major fatty acids were C18 : 1ω7c and C18 : 0. The polar lipids profile of strain 12N15T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminolipid, phosphatidylcholine, one lipid and three phospholipids. The genomic DNA G+C content was 69.6 mol%. Phylogenetic analyses based on the 16S rRNA gene showed that the strain 12N15T was affiliated within the genus Jannaschia , and was most closely related to Jannaschia seohaensis KCTC 22172T. The average amino acid identity and percentage of conserved protein values between strain 12N15T and the type strain of the type species, Jannaschia helgolandensis DSM 14858T, were 70.2 % and 64.1 %, respectively. The average nucleotide identity value between strain 12N15T and J.annaschia seohaensis KCTC 22172T was 81.9 %. The phenotypic, phylogenetic and genomic analyses supported the hypothesis that strain 12N15T represents a novel species of the genus Jannaschia , for which the name Jannaschia formosa sp. nov. is proposed. The type strain is 12N15T (=MCCC 1H00325T=KCTC 62582T).
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Yersinia hibernica sp. nov., isolated from pig-production environments
A Gram-stain-negative, rod-shaped strain isolated from pig-production environments was identified as a new species within the genus Yersinia using multifaceted genomic and biochemical approaches. The genome of this strain was closed using a hybrid assembly approach combining both high accuracy short read sequencing data with long read sequencing technology. Phylogenetic analysis of the 16S rRNA gene showed ~98 % similarity to Yersinia kristensenii and ~98 % similarity to Yersinia enterocolitica . Average nucleotide identity (OrthoANI) values were calculated as 85.79 % to Y. kristensenii ATCC 33638T and 85.73 % to Y. enterocolitica ATCC 9610T thereby providing evidence that this isolate should be considered as a novel species. The type strain is CFS1934T (=NCTC 14222T=LMG 31076T).
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Pelagibaculum spongiae gen. nov., sp. nov., isolated from a marine sponge in South-West Iceland
More LessA Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, designated Hp12T, was isolated from a marine sponge in the intertidal zone off the coast of Seltjarnarnes (64° 16′ N 22° 00′ W), Iceland. Strain Hp12T grew optimally at 20–22 °C, at pH 7–8 and in the presence of 1–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Hp12T in the class Gammaproteobacteria , related to members of the genus Alcanivorax in the order Oceanospirillales with 90.3–88.5 % sequence similarity. The strain had a draft genome size of 4.99 Mbp with a DNA G+C content of 43.0 mol%. Cellular fatty acids were dominated by C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The major respiratory lipoquinones were ubiquinone Q8 and menaquinone MK8. From the taxonomic information and phenotypic properties obtained in this study, it is proposed that strain Hp12T be placed into a novel genus and species named Pelagibaculum spongiae gen. nov., sp. nov. The type strain of Pelagibaculum spongiae is Hp12T (=DSM 104963T=CECT 9367T).
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Massilia atriviolacea sp. nov., a dark purple-pigmented bacterium isolated from soil
More LessA bacterial strain, designated SODT, with Gram-stain-negative and motile rod-shaped cells, was isolated from soil in Hefei, PR China, and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SODT belonged to the genus Massilia and showed the highest similarities to Massilia violaceinigra B2T (99.3 %), followed by Massilia glaciei B448-2T (98.7 %), Massilia eurypsychrophila CGMCC 1.12828T (98.6 %) and Rugamonas rubra CCM3730T (97.8 %). Average nucleotide identity and digital DNA–DNA hybridization values between genome sequences of strain SODT and the closely related species ranged from 77.1 to 89.3% and from 22.2 to 34.7 %. The DNA G+C content of strain SODT was 65.4 mol%. Strain SODT contained Q-8 as the major ubiquinone and the dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C15 : 0iso 2-OH; 58.5 %), C16 : 0 (26.8 %) and C18 : 1ω7c (5.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. On the basis of the evidence presented in this study, strain SODT represents a novel species of the genus Massilia , for which the name Massilia atriviolacea sp. nov. is proposed. The type strain is SODT (=KCTC 62720T=LMG 30840T).
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Sphingomonas crocodyli sp. nov., isolated from a crocodile pond
More LessStrain CCP-7T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CCP-7T formed a phylogenetic lineage in the genus Sphingomonas . Strain CCP-7T was most closely related to Sphingomonas starnbergensis 382T and Sphingomonas naphthae DKC-5-1T with 96.2 % 16S rRNA gene sequence similarity. Strain CCP-7T showed 65.5–76.7 % average nucleotide identity and 20.2–22.5 % digital DNA–DNA hybridization identity with the strains of other related Sphingomonas species. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acid of strain CCP-7T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, three uncharacterized sphingoglycolipids, two uncharacterized phospholipids and six uncharacterized lipids. The predominant polyamine was homospermidine. The only isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CCP-7T was 64.5 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-7T should be classified in a novel species of the genus Sphingomonas , for which the name Sphingomonas crocodyli sp. nov. is proposed. The type strain is CCP-7T (=BCRC 81096T=LMG 30311T=KCTC 62190T).
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- Eukaryotic Micro-Organisms
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Mucor chuxiongensis sp. nov., a novel fungal species isolated from rotten wood
More LessThree strains of a novel mucoralean fungus were isolated from samples of decayed wood, which were collected from three locations near the city of Chuxiong, Yunnan province, China. These isolates were identified as a novel species through comparison of sequences in the ITS sequence, the D1/D2 domains of the LSU rRNA gene, and other taxonomic characteristics. The results demonstrated that these isolates represent a novel mucoralean fungus species belonging to the genus Mucor. The ITS sequence of Mucor chuxiongensissp. nov. differed from its closest relative, Mucor guilliermondii CBS 174.27T, by 13.1 % sequence divergence (39 substitutions and 38 gaps), and the D1/D2 sequences of the novel strains differed by 13 nt substitutions and one gap (1.9 %) from the ex-type strain. On potato dextrose agar, malt extract agar and synthetic mucor agar, the isolates grew slowly below 10 °C, rapidly at 25–30 °C, and could not grow well at 35 °C. The holotype strain of Mucor chuxiongensis sp. nov. is NYNU 174111 (CICC 41666T=CBS 143707T).
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Volumes and issues
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Volume 74 (2024)
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