- Volume 71, Issue 7, 2021
Volume 71, Issue 7, 2021
- Validation List
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- Notification List
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- List of Changes in Taxonomic Opinion
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- New Taxa
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- Actinobacteria
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Enorma shizhengliae sp. nov. and Eggerthella guodeyinii sp. nov., two new members of the family Coriobacteriaceae
Four obligatory anaerobic, Gram-stain-positive, non-motile and rod-shaped organisms (HF-1365T, HF-1362, HF-1101T and HF-4214) were isolated from faecal samples of healthy Chinese subjects. Results of 16S rRNA gene sequence analyses showed that these isolates belong to the genera Enorma (strains HF-1365T and HF-1362) and Eggerthella (strains HF-1101T and HF-4214), closest to Enorma massiliensis (both 98.6 %) and Eggerthella sinensis (98.0 and 97.8 %), respectively. The whole genome sequences of strains HF-1365T and HF-1101T were 2.3 and 4.2 Mb in size with 61.7 and 66.2 mol% DNA G+C content, respectively. The average nucleotide identity and digital DNA–DNA hybridization values indicated that strains HF-1365T and HF-1101T represent novel species in the genera Enorma and Eggerthella . Major fatty acid constituents (>10 %) of strains HF-1365T and HF-1362 were C12 : 0 (24.7 and 23.9 %), C14 : 0 (21.9 and 20.6 %) and summed feature 1 (C15 : 1iso H/C13 : 0 3OH; 12.8 and 10.8 %); those of strains HF-1101T and HF-4214 were C18 : 1 ω9c (32.4 and 33.1 %) and C16 : 0 (13.9 and 14.0 %). Strain HF-1365T had phospholipid, glycolipid, lipid and phosphoglycolipid without any known quinones, while strain HF-1101T had diphosphatidylglycerol as the major polar lipid and MK-7 (80.7 %) as the predominant quinone. On the basis of their phylogenetic and phenotypic characteristics, strains HF-1365T and HF-1101T represent two distinct species, respectively, in the genera Enorma and Eggerthella , for which the names Enorma shizhengliae sp. nov. (type strain HF-1365T=CGMCC 1.17435T=GDMCC 1.1705T=JCM 33601T) and Eggerthella guodeyinii sp. nov. (type strain HF-1101T=CGMCC 1.17436T=GDMCC 1.1668T=JCM 33773T) are proposed.
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Streptomyces acididurans sp. nov., isolated from peat swamp forest soil
More LessA novel actinomycete, designated strain KK5PA1T, was isolated from a soil sample collected from Kuan Kreng peat swamp forest, Nakhon Si Thammarat Province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . Strain KK5PA1T was most closely related to Streptomyces bryophytorum NEAU-HZ10T (98.0 %) and Streptomyces guanduensis 701T (97.6 %). The G+C content of the genomic DNA was 72.3 mol%. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain KK5PA1T and those of S. bryophytorum DSM 42138T(25.1 and 79.1 %) and S. guanduensis DSM 41944T(25.1 and 79.7%) were below the thresholds of 70 and 96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain KK5PA1T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, mannose and ribose as whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside, two unidentified aminolipids, five unidentified phospholipids and an unidentified lipid. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and C16 : 0. On the basis of these genotypic and phenotypic data, it is proposed that strain KK5PA1T represents a novel species of the genus Streptomyces , for which the name Streptomyces acididurans sp. nov. is proposed. The type strain is strain KK5PA1T (=TBRC 13094T=NBRC 114802T).
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Nocardioides malaquae sp. nov., a novel actinobacterium isolated from sewage sludge of a fisheries processing factory
More LessA Gram-stain-positive, rod-shaped, strictly aerobic bacterial strain (Y6T) was isolated from a sewage sludge sample collected from a fisheries processing factory in Zhoushan, Zhejiang Province, PR China. The growth range of NaCl concentration was 0–6.0 % (w/v), with an optimum at 3.0 % (w/v). The temperature range for growth was 10–42 °C, with an optimum at 37 °C. The pH range for growth was pH 7.0–10.0, with an optimum at pH 9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y6T belonged to the genus Nocardioides and showed the highest sequence similarity of 97.8 % to Nocardioides jishulii dk3136T. The average nucleotide identity and in silico DNA–DNA hybridization values between strain Y6T and the reference strains were 76.9–81.2 % and 20.6–23.6 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-8(H4) and the predominant cellular fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and C18 : 1 ω9c. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified phospholipids, three unidentified aminolipids and five unidentified lipids. The peptidoglycan was ll-2,6-diaminopimelic acid. On the basis of the phenotypic, genotypic, phylogenetic and chemotaxonomic features, strain Y6T is considered to represent a novel species, for which the name Nocardioides malaquae sp. nov. is proposed. The type strain is Y6T (=KCTC 49504T=MCCC 1K04765T).
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Streptomyces musisoli sp. nov., an actinomycete isolated from soil
An actinobacterium, strain CH5-8T, which formed spiral chains of spore arising from the aerial mycelium, was isolated from rhizosphere soil of Musa spp. The organism exhibited vivid greenish yellow substrate mycelium and easily produced the medium grey aerial spore mass on ISP2 medium. The typical chemotaxonomic properties of members of the genus Streptomyces were observed for strain CH5-8T, e.g. ll-diaminopimelic acid in cell peptidoglycan, MK-9(H8), MK-9(H6), and MK-9(H4) as major menaquinones and anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside were detected in the cells. A combination of morphological and chemotaxonomic data supported the assignment to the genus Streptomyces . The analysis result obtained for the 16S rRNA gene sequence confirmed the taxonomic affiliation at the genus level of this strain. The novel strain CH5-8T showed the highest 16S rRNA gene sequence values to Streptomyces echinatus NBRC 12763T (98.9 %), followed by Streptomyces actinomycinicus RCU-197T (98.9 %). The average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization values between CH5-8T and its closest relatives, S. echinatus CECT 3313T and S. actinomycinicus RCU-197T, were ≤91.6 % and ≤47.4 %, respectively. The digital DNA G+C content of genomic DNA was 72.1 mol%. On the basis of these phenotypic and genotypic data, strain CH5-8T represents a novel species, for which the name Streptomyces musisoli sp. nov. is proposed. The type strain is CH5-8T (=TBRC 9950T=NBRC 113997T).
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Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species
Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.
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Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum
A novel actinomycete, designated NUM-2625T, was isolated as an endophytic bacterium in aerial parts of Comarum salesowianum, an endemic species in the Altai, Himalaya mountain chain area, collected from Khasagt Khairkhan Mountain in Mongolia. The 16S rRNA gene sequence of strain NUM-2625T showed the highest similarity to Actinocatenispora thailandica TT2-10T (99.4 %), Actinocatenispora sera KV-744T (99.3 %), and Actinocatenispora rupis CS5-AC17T (97.7 %). Chemotaxonomic properties of strain NUM-2625T were essentially consistent with those of the genus Actinocatenispora, such as the presence of meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, MK-9(H4) and MK-9(H6) as the major menaquinones, and iso-C16 : 0, iso-C15 : 0, iso-C14 : 0 3-OH, and anteiso-C17 : 0 as the major fatty acids. Meanwhile, digital DNA–DNA hybridization and average nucleotide identity values revealed a low relatedness between strain NUM-2625T and the other type strains of the genus Actinocatenispora . In addition, strain NUM-2625T exhibited several phenotypic properties that could be used to distinguish it from its closest relatives. Based on the results of polyphasic analyses, strain NUM-2625T represents a novel species in the genus Actinocatenispora , for which the name Actinocatenispora comari sp. nov. is proposed. The type strain is NUM-2625T (=NBRC 114660T=TBRC 13496T).
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Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges
More LessTwo novel Rhodococcus strains, LHW50502T and LHW51113T, were isolated from marine sponges obtained on Xisha Island, Hainan Province, PR China. Rods and cocci, typical characteristics of the genus Rhodococcus , were observed. The strains contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall hydrolysates and galactose, arabinose, ribose and glucose as the whole-cell sugars. The major fatty acid identified was C16 : 0. MK-8(H4) was the predominat menaquinone of both strains. Stains LHW50502T and LHW51113T had almost identical (99.6 %) 16S rRNA gene sequences but shared relatively low similarities with previously characterized Rhodococcus species (well below 98.7 %). The results of phylogenetic analysis supported their closest relationship; however, the average nucleotide identity and digital DNA–DNA hybridization values between these two strains indicated that they belonged to distinct species. Taken together, the results of this study indicate that strains LHW50502T and LHW51113T represent two novel species of the genus Rhodococcus , for which the names Rhodococcus spongiicola sp. nov. (type strain LHW50502T=DSM 106291T=CCTCC AA 2018033T) and Rhodococcus xishaensis sp. nov. (type strain LHW51113T=DSM 106204T=CCTCC AA 2018034T) are proposed.
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Euzebya pacifica sp. nov., a novel member of the class Nitriliruptoria
More LessA Gram-stain-positive, aerobic, chemo-organotrophic, rod-shaped, non-spore-forming strain, which produced convex, circular, pink-pigmented colonies, designated as DY32-46T, was isolated from seawater collected from the Pacific Ocean. DY32-46T was found to grow at 20–40 °C (optimum, 30–35 °C), pH 6.0–8.0 (optimum, pH 6.5) and with 0–5 % (w/v) NaCl (optimum, 1–2 %). The results of chemotaxonomic analysis indicated that the respiratory quinone of DY32-46T was MK-9(H4), and major fatty acids (>10 %) were C17 : 1 ω8c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C15 : 1 ω6c. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified glycolipids, three unidentified phospholipids, one unidentified phosphoglycolipid and five unidentified lipids. The DNA G+C content of DY32-46T was 70.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences and genomic data indicated that DY32-46T should be assigned to the genus Euzebya . ANI and in silico DNA–DNA hybridization values between strain DY32-46T and type strains of Euzebya species were 73.1–87.2 % and 20.2–32.4 %, respectively. Different phenotypic properties, together with genetic distinctiveness, demonstrated that strain DY32-46T was clearly distinct from recognized species of the genus Euzebya . Therefore, DY32-46T represents a novel species within the genus Euzebya , for which the name Euzebya pacifica sp. nov is proposed. The type strain is DY32-46T (=MCCC 1K03476T=KCTC 49091T).
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Characterization of isolates of members of the genus Actinomyces from Marmota himalayana: description of Actinomyces faecalis sp. nov., Actinomyces respiraculi sp. nov., and Actinomyces trachealis sp. nov.
Six novel strains (ZJ34T, ZJ561, ZJ750T, ZJ1629, zg-993T and zg-987) isolated from faeces and respiratory tracts of Marmota himalayana from the Qinghai–Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus Actinomyces , and are closely related to Actinomyces urogenitalis DSM 15434T (16S rRNA gene sequences similarities, 94.9–98.7 %), Actinomyces weissii CCUG 61299T (95.6–96.6 %), Actinomyces bovis CCTCC AB2010168T (95.7 %) and Actinomyces bowdenii DSM 15435T (95.2–96.4 %), with values of digital DNA–DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34T/ZJ561, ZJ750T/ZJ1629 and zg-993T/zg-987). All the novel strains had C18 : 1 ω9c and C16 : 0 as the two most abundant major fatty acids. MK-9(H4) or MK-8(H4) was the sole or predominant respiratory quinone of strains ZJ34T, ZJ750T and zg-993T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750T shared identical peptidoglycan amino acid profile with ZJ34T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993T (glucose, rhamnose and ribose). Strain zg-993T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34T was ribose. The DNA G+C contents of the novel strains were within the range of 65.8–70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus Actinomyces , for which the names Actinomyces faecalis sp. nov. [type strain ZJ34T (=GDMCC 1.1952T=JCM 34355T)], Actinomyces respiraculi sp. nov. [type strain ZJ750T (=GDMCC 1.1950T=JCM 34356T)] and Actinomyces trachealis sp. nov. [type strain zg-993T (=GDMCC 1.1956T=JCM 34357T)] were proposed, respectively.
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Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonyms of Rhodococcus erythropolis, and Rhodococcus percolatus and Rhodococcus imtechensis are later synonyms of Rhodococcus opacus
More LessTwo novel actinobacterial strains, designated C9-5T and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod–coccus developmental cycle during growth and grew at 10–30 °C, pH 5–9 and 0–3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5T was loosely associated with Rhodococcus tukisamuensis , albeit sharing low 16S rRNA gene sequence similarity (97.4 %). A combination of morphological and chemotaxonomic characteristics supported assignment with the genus Rhodococcus . With respect to 16S rRNA gene sequence similarity, the novel isolates showed the highest identity to the type strain of Rhodococcus subtropicus (98.7 % sequence similarity), followed by Rhodococcus olei (98.5 %) and Rhodococcus pedocola (98.4 %).The average nucleotide identity and digital DNA–DNA hybridization values between strain C9-5T and members of the genus Rhodococcus were ≤81.5 and ≤37.1 %, respectively. A set of physiological and chemotaxonomic properties together with overall genomic relatedness differentiated the novel isolates from members of the genus Rhodococcus , for which the name Rhodococcus spelaei sp. nov. is proposed. The type strain is C9-5T (=KACC 19822T=DSM 107558T). Based on genome analysis performed here, it is also proposed that Rhodococcus biphenylivorans Su et al. 2015 is a later heterotypic synonym of Rhodococcus pyridinivorans Yoon et al. 2000, Rhodococcus qingshengii Xu et al. 2007 and Rhodococcus baikonurensis Li et al. 2004 are later heterotypic synonyms of Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980), and Rhodococcus percolatus Briglia et al. 1996 and Rhodococcus imtechensis Ghosh et al. 2006 are later heterotypic synonyms of Rhodococcus opacus Klatte et al. 1995.
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Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife
Four mesophilic and Gram-stain-positive strains (zg-686T/zg-691 and HY186T/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus Gordonia according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4–68.3 mol% and low DNA relatedness (19.2–27.6 %) with all available genomes in the genus Gordonia . Strains zg-686T/zg-691 and HY186T/HY189 had C18 : 1ω9c, C18 : 0 10-methyl, C16 : 1 ω7c/C16 : 1ω6c and C16 : 0 as major cellular fatty acids. The polar lipids detected in strains zg-686T and HY186T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H2) (10.8 %) and MK9(H2) (89.2 %) for strain zg-686T, and MK6 (7.7 %), MK8(H2) (8.4 %), MK8(H4) (3.1 %) and MK9(H2) (80.8 %) for strain HY186T. Optimal growth conditions were pH 7.0, 35–37 °C and 0.5–1.5 % NaCl (w/v) for strains pair zg-686T/zg-691, and pH 7.0, 28 °C and 1.5 % (w/v) NaCl for strains pair HY186T/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus Gordonia , for which the names Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov. are proposed. The type strains are zg-686T (=GDMCC 1.1715T =JCM 33890T) and HY186T (=CGMCC 4.7607T =JCM 33466T), respectively.
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Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.
Three novel actinomycete strains, designated as DR6-1T, DR6-2 and DR6-4, isolated from the roots of Dendrobium heterocarpum Lindl in Thailand were studied using a polyphasic taxonomic approach. The strains grew at 20–37 °C, at pH 5–10 and with 5 % (w/v) NaCl. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and MK-9(H4) was a major menaquinone. Arabinose and galactose were the major sugars in the cell wall. The predominant cellular fatty acids were iso-C16 : 0 and iso-C15 : 0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1T, DR6-2 and DR6-4 shared 99.9–100 % 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831T (98.7-98.8%). The approximate genome size of strain DR6-1T was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1T and Amycolatopsis echigonensis JCM21831T, Amycolatopsis rubida JCM 10871T and Amycolatopsis nivea KCTC 39515T were 90.55, 92.25, 92.60%, and 47.20, 52.10 and 52.50%, respectively. Based on the phenotypic, chemotaxonomic and genotypic characteristics, it has been concluded that strains DR6-1T, DR6-2 and DR6-4 represent a novel species of the genus Amycolatopsis for which the name Amycolatopsis dendrobii sp. nov. is proposed. The type strain is DR6-1T (=JCM 33742T=KCTC 49546T=TISTR 2840T).
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Cellulosimicrobium composti sp. nov., a thermophilic bacterium isolated from compost
Lin Hu, Mengli Xia, Xi Gao, Yi-Xin Huo and Yu YangA Gram-stain-positive, yellow-pigmented, non-motile actinobacterial strain, designated as BIT-GX5T, was isolated from a sesame husks compost collected in Beijing, PR China. This bacterium was found to be able to grow in the temperature range from 16 to 50 °C and had an optimal growth temperature at 45 °C. Its taxonomic position was analysed using a polyphasic approach. The 16S rRNA gene sequence (1482 bp) of strain BIT-GX5T was most similar to Cellulosimicrobium funkei ATCC BAA-886T (99.45%), Cellulosimicrobium cellulans LMG 16121T (99.17%) and Cellulosimicrobium marinum RS-7-4T (98.75%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (gyrB, rpoB, recA, atpD and trpB) and genome sequences, placed strain BIT-GX5T in a separate lineage among the genus Cellulosimicrobium within the family Promicromonosporaceae . The major polar lipids of strain BIT-GX5T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The major isoprenoid quinone was MK-9(H4), while the cell-wall sugars were galactose, rhamnose, glucose and mannose. The peptidoglycan type was A4α l-Lys–d-Ser–d-Asp. The major fatty acids were anteiso-C15:0 and iso-C15: 0, which were similar to other members in the genus Cellulosimicrobium. Results of in silico DNA–DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-GX5T from the other members of the genus Cellulosimicrobium . Therefore, strain BIT-GX5T is considered to represent a novel species within the genus Cellulosimicrobium , for which the name Cellulosimicrobium composti sp. nov. is proposed. The type strain is BIT-GX5T (= CGMCC 1.17687T = KCTC 49391T).
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Gulosibacter sediminis sp. nov., isolated from Indian Ocean marine sediment
A novel Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, non-motile, rod-shaped bacterium, designated strain YIM M12148T, was isolated from a marine sediment sample collected from the Indian Ocean. The strain grew optimally at 28 °C, pH 8.0 and in the presence of 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M12148T belongs to the genus Gulosibacter , with the highest sequence similarity to Gulosibacter faecalis NBRC 15706T (96.12 %). The cell-wall sugars of strain YIM M12148T were rhamnose, ribose, glucose and mannose. The predominant isoprenoid quinones were MK-8 and MK-9. The polar lipids consisted of major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown lipid. Major fatty acids (>5 % of the total) of the novel isolate were anteiso-C15 : 0, iso-C15 : 0, iso-C13 : 0 and anteiso-C13 : 0. The genomic DNA G+C content of strain YIM M12148T was 67.15 mol%. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M12148T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter sediminis sp. nov. is proposed. The type strain is YIM M12148T (=KCTC 29660T=DSM 29154T).
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Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai–Tibet Plateau
In the present study, four bacterial strains, two (S-713T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531T and 1598) from leaves of dandelion collected on the Qinghai–Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713T/406 and S-531T/1598 form two independent branches belonging to the genus Nocardioides , and are closest to Nocardioides lianchengensis , Nocardioides dokdonensis , Nocardioides salarius , Nocardioides marinisabuli , Nocardioides psychrotolerans and Nocardioides szechwanensis . Although sharing MK8-(H4) as their major isoprenoid quinone, strains S-713T and S-531T contained C18 : 1 ω9c (24.64 and 16.34 %) and iso-C16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713T and S-531T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides , for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713T (=JCM 33698T=CGMCC 4.7660T) and S-531T (=JCM 33468T=CGMCC 4.7659T) as the respective type strains.
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Actinoplanes lichenicola sp. nov. and Actinoplanes ovalisporus sp. nov., isolated from lichen in Thailand
Two actinobacteria, designated as strain LDG1-01T and LDG1-06T, were isolated from lichen samples collected in Thailand. Results of morphological characterization, chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains were members of the genus Actinoplanes . MK-9(H4) was found as the major menaquinone. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were observed as the polar lipids, but differences in minor unidentified polar lipids were found between the strains. Results of comparative genome analysis based on average nucleotide identity and digital DNA–DNA hybridization calculations revealed that both strains showed values below 95 and 70 %, respectively, from each other and closely related Actinoplanes type strains. Based on data from this polyphasic study, strains LDG1-01T and LDG1-06T represent novel species of the genus Actinoplanes . The names proposed are Actinoplanes lichenicola sp. nov. (type strain, LDG1-01T (=JCM 33066T=TISTR 2982T) and Actinoplanes ovalisporus sp. nov. (type strain, LDG1-06T=JCM 33067T=TISTR 2983T).
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Leucobacter chromiisoli sp. nov., isolated from chromium-containing chemical plant soil
More LessA Gram-stain-positive, rod-shaped, aerobic, non-motile, non-sporulating bacterial strain, designated CSA1T, was isolated from chromium-containing soil sampled at a chemical plant. Growth of strain CSA1T occurred at pH 6–10 (optimum, pH 7), 15–45 °C (optimum, 30 °C) and in the presence of 0.5–6.5 % (w/v) NaCl (optimum, 2 %). The 16S rRNA gene sequence of strain CSA1T revealed the highest similarity to Leucobacter ruminantium A2T (97.5 %), Leucobacter tardus K 70/01T (97.3 %), Leucobacter humi Re6T (96.6 %), Leucobacter kyeonggiensis F3-P9T (96.2 %), Leucobacter zeae CC-MF41T (96.1 %) and Leucobacter weissii S27T (96.0 %). The draft genome of CSA1T was approximately 3 350 931 bp in size with a G+C content of 70.6 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values among strain CSA1T and the selected Leucobacter species were 74.0–79.2 % (ANIb), 84.3–87.1 % (ANIm) and 21.5–25.4 % (dDDH), which are below the recommended cutoff values for species delineation. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The predominant menaquinones were MK-11, MK-8 and MK-6. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. From the phenotypic, chemotaxonomic and molecular features, strain CSA1T was considered to represent a novel species of the genus Leucobacter , for which the name Leucobacter chromiisoli sp. nov. is proposed. The type strain is CSA1T (=JCM 34359T=CGMCC 1.18746T).
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- Archaea
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Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge
A coccoid-shaped, strictly anaerobic, hyperthermophilic and piezophilic organoheterotrophic archaeon, strain Iri35cT, was isolated from a hydrothermal chimney rock sample collected at a depth of 2300 m at the Mid-Atlantic Ridge (Rainbow vent field). Cells of strain Iri35cT grew at NaCl concentrations ranging from 1–5 % (w/v) (optimum 2.0 %), from pH 5.0 to 9.0 (optimum 7.0–7.5), at temperatures between 50 and 90 °C (optimum 75–80 °C) and at pressures from 0.1 to at least 50 MPa (optimum: 10–30 MPa). The novel isolate grew on complex organic substrates, such as yeast extract, tryptone, peptone or beef extract, preferentially in the presence of elemental sulphur or l-cystine; however, these molecules were not necessary for growth. Its genomic DNA G+C content was 54.63 mol%. The genome has been annotated and the metabolic predictions are in accordance with the metabolic characteristics of the strain and of Thermococcales in general. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain Iri35cT belongs to the genus Thermococcus, and is closer to the species T. celericrescens and T. siculi . Average nucleotide identity scores and in silico DNA–DNA hybridization values between the genome of strain Iri35cT and the genomes of the type species of the genus Thermococcus were below the species delineation threshold. Therefore, and considering the phenotypic data presented, strain Iri35cT is suggested to represent a novel species, for which the name Thermococcus camini sp. nov. is proposed, with the type strain Iri35cT (=UBOCC M-2026T=DSM 111003T).
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Thermococcus henrietii sp. nov., a novel extreme thermophilic and piezophilic sulfur-reducing archaeon isolated from a deep-sea hydrothermal chimney
A novel extreme thermophilic and piezophilic chemoorganoheterotrophic archaeon, strain EXT12cT, was isolated from a hydrothermal chimney sample collected at a depth of 2496 m at the East Pacific Rise 9° N. Cells were strictly anaerobic, motile cocci. The strain grew at NaCl concentrations ranging from 1 to 5 % (w/v; optimum, 2.0%), from pH 6.0 to 7.5 (optimum, pH 6.5–7.0), at temperatures between 60 and 95 °C (optimum, 80–85 °C), and at pressures from 0.1 to at least 50 MPa (optimum, 30 MPa). Strain EXT12cT grew chemoorganoheterotrophically on complex proteinaceous substrates. Its growth was highly stimulated by the presence of elemental sulphur or l-cystine, which were reduced to hydrogen sulfide. The DNA G+C content was 54.58 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain EXT12cT falls into the genus Thermococcus and is most closely related to Thermococcus nautili strain 30-1T. Overall genome relatedness index analyses (average nucleotide identity scores and in silico DNA–DNA hybridizations) showed a sufficient genomic distance between the new genome and the ones of the Thermococcus type strains for the delineation of a new species. On the basis of genotypic and phenotypic data, strain EXT12cT is considered to represent a novel species, for which the name Thermococcus henrietii sp. nov. is proposed, with the type strain EXT12cT (=UBOCC M-2417T=DSM 111004T).
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Halobaculum halophilum sp. nov. and Halobaculum salinum sp. nov., isolated from salt lake and saline soil
More LessTwo halophilic archaeal strains, Gai3-2T and NJ-3-1T, were isolated from salt lake and saline soil samples, respectively, collected in PR China. The 16S rRNA gene sequences of the two strains were 97.5% similar to each other. Strains Gai3-2T and NJ-3-1T had the highest sequence similarities to ‘ Halobonum tyrrellense ’ G22 (96.7 and 97.8%, respectively), and displayed similarities of 91.5–93.5% and 92.3–94.7%, respectively, to Halobaculum members. Phylogenetic analysis revealed that the two strains formed different branches and clustered tightly with ‘ H. tyrrellense ’ G22 and Halobaculum members. The average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and amino acid identity (AAI) values between the two strains were 83.1, 26.9 and 77.9%, respectively, much lower than the threshold values proposed as a species boundary. These values between the two strains and ‘ H. tyrrellense ’ G22 (ANI 77.9–78.2%, isDDH 22.5–22.6% and AAI 68.8–69.3%) and Halobaculum members (ANI 77.53–77.63%, isDDH 21.8–22.3% and AAI 68.4–69.4%) were almost identical, and much lower than the recommended threshold values for species delimitation. These results suggested that strains Gai3-2T and NJ-3-1T represent two novel species of Halobaculum . Based on phenotypic, chemotaxonomic and phylogenetic properties, strains Gai3-2T (=CGMCC 1.16080T=JCM 33550T) and NJ-3-1T (=CGMCC 1.16040T=JCM 33552T) represent two novel species of the genus Halobaculum , for which the name Halobaculum halophilum sp. nov. and Halobaculum salinum sp. nov. are proposed.
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- Bacteroidetes
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Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola
More LessA novel Gram-stain-negative, aerobic, asporogenous, catalase-positive and oxidase-negative, non-motile, golden-yellow pigmented, rod-shaped bacterium with casein-degrading ability, designated strain GCR10T, was isolated from roots of rice plants collected from a paddy field near Dongguk University, Republic of Korea. The results of subsequent 16S rRNA gene sequence analysis indicated that GCR10T shares the highest sequence identity with Chryseobacterium piscicola VQ-6316sT (98.3%). Strain GCR10T grew at 2–32 °C (optimum, 25 °C), at pH 6.0–8.0 (optimum, pH 7.0) and in the presence of 0–2.0% (w/v) NaCl (optimum in the absence of NaCl). The novel strain was able to produce carotenoid and flexirubin-type pigments. The predominant menaquinone was MK-6 and the major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The polar lipids were phosphatidylethanolamine, four unidentified aminoglycolipids, two unidentified aminolipids and two unidentified glycolipids. The genome of GCR10T is 4.3 Mb in length with a DNA G+C content of 36.5 mol%. Average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between GCR10T and Chryseobacterium piscicola VQ-6316sT were 82.1, 25.2 and 84.3 %, respectively, which clearly indicates that the novel strain is distinct from its closest relative. The demand for natural biodegradable pigments isolated frominsects, plants or microorganisms is increasing day by day because of their beneficial pharmacological properties. Here, we describe a novel strain that produces two types of pigment, carotenoid and flexirubin. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain GCR10T represents a novel species of the genus Chryseobacterium , and the name Chryseobacterium caseinilyticum sp. nov. is proposed. The type strain is GCR10T (=KACC 21707T=NBRC 114715T).
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Chitinophaga silvatica sp. nov., isolated from forest soil, and reclassification of Chitinophaga extrema as a later heterotypic synonym of Chitinophaga solisilvae
More LessA novel bacterial strain, designated K2CV101002-2T, was isolated from forest soil collected at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that it belonged to the genus Chitinophaga and was most closely related to Chitinophaga terrae KP01T (99.0 %), followed by Chitinophaga extrema Mgbs1T (98.3 %) and Chitinophaga solisilvae O9T (98.1 %). The draft genome sequence was 6.8 Mb long with a relative low G+C content of 39.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the novel strain and closely related type strains were 71.4‒76.2 % and 18.4‒19.6 %, respectively. Meanwhile the corresponding values between C. extrema Mgbs1T and C. solisilvae O9T were 98.6 and 88.1 %, respectively. The novel strain contained iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH as the major fatty acids and MK-7 as the predominant respiratory quinone. The polyphasic study clearly supported that strain K2CV101002-2T represents a new species of the genus Chitinophaga , for which the name Chtinophaga silvatica sp. nov. (type strain K2CV101002-2T=GDMCC 1.1288T=JCM 32696T) is proposed. In addition, Chitinophaga extrema Goh et al. 2020 should be taken as a later heterotypic synonym of Chitinophaga solisilvae Ping et al. 2020.
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Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov.
More LessA strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain R1DC9T, was isolated from sediments of a mangrove stand on the Red Sea coast of Saudi Arabia via diffusion chamber cultivation. Strain R1DC9T grew at 20–40 °C (optimum, 37 °C), pH 6–10 (optimum, pH 8) and 3–11 % NaCl (optimum, 7–9 %) in the cultivation medium. The genome of R1DC9T was 4 661 901 bp long and featured a G+C content of 63.1 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis using 120 concatenated single-copy genes revealed that R1DC9T represents a distinct lineage in the order Cytophagales and the phylum Bacteroidetes separated from the Roseivirgaceae and Marivirgaceae families. R1DC9T displayed 90 and 89 % 16S rRNA gene sequence identities with Marivirga sericea DSM 4125T and Roseivirga ehrenbergii KMM 6017T, respectively. The predominant quinone was MK7. The polar lipids were phosphatidylethanolamine, two unknown phospholipids and two unknown lipids. The predominant cellular fatty acids were the saturated branch chain fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 0, along with a low percentage of the monounsaturated fatty acid C16 : 1 ω5c. Based on differences in phenotypic, physiological and biochemical characteristics from known relatives, and the results of phylogenetic analyses, R1DC9T (=KCTC 72349T=JCM 33609T=NCCB 100698T) is proposed to represent a novel species in a new genus, and the name Mangrovivirga cuniculi gen. nov., sp. nov. is proposed. The distinct phylogenetic lineage among the families in the order Cytophagales indicates that R1DC9T represents a new family for which the name Mangrovivirgaceae fam. nov. is proposed.
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Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil
More LessTwo Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27T and SE-s28T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25–30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28T produced flexirubin-type pigments, but strain SE-s27T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27T contained iso-C15 : 1 and iso-C15 : 1G, whereas SE-s28T contained iso-C15 : 0 and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH. The DNA G+C contents of strains SE-s27T and SE-s28T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27T and SE-s28T formed respective distinct phylogenetic lineages within the genus Flavobacterium . Strains SE-s27T and SE-s28T were most closely related to Flavobacterium macrobrachii an-8T and Flavobacterium piscinae ICH-30T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27T and SE-s28T represent novel species of the genus Flavobacterium , for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27T (=KACC 18802T=JCM 31544T) and SE-s28T (=KACC 18803T=JCM 31545T), respectively.
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Flavobacterium franklandianum sp. nov. and Flavobacterium gawalongense sp. nov., isolated from glaciers on the Tibetan Plateau
More LessThe genus Flavobacterium (family Flavobacteriaceae ) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium . None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium . Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95–96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).
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Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree
More LessA Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20–37 °C, at pH 5.0–8.5 and at 0–2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2–83.2 % and 22.1–27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA–DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus Niastella , for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.
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Muriicola soli sp. nov., isolated from soil
More LessA Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).
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Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout
More LessTwo yellow-pigmented isolates, F-60T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium . Digital DNA–DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium . The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623T while those values for F. crassostreae LPB0076T were obtained as 21.4–21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60T as the type strain (=JCM 34196T=KCTC 82256T).
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Chryseobacterium pennae sp. nov., isolated from poultry feather waste
A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178T. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jejuense (99.1%) and Chryseobacterium nakagawai (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity) revealed greatest similarity to the C. jejuense and C. nakagawai type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178T were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178T had a typical fatty acid composition for Chryseobacterium species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178T constitutes a novel species of Chryseobacterium , for which the name Chryseobacterium pennae sp. nov. is proposed. The type strain is 1_F178T (=LMG 30779T=KCTC 62759T).
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Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond
More LessTwo Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.
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Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila
An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27T (98.0 %) and Pedobacter agri PB92T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12T were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12T is proposed to represent a novel species of the genus Pedobacter , for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12T (=KCTC 82363T=NBRC 114901T).
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Dyadobacter subterraneus sp. nov., isolated from hydrocarbon-polluted groundwater from an oil refinery in Hungary
A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterial strain (UP-52T) was isolated from hydrocarbon-polluted groundwater located near an oil refinery in Tiszaujvaros, Hungary. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Dyadobacter in the family Cytophagaceae . Its closely related species are Dyadobacter frigoris (98.00 %), Dyadobacter koreensis (97.64 %), Dyadobacter psychrophilus (97.57 %), Dyadobacter ginsengisoli (97.56 %) and Dyadobacter psychrotolerans (97.20 %). The predominant fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω7c/C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and C17 : 0 iso 3OH. The predominant respiratory quinone detected in strain UP-52T is quinone MK-7. The dominant polar lipids are glycolipid, phosphoaminolipid, phospholipid and aminolipid. The DNA G+C content is 40.0 mol%. Flexirubin-type pigment was present. Based on these phenotypic, chemotaxonomic and phylogenetic results, UP-52T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter subterraneus sp. nov. is proposed. The type strain is UP-52T (=NCAIM B.02653T=CCM 9030T).
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Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea
More LessA novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1MT, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1MT was closely related to Mariniflexile gromovii KMM 6038T (95.3 %), Mariniflexile fucanivorans SW5T (95.2 %), Mariniflexile soesokkakense RSSK-9T (95.1 %), Yeosuana aromativorans GW1-1T (94.6 %) and Confluentibacter lentus HJM-3T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1MT formed a distinct cluster with the type strains of the genus Mariniflexile . The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C15:0, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, iso-C16:03-OH and iso-C17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1MT was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1MT is considered to represent a novel species within the genus Mariniflexile , for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1MT (=KCTC 72895T=JCM 33982T).
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Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces
More LessTwo Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1 ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).
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- Firmicutes and Related Organisms
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Facklamia lactis sp. nov., isolated from raw milk
More LessTwo strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842T (96.9 %), and Facklamia hominis CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10–40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l−1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.
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Sulfobacillus harzensis sp. nov., an acidophilic bacterium inhabiting mine tailings from a polymetallic mine
More LessA mixotrophic and acidophilic bacterial strain BGR 140T was isolated from mine tailings in the Harz Mountains near Goslar, Germany. Cells of BGR 140T were Gram-stain-positive, endospore-forming, motile and rod-shaped. BGR 140T grew aerobically at 25–55 °C (optimum 45 °C) and at pH 1.5–5.0 (optimum pH 3.0). The results of analysis of the 16S rRNA gene sequences indicated that BGR 140T was phylogenetically related to different members of the genus Sulfobacillus , and the sequence identities to Sulfobacillus acidophilus DSM 10332T, Sulfobacillus thermotolerans DSM 17362T, and Sulfobacillus benefaciens DSM 19468T were 94.8, 91.8 and 91.6 %, respectively. Its cell wall peptidoglycan is A1γ, composed of meso-diaminopimelic acid. The respiratory quinone is DMK-6. The major polar lipids were determined to be glycolipid, phospholipid and phosphatidylglycerol. The predominant fatty acid is 11-cycloheptanoyl-undecanoate. The genomic DNA G+C content is 58.2 mol%. On the basis of the results of phenotypic and genomic analyses, it is concluded that strain BGR 140T represents a novel species of the genus Sulfobacillus , for which the name Sulfobacillus harzensis sp. nov. is proposed because of its origin. Its type strain is BGR 140T (=DSM 109850T=JCM 39070T).
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Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage
A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0–3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0–7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes , class Clostridia , family Peptococcaceae , genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus , for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В−3021T).
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Paraliobacillus salinarum sp. nov., isolated from saline soil in Yingkou, China
More LessA novel Gram-stain-positive, facultatively aerobic, slightly halophilic, endospore-forming bacterium, designated G6-18T, was isolated from saline soil collected in Yingkou, Liaoning, PR China. Cells of strain G6-18T grew at 10–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 8.0) and in the presence of 2–15 % (w/v) NaCl (optimum, 5 %). The strain could be clearly distinguished from the related species of the genus Paraliobacillus by its phylogenetic position and biochemical characteristics. It presented MK-7 as the major quinone and the dominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 0 and iso-C14 : 0. The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol as the major components. The G+C content of strain G6-18T genome was 35.3 mol%. 16S rRNA analysis showed that strain G6-18T had the highest similarity to Paraliobacillus ryukyuensis DSM 15140T, reaching 97.0 %, followed by Paraliobacillus quinghaiensis CGMCC 1.6333T with a value of 96.3 %. The average nucleotide identity values between strain G6-18T and Paraliobacillus ryukyuensis DSM 15140T, Paraliobacillus sedimins KCTC 33762T, Paraliobacillus quinghaiensis CGMCC 1.6333T and Paraliobacillus zengyii DSM 107811T were 74.3, 72.0, 73.2 and 72.8 %, respectively, and the digital DNA–DNA hybridization values between strain G6-18T and the neighbouring strains were 15.6, 13.8, 14.2 and 14.2 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G6-18T represents a novel species of the genus Paraliobacillus , for which the name Paraliobacillus salinarum sp. nov. (=CGMCC 1.12058T=DSM 25428T) is proposed.
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Staphylococcus caledonicus sp. nov. and Staphylococcus canis sp. nov. isolated from healthy domestic dogs
More LessTwo strains, H8/1T and H16/1AT, of Gram-stain-positive, coagulase-negative staphylococci were isolated from separate healthy domestic dogs in Scotland. Both strains were genome sequenced and their inferred DNA–DNA hybridisation indicates that H8/1T and H16/1AT represent two novel species of the genus Staphylococcus . On the basis of the results of genome sequence analysis (genome blast distance phylogeny and single nucleotide polymorphism analysis) H8/1T is most closely related to Staphylococcus devriesei and H16/1AT most closely related to Staphylococcus felis . Also, average nucleotide identity distinguished H8/1T and H16/1AT from S. devriesei and S. felis as did minor phenotypic differences. On the basis of these results, it is proposed that H8/1T and H16/1AT represent novel species with the respective names Staphylococcus caledonicus and Staphylococcus canis. The type strain of S. caledonicus is H8/1T (=NCTC 14452T=CCUG 74789T). The type strain of S. canis is H16/1AT (=NCTC 14451T=CCUG 74790T)
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Lactobacillus corticis sp. nov., isolated from hardwood bark
During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40T from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40T, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30–50 °C, at pH 3.5–7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C16:0, C18:1 ω9c and summed feature 8. The genomic DNA G+C content of strain B40T is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40T belongs to the genus Lactobacillus and the closest neighbours of strain B40T are Lactobacillus gigeriorum 202T (95.7 %), Lactobacillus pasteurii CRBIP 24.76T (95.6 %), Lactobacillus psittaci DSM 15354T (95.4 %), Lactobacillus fornicalis TV1018T (95.4 %) and Lactobacillus jensenii ATCC 25258T (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus Lactobacillus but could not be assigned to any known species. Strain B40T has an average nucleotide identify of <70.2 % and a digital DNA–DNA hybridization value of 19.2 % compared with the strains of other closely related Lactobacillus species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus corticis sp. nov. is proposed. The strain type is B40T (=JCM 32597T=DSM 107967T).
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Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., isolated from traditional Chinese pickle and the gut of honeybee (Apis mellifera)
More LessThirteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that 12 of the 13 strains represented eight novel species belonging to the genera Apilactobacillus , Secundilactobacillus , Levilactobacillus and Lacticaseibacillus ; strains HN36-1T, 887-11T, F79-211-2T, 866-3T, 6-5(1)T, 13B17T, 117-1T and ZW152T were designated as the type strains. Based upon the data of polyphasic characterization obtained in the present study, eight novel species, Apilactobacillus nanyangensis sp. nov., Secundilactobacillus hailunensis sp. nov., Secundilactobacillus yichangensis sp. nov., Levilactobacillus andaensis sp. nov., Levilactobacillus wangkuiensis sp. nov., Levilactobacillus lanxiensis sp. nov., Lacticaseibacillus mingshuiensis sp. nov. and Lacticaseibacillus suilingensis sp. nov., are proposed and the type strains are HN36-1T (=JCM 33867T=CCTCC AB 2019385T), 887-11T (=NCIMB 15201T=CCM 8950T=JCM 33864T=CCTCC AB 2018396T), F79-211-2T (=NCIMB 15254T=JCM 33866T=CCTCC AB 2019384T), 866-3T (=JCM 33863T=CCTCC AB 2019383T), 6-5(1)T (=NCIMB 15229T=CCM 8977T=JCM 33564T=CCTCC AB 2019168T), 13B17T (=NCIMB 15230T=CCM 8979T=JCM 33565T=CCTCC AB 2019167T), 117-1T (=NCIMB 15232T=CCM 8980T=JCM 33567T) and ZW152T (=JCM 34363T=CCTCC AB 2020299T=LMG 32143T=CCM 9110T), respectively.
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- Other Bacteria
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Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria
The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter , with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinct clade within the order Ktedonobacterales , showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040T=CGMCC 1.17052T=BCRC 81202T) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales ; strain SOSP1-1T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1T=CGMCC 1.17205T=BCRC 81203T) and strain SOSP1-30T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30T=CGMCC 1.17733T=BCRC 81205T) within the family Ktedonobacteraceae ; strain Uno17T as Dictyobacter arantiisoli sp. nov. (type strain Uno17T=NBRC 113155T=BCRC 81116T); and strain SOSP1-9T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9T=CGMCC 1.17206T=BCRC 81204T) within the family Dictyobacteraceae .
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Thermosipho ferrireducens sp.nov., an anaerobic thermophilic iron(III)-reducing bacterium isolated from a deep-sea hydrothermal sulfide deposits
More LessA thermophilic, anaerobic, iron-reducing bacterium strain JL129W03T (=KCTC 15905T=MCCC 1A14213T) was isolated from a sulfide sample collected from the Daxi hydrothermal field (60.5° E, 6.4° N, 2919 m depth) on the Carlsberg Ridge, northwest Indian Ocean. Cells grew at 55–75 °C(optimum, 70 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and at NaCl concentrations of 1.5–4.5 % (w/v; optimum 3.0 %). Under optimal growth conditions, the generation time was around 85 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, carbohydrates, organic acids and one amino acid. It was anaerobic and facultatively dependent on elemental sulphur and various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulphate, thiosulfate or nitrate. The G+C content of its genomic DNA was 34.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that its closest relative was Thermosipho atlanticus DV1140T with 95.81 % 16S rRNA sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Thermosipho , for which the name Thermosipho ferrireducens sp. nov. is proposed. The type strain is strain JL129W03T (=KCTC 15905T;=MCCC 1A14213T).
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- Proteobacteria
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Aureimonas mangrovi sp. nov., a marine alphaproteobacterium isolated from mangrove sediment in Thailand
Two bacterial strains, designated as 1-4-3T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4–37 °C, pH 7.0–9.0, and 0–7% NaCl. The predominant fatty acids of the novel strains were C18 : 1 ω7c, C19 : 0 cyclo ω8c, C18 : 0, and C16 : 0. A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas , with closest sequence similarity to A. populi 4M3-2T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3T was 66.80 mol%. Strain 1-4-3T displayed low DNA–DNA relatedness to A. populi 4M3-2T, with an average nucleotide identity value of 77.47 % and digital DNA–DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3T and 1-4-4 represent a novel species of the genus Aureimonas , for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3T (=LMG 31693T=CGMCC 1.18507T).
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Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust
Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6T and T18T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6T and T18T showed similarities with Belnapia rosea CGMCC 1.10758T and Belnapia moabensis CP2CT (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6T and T18T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia . The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C18 : 1 2-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to he results of the polyphasic study, strains T6T and T18T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6T = CECT 30228T=DSM 112073T) and Belnapia arida sp. nov. (type strain T18T=CECT 30229T=DSM 112074T) are proposed, respectively.
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Niveibacterium microcysteis sp. nov., isolated from a cyanobacterial bloom sample
More LessA novel bacterial strain, named HC41T, was isolated from a cyanobacterial bloom sample and was characterized as Gram-stain-negative, rod-shaped and non-motile. According to 16S rRNA phylogenetic analyses, this strain HC41T belongs to the family Rhodocyclaceae and is most closely related to Niveibacterium umoris KACC 17062T (=MIC 2059T; 98.63 %) and Uliginosibacterium gangwonense 5YN10-9 T (=KACC 11603T; 93.64 %). The genome size and DNA G+C content of strain HC41T were 4.8 Mbp and 64.17 mol%, respectively. Moreover, the average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values between strain HC41T and N. umoris KACC 17062T were 81.8, 43.1 and 90.89 %, respectively. Additionally, strain HC41T exhibited weak catalase and oxidase activities and had no motility (swimming and swarming motilities). The cells grew at 11–40 °C (optimum, 30 °C), pH 5.5–8.0 (optimum, pH 7) and with 0–1.0 % (w/v) NaCl (optimum, 0 % NaCl) in Reasoner’s 2A medium. Its major respiratory quinone was ubiquinone-8 and its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Furthermore, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; C16 : 1 ω6c and/or C16 : 1 ω7c) were the predominant cellular fatty acids in strain HC41T according to fatty acid methyl ester analysis. Based on its genotypic and phenotypic characteristics, strain HC41T was identified as representing a novel Niveibacterium species, for which the name Niveibacterium microcysteis sp. nov. is proposed (=KACC 22091T=DSM 111425T).
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Mesorhizobium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa
More LessStrain MaA-C15T, a Gram-stain-negative, non-spore-forming and strictly aerobic bacterium, was isolated from a xenic culture of Microcystis aeruginosa in the Republic of Korea. Cells were motile rods showing positive reactions in catalase and oxidase tests. Growth was observed between 15 and 37 °C (optimum, 30 °C), between pH 6.0 and pH 11.0 (optimum, pH 7.5) and in the presence of 0–2.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-C15T contained C16 : 0, 11-methyl-C18 : 1 ω7c, cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) as the major cellular fatty acids and ubiquinone-10 as the sole respiratory quinone. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids were detected as the major polar lipids. The G+C content of the genomic DNA was 64.1 mol%. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences revealed that strain MaA-C15T formed a phyletic lineage with Mesorhizobium sediminum YIM M12096T within the family Phyllobacteriaceae . Strain MaA-C15T was most closely related to Mesorhizobium albiziae DSM 21822T with a 98.2 % 16S rRNA sequence similarity. Average nucleotide identity and in silico DNA–DNA hybridization values between strain MaA-C15T and M. albiziae DSM 21822T were 75.4 and 20.1 %, respectively. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain MaA-C15T represents a novel species of the genus Mesorhizobium , for which the name Mesorhizobium microcysteis sp. nov. is proposed. The type strain is MaA-C15T (=KACC 21226T=JCM 33503T).
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Volumes and issues
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Volume 74 (2024)
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