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  • Microbiology Society  (12)
  • 1
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    Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov., two novel species isolated from forest soil
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 10 ( 2021-10-22)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 10 ( 2021-10-22)
    Abstract: Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178 T , RXD172-2 and RLT1W51 T , were isolated from two forest soil samples of Nanling National Nature Reserve in Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that they belonged to the genus Collimonas , and were most closely related to four validly published species with similarities ranging from 99.4 to 98.2 %. The genomic DNA G+C contents of strains RXD178 T , RXD172-2 and RLT1W51 T were 57.1, 59.5 and 59.4 mol%, respectively. The genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel strains and closely related type species were below 37.90 and 89.34 %, respectively. Meanwhile, the ANI and dDDH values between strains RXD172-2 and RLT1W51 T were 98.27 and 83.50 %, respectively. The three novel strains contained C 16 : 0 , C 17 : 0 cyclo and summed feature 3 (C 16 : 1 ω 6 c and/or C 16 : 1 ω 7 c ) as the major fatty acids, and summed feature 8 (C 18 : 1 ω 6 c and/or C 18 : 1 ω 7 c ) comprised a relative higher proportion in strain RXD178 T than in other strains. Both strains RXD172-2 and RLT1W51 T had phosphatidylglycerol (PG), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG) and an unidentified aminophospholipid (APL) as the main polar lipids while only PE and APL were detected in strain RXD178 T . Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178 T should be considered as representing one novel species within the genus Collimonas and strains RXD172-2 and RLT1W51 T as another one, for which the names Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov. are proposed, with RXD178 T (=GDMCC 1.1925 T =KACC 21987 T ) and RLT1W51 T (=GDMCC 1.1923 T =KACC 21985 T ) as the type strains, respectively.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005061
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
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  • 2
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    Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov.
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 10 ( 2022-10-07)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 10 ( 2022-10-07)
    Abstract: A lemon-chiffon strain, designated QH1ED-6-2 T , was isolated from a soil sample collected from Qinghai Virgin Forests, Qinghai Province, PR China. The strain was Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain QH1ED-6-2 T belongs to the family Fulvivirgaceae , and has the highest similarity values of 93.6–92.0 % to Ohtaekwangia koreensis CCUG 58939 T , Ohtaekwangia kribbensis CCUG 58938 T , Chryseolinea flava SDU1-6 T and Chryseolinea serpens DSM 24574 T , respectively. The major cellular fatty acids included iso-C 15 : 0 , C 16 : 1  ω 5 c , iso-C 17 : 0 3-OH and summed feature 3. The major polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone-7. The average amino acid identity values and percentages of conserved proteins between QH1ED-6-2 T and its closely related genera were 66.4–69.6 % and 58.9–64.9 %, respectively, which are interspersed in the intra-genera cutoff values. The digital DNA–DNA hybridization values were 17.6–19.2 %. The draft genome size of strain QH1ED-6-2 T was 7.98 Mbp with a DNA G+C content of 51.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic data, genomic DNA G+C content, as well as AAI, POCP and dDDH results, strain QH1ED-6-2 T represents a novel species of a new genus in the family Fulvivirgaceae , for which the name Parachryseolinea silvisoli sp. nov. is proposed. The type strain is QH1ED-6-2 T (=GDMCC 1.2318 T =JCM 35041 T ). We also propose the reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov. (type strain SDU1-6 T =CGMCC 1.13492 T =JCM 32520 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005523
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
    detail.hit.zdb_id: 215062-1
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  • 3
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    Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil
    Microbiology Society ; 2023
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 73, No. 5 ( 2023-05-31)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 5 ( 2023-05-31)
    Abstract: Two aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20 T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20 T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39 T , Sphingomonas mucosissima DSM 17494 T and Sphingomonas dokdonensis DSM 21029 T . The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains MMSM20 T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20 T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C 14 : 0 2OH, summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20 T and MMSM24 represent a novel species of the genus Sphingomonas , for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20 T (=GDMCC 1.3401 T =JCM 35647 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005920
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
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  • 4
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    Deminuibacter soli gen. nov., sp. nov., isolated from forest soil, and reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov.
    Microbiology Society ; 2019
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 69, No. 6 ( 2019-06-01), p. 1650-1655
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 69, No. 6 ( 2019-06-01), p. 1650-1655
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.003374
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2019
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  • 5
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    Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 8 ( 2022-08-25)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 8 ( 2022-08-25)
    Abstract: Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7 T , RRHST34 T and RHCKR47 T , were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus Sphingomonas , among which both strains RHCKR7 T and RRHST34 T showed a close relationship with Sphingomonas yunnanensis YIM 003 T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47 T was most closely related to Sphingomonas palmae KACC 17591 T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7 T and RRHST34 T were 90.43 and 40.80 %, respectively, and their most closely related type strain, S. yunnanensis YIM 003 T , showed 90.43 % ANI and 40.7 % dDDH with RHCKR7 T and 90.21 % and 42.9 % with RRHST34 T , respectively, and the corresponding values between strain RHCKR47 T and S. palmae KACC 17591 T were 85.53 % and 29.30%, respectively. They all took C 14 : 0 2-OH and summed feature 8 (C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c ) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym -Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus Sphingomonas , for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7 T (=GDMCC 1.2663 T =JCM 34794 T ), RRHST34 T (=GDMCC 1.2665 T =JCM 34796 T ) and RHCKR47 T (=GDMCC 1.2664 T =JCM 34795 T ) as the type strains, respectively.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005492
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
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  • 6
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    Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water
    Microbiology Society ; 2021
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 71, No. 11 ( 2021-11-15)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 11 ( 2021-11-15)
    Abstract: Two novel bacterial strains, designated as DN00404 T and DN04309 T , were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404 T and DN04309 T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404 T were short rod-shaped and those of DN04309 T were long rod-shaped. Strain DN00404 T was found to grow at 15–37 °C (optimum, 25–30 °C), at pH 6.0–11.0 (optimum, pH 7.5) and in 0–2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309 T was found to grow at 15–45 °C (optimum, 20–37 °C), at pH 5.5–11.0 (optimum, 7.5) and in 0–4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus Sphingobacterium and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0–96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404 T and DN04309 T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C 15 : 0 and summed feature 3 (C 16 : 1  ω 6 c and/or C 16 : 1  ω 7 c ), which were similar to those of other species of this genus. The two major fatty acids C 16 : 0 and iso-C 17 : 0 3-OH were also found in strain DN00404 T . Based on genotypic and phenotypic characteristics, two novel species of the genus Sphingobacterium are proposed: Sphingobacterium micropteri sp. nov. with DN00404 T (=GDMCC 1.1865 T =KACC 21924 T ) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309 T (=GDMCC 1.1984 T =KCTC 82348 T ) as the type strain.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005091
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2021
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  • 7
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    Erwinia phyllosphaerae sp. nov., a novel bacterium isolated from phyllosphere of pomelo (Citrus maxima)
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 4 ( 2022-04-13)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 4 ( 2022-04-13)
    Abstract: A novel phosphate-solubilizing and 3-indoleacetic acid producing bacterium, designated strain CMYE1 T , was isolated from the phyllosphere of pomelo ( Citrus maxima ) in Meizhou, Guangdong Province, PR China. Cells were Gram-stain-negative, facultative aerobic, non-spore-forming, rod-shaped and motile with peritrichous flagella. It had the highest 16S rRNA gene sequence similarity to Kalamiella piersonii NRRL B-65522 T (99.0 %), followed by Pantoea cypripedii LMG 2657 T (98.1 %), Erwinia iniecta B120 T (97.7 %), Mixta intestinalis 29Y89B T (97.6 %) and other species ( 〈 97.6 %). However, phylogenomic analyses clearly showed that strain CMYE1 T should be assigned into the genus Erwinia , and was most closely related to Erwinia oleae LMG 25322 T (96.7 %). Genome comparisons showed that the novel strain shared ≤83.2 % average nucleotide identity and ≤26.5 % digital DNA–DNA hybridization values with closely related strains, respectively. It contained C 16 : 0 , C 17 : 0 cyclo, summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ) and summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ) as the major fatty acids. Based on the results of phylogenetic, phenotypic and chemotaxonomic analyses, as well as genome comparisons, strain CMYE1 T belongs to a novel species of the genus Erwinia , for which the name Erwinia phyllosphaerae sp. nov. is proposed with the type strain CMYE1 T (=GDMCC 1.2674 T =JCM 34792 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005316
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
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  • 8
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    Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil
    Microbiology Society ; 2023
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 73, No. 5 ( 2023-05-15)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 5 ( 2023-05-15)
    Abstract: Four novel bacterial strains, designated RBB1W86 T , RXD159 T , RBB189 T and RLT163 T , were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella , among which strains RBB1W86 T and RXD159 T were closely related to Dyella halodurans CGMCC 1.15435 T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189 T and RLT163 T were closely related to Dyella tabacisoli CGMCC 1.16273 T (98.8 %) and Dyella japonica JCM 21530 T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86 T , RBB189 T and RLT163 T , while strain RXD159 T showed a closer relationship with D. tabacisoli CGMCC 1.16273 T and strain RBB189 T . The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA–DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C 15 : 0 and summed feature 9 (10-methyl C 16  : 0 and/or iso-C 17  : 1 ω 9 c ) as the major fatty acids. Moreover, C 16 : 0 , iso-C 16 : 0 , iso-C 17 : 0 and summed feature 3 (C 16 : 1 ω 7 c and/or C 16 : 1 ω 6 c ) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189 T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella , for which the names Dyella humicola sp. nov. (type strain RBB1W86 T =GDMCC 1.1901 T =KACC 21988 T ), Dyella subtropica sp. nov. (type strain RXD159 T =GDMCC 1.1902 T =KACC 21989 T ), Dyella silvatica sp. nov. (type strain RBB189 T =GDMCC 1.1900 T =KACC 21990 T ) and Dyella silvae sp. nov. (type strain RLT163 T =GDMCC 1.1916 T =KACC 21991 T ) are proposed.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005878
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
    detail.hit.zdb_id: 215062-1
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  • 9
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    Chryseobacterium vietnamense sp. nov., isolated from forest soil
    Microbiology Society ; 2012
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 62, No. Pt_4 ( 2012-04-01), p. 827-831
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 62, No. Pt_4 ( 2012-04-01), p. 827-831
    Abstract: A Gram-reaction-negative bacterial strain, designated GIMN1.005 T , was isolated from a forest soil sample in Vietnam. The isolate was yellow-pigmented, strictly aerobic, and unable to grow below 5 °C or above 37 °C and in the presence of more than 2.0 % NaCl. Cells were non-motile, non-gliding and non-spore-forming. The yellow pigment was of the flexirubin type, non-diffusible and non-fluorescent. Analysis of 16S rRNA gene sequences showed that strain GIMN1.005 T occupied a distinct lineage within the genus Chryseobacterium , with sequence similarity values of 98.6, 98.5 and 98.3 % to Chryseobacterium aquifrigidense KCTC 12894 T , Chryseobacterium jejuense KACC 12501 T and Chryseobacterium indologenes GIFU 1347 T , respectively. The level of DNA–DNA relatedness between strain GIMN1.005 T and C. jejuense KACC 12501 T was 〈 30 %. The DNA G+C content of strain GIMN1.005 T was 42.1 mol%. The predominant cellular fatty acids were iso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ); menaquinone 6 (MK-6) was the sole respiratory quinone. On the basis of phenotypic properties and phylogenetic distinctiveness, strain GIMN1.005 T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium vietnamense sp. nov. is proposed. The type strain is GIMN1.005 T ( = CCTCC M 209230 T  = NRRL B-59550 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijs.0.027201-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2012
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  • 10
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    Chitinophaga silvisoli sp. nov., isolated from forest soil
    Microbiology Society ; 2019
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 69, No. 4 ( 2019-04-01), p. 909-913
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 69, No. 4 ( 2019-04-01), p. 909-913
    Abstract: A Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901 T , was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10′ 24′′ N; 112° 32′ 10′′ E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901 T belongs to the genus Chitinophaga , and showed the highest similarities to Chitinophaga sancti NBRC 15057 T (98.6 %) and Chitinophaga oryziterrae JCM 16595 T (96.9 %). The major fatty acids ( 〉 10 %) were iso-C 15 : 0 , C 16 : 1 ω5 c , summed feature 3 (C 16 : 1 ω6 c and/or C 16 : 1 ω7 c ) and iso-C 17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901 T was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain K20C18050901 T and C. sancti NBRC 15057 T were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901 T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga silvisoli sp. nov. is proposed. The type strain is K20C18050901 T (=GDMCC 1.1411 T =KCTC 62860 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.003212
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2019
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