scholarly journals Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater

2020 ◽  
Vol 70 (12) ◽  
pp. 6060-6066 ◽  
Author(s):  
Xiaolei Wang ◽  
Feng Guo ◽  
Peng Tian ◽  
Shuangen Yu ◽  
Chun-Xu Xue ◽  
...  

A Gram-stain-negative, aerobic, gliding, reddish-orange-coloured, rod-shaped strain, designated SR4T, was isolated from surface seawater sampled at Luhuitou fringing reef (South China Sea). Phylogenetic analyses based on the 16S rRNA gene, phylogenomic analysis of single-copy gene families and whole genome data affiliated it to the genus Flammeovirga . It was most closely related to Flammeovirga yaeyamensis NBRC 100898T (97.99 % 16S rRNA gene similarity). The genome average nucleotide identity and DNA–DNA relatedness values between strain SR4T and its reference strains were less than 74.2 and 16.3 %, respectively. Growth occurred at 20–35 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 1–6 % (w/v) NaCl (optimum, 2–4 %). The dominant fatty acids were C16 : 0, iso-C15 : 0 and C20 : 4  ω6,9,12,15c. The polar lipid profile of strain SR4T comprised phosphatidylethanolamine, two glycolipids, two aminophospholipids and three unidentified lipids. The major respiratory quinone was MK-7. The DNA G+C content of strain SR4T was 34.20 mol%. On the basis of the polyphasic evidence, strain SR4T is proposed as representing a novel species of the genus Flammeovirga , for which the name Flammeovirga agarivorans sp. nov. is proposed. The type strain is SR4T (=KCTC 82075T=MCCC 1A17137T).

Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).


2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to Methylobacterium organophilum ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus Methylobacterium , for which the names Methylobacterium haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and Methylobacterium brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.


2020 ◽  
Vol 70 (5) ◽  
pp. 3335-3339 ◽  
Author(s):  
Guanghua Wang ◽  
Dahao Tang ◽  
Guangyu Li ◽  
Shuailiang Xu ◽  
Ge Dang ◽  
...  

A Gram-stain-negative, non-spore-forming, aerobic, motile, curved rod-shaped bacterium, designed strain R148T was isolated from a coralline algae Tricleocarpa sp. collected from Weizhou island, PR China. The optimal growth of R148T occurred at 25 °C, pH 8–9 in the presence of 0.5 % (w/v) NaCl on the basis of amended marine broth 2216. The genomic DNA G+C content was 59.5 mol%. The only detected respiratory quinone was Q-10. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and three unidentified ninhydrin-positive lipids. The major cellular fatty acids were C18 : 1ω7c, C16 : 1ω7c, C19 : 0cyclo 9, 10 DMA and C18 : 0. The results of 16S rRNA gene-based global alignment indicated that the closest neighbour of strain R148T was Pelagibius litoralis DSM 21314T (93.1 % similarity), the second is Limibacillus halophilus KCTC 42420T (92.2 %). The results of phylogenetic analysis indicated that R148T forms a distinct branch in the robust clade of R148T and P. litoralis DSM 21314T, while the taxonomic position of this clade in the family Rhodospirillaceae is ambiguous among phylogenetic approaches. The low 16S rRNA gene similarity and distinct polar lipid and cellular fatty acid profile could readily distinguish R148T from closely related type strains. So R148T is suggested to represent a novel species in a novel genus, for which the name Denitrobaculum tricleocarpae gen. nov., sp. nov. is proposed. The type strain is R148T (=MCCC 1K03781T=KCTC 72137T).


2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1127-1132 ◽  
Author(s):  
Jing Liang ◽  
Ji Liu ◽  
Xiao-Hua Zhang

A Gram-stain-negative, strictly aerobic and rod-shaped motile bacterium with peritrichous flagella, designated strain LZB041T, was isolated from offshore surface seawater of the East China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LZB041T formed a lineage within the family ‘ Aurantimonadaceae ’ that was distinct from the most closely related genera Aurantimonas (96.0–96.4 % 16S rRNA gene sequence similarity) and Aureimonas (94.5–96.0 %). Optimal growth occurred in the presence of 1–7 % (w/v) NaCl, at pH 7.0–8.0 and at 28–37 °C. Ubiquinone-10 was the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8) and cyclo-C19 : 0ω8c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unknown aminolipid, one unknown phospholipid and one unknown polar lipid. The DNA G+C content of strain LZB041T was 71.3 mol%. On the basis of polyphasic analysis, strain LZB041T is considered to represent a novel species of a new genus in the class Alphaproteobacteria , for which the name Jiella aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is LZB041T ( = JCM 30119T = MCCC 1K00255T).


Author(s):  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
Shan Lu ◽  
...  

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353T (97.51 %), zg-917T/zg-910 to Corynebacterium coyleae DSM 44184T (98.68 %), and zg-913T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2–64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs. Corynebacterium auriscanis CIP 106629T, Corynebacterium resistens DSM 45100T and Corynebacterium suicordis DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs. C. coyleae DSM 44184T and Corynebacterium jeddahense JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs. Corynebacterium mucifaciens ATCC 700355T and C. afermentans subsp. lipophilum CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1  ω9c and C18 : 0 ante/C18 : 2  ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35–37 °C, 0.5 % (w/v) NaCl and pH 7.0–8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).


2020 ◽  
Vol 70 (6) ◽  
pp. 3606-3613 ◽  
Author(s):  
Zixiao Xu ◽  
Yuxiao Zhang ◽  
Yasir Muhammad ◽  
Gejiao Wang

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of Sphingomonas crocodyli CCP-7T (97.0%), Sphingomonas jatrophae S5-249T (96.6%) and Sphingomonas starnbergensis 382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with S. crocodyli CCP-7T, S. jatrophae S5-249T and S. starnbergensis 382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains ( S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with S. crocodyli BCRC 81096T and S . jatrophae DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).


Author(s):  
Ruijuan Yang ◽  
De Zhou ◽  
Qiaomei Wang ◽  
Wenshu Peng ◽  
Wanying Gong ◽  
...  

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia . The closest phylogenetic relative was Massilia arenae CICC 24458T (99.5 %), followed by M. timonae CCUG45783T (97.9 %), M. oculi CCUG43427AT (97.8 %), and M. aurea DSM 18055T (97.8 %). The major fatty acids were C16 : 0 and C16 : 1  ω7c and/or C16 : 1  ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA–DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3T and Massilia arenae CICC 24458T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3T (=CGMCC 1.17158T=KCTC 82193T).


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 479-484 ◽  
Author(s):  
Linfang Wei ◽  
Meiru Si ◽  
Mingxiu Long ◽  
Lingfang Zhu ◽  
Changfu Li ◽  
...  

A yellowish-pigmented bacterium, designated strain PLGR-1T, was isolated from the root of Bergenia scopulosa collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain PLGR-1T were Gram-stain-negative, strictly aerobic, rod-shaped, non-spore-forming and motile with a single polar flagellum. Growth occurred at 7–33 °C (optimum, 25–28 °C), at pH 5.0–10.0 (optimum, pH 6.0–7.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). The predominant respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polyamines were putrescine and 2-hydroxyputrescine and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PLGR-1T belonged to the class Betaproteobacteria and formed a tight phyletic lineage with members of the genus Rhizobacter . Strain PLGR-1T was most closely related to Rhizobacter dauci DSM 11587T and Rhizobacter fulvus DSM 19916T, with 16S rRNA gene sequence similarities of 98.5 and 98.0 %, respectively. The DNA–DNA relatedness values between strain PLGR-1T and the type strains of Rhizobacter dauci and Rhizobacter fulvus were 46.3 and 14.7 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain PLGR-1T is considered to represent a novel species of the genus Rhizobacter , for which the name Rhizobacter bergeniae sp. nov. is proposed. The type strain is PLGR-1T ( = CCTCC AB 2013018T = KCTC 32299T = LMG 27607T).


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 353-358 ◽  
Author(s):  
Maki Teramoto ◽  
Ken-ichi Yagyu ◽  
Miyuki Nishijima

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2-9T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain was transparent on 1/5 strength marine broth plate but became easily visible when the plate was supplemented with pyruvate. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the strain fell within the class Gammaproteobacteria and was most closely related to the genus Arenicella (92.7–93.0 % 16S rRNA gene sequence similarities to type strains of species of this genus) of an unclassified order within this class. The DNA G+C content of strain 2-9T was 41.7 mol%. The major fatty acids were C18 : 1ω7c (37.6 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3; 19.1 %), C18 : 0 (10.8 %), C16 : 0 (10.2 %) and an unidentified fatty acid with an equivalent chain-length value of 11.799 (9.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. Ubiquinone-8 (Q-8) was detected as the sole isoprenoid quinone. From these taxonomic data, it is proposed that strain 2-9T represents a novel species of a new genus, Perspicuibacter marinus gen. nov., sp. nov. The type strain of the type species is 2-9T ( = NBRC 110144T = KCTC 42196T). A new family, Arenicellaceae fam. nov. (type genus Arenicella ), and order, Arenicellales ord. nov., of the class Gammaproteobacteria are proposed to accommodate the novel taxon.


2020 ◽  
Vol 70 (5) ◽  
pp. 3483-3490 ◽  
Author(s):  
Jianyang Li ◽  
Mingming Qi ◽  
Qiliang Lai ◽  
Chunming Dong ◽  
Xiupian Liu ◽  
...  

Two Gram-stain-negative, short rod-shaped and non-flagellated strains, designated 17-4AT and L52-1-41, were isolated from the surface seawater of the Indian Ocean and South China Sea, respectively. The 16S rRNA genes of the two strains shared sequence similarity of 99.45 %. Strain 17-4AT shared the highest 16S rRNA gene similarity of 98.02 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.93 %), Parapusillimonas granuli Ch07T (96.68 %), Pusillimonas ginsengisoli DCY25T (96.65 %), Eoetvoesia caeni PB3-7BT (96.63 %), Paracandidimonas caeni 24T (96.34 %), Castellaniella defragrans 54PinT (96.28 %) and Pusillimonas harenae B201T (96.05 %). L52-1-41 shared the highest 16S rRNA gene similarity of 97.74 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.65 %), Parapusillimonas granuli Ch07T (96.41 %), Pusillimonas ginsengisoli DCY25T (96.37 %), Eoetvoesia caeni PB3-7BT (96.35 %), Pusillimonas harenae B201T (96.28 %), and Paracandidimonas caeni 24T (96.06 %). The results of phylogenetic analyses indicated that 17-4AT and L52-1-41 formed a stable, distinct and highly supported lineage affiliated to the genus Pusillimonas . The results of the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses indicated that they represented a single species. They featured similar genomic DNA G+C contents of 53.2–53.4 mol%. Activities of catalase and oxidase were negative for both strains. The fatty acids patterns of 17-4AT and L52-1-41 were most similar, mostly comprised of C16 : 0, C17 : 0cyclo, C18 : 0, C18 : 1ω9c and summed feature 8 (C18 : 1ω7c and/or C18 : 1  ω6c). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The respiratory quinone of the two strains was Q-8. Hence, on the basis of the phenotypic, chemotaxonomic and genotypic data presented in this study, we proposed the classification of both strains as representatives of a novel species named Pusillimonas maritima sp. nov., with the type strain 17-4AT (=MCCC 1A12670T=KCTC 62121T=NBRC 113794T), and another strain L52-1-41 (=MCCC 1A05046=KCTC 52313).


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