Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2690-2699 ◽  
Author(s):  
S. Wellner ◽  
N. Lodders ◽  
S. P. Glaeser ◽  
P. Kämpfer

Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium . The closest relatives of strains C34T and T5 were Methylobacterium gnaphalii 23eT (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833T (97.0 and 97.2 %, respectively). Strain TA73T showed the highest sequence similarities to Methylobacterium marchantiae JT1T and Methylobacterium bullatum F3.2T (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27T and Methylobacterium brachiatum DSM 19569T (both 97.8 %), Methylobacterium cerastii C15T and Methylobacterium radiotolerans JCM 2831T (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73T and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34T and T5. Physiological and biochemical analysis, including DNA–DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA–DNA hybridization studies also showed high similarities between strains C34T and T5 (59.6–100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium , for which the names Methylobacterium trifolii sp. nov. (type strain TA73T = LMG 25778T = CCM 7786T) and Methylobacterium thuringiense sp. nov. (type strain C34T = LMG 25777T = CCM 7787T) are proposed.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2624-2630 ◽  
Author(s):  
Vikram Surendra ◽  
Pant Bhawana ◽  
Korpole Suresh ◽  
T. N. R. Srinivas ◽  
Pinnaka Anil Kumar

A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia , Coenonia and Capnocytophaga , being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.


2020 ◽  
Vol 70 (3) ◽  
pp. 1496-1502 ◽  
Author(s):  
Jin Li ◽  
Yan Xu ◽  
Jiarong Feng ◽  
Mingqi Zhong ◽  
Qingyi Xie ◽  
...  

A Gram-stain-negative, aerobic, non-motile and rod-shaped marine bacterium, CW2-9T, was isolated from algae collected from Fujian Province in PR China. 16S rRNA gene sequence analysis showed that this strain was affiliated with the genus Tamlana in the family Flavobacteriaceae of the class Flavobacteriia and was very similar to the type strain Tamlana sedimentorum MCCC 1A10799T (96.3 % sequence similarity). The whole genome of strain CW2-9T comprised 3 997 513 bp with a G+C content of 34.3 mol%. The average nucleotide identity value between strain CW2-9T and T. sedimentorum MCCC 1A10799T was 73.8 %. Growth was observed from 15 to 40 °C (optimum, 30 °C), at pH from pH 5.0 to 10.0 (pH 8.0) and in the presence of 0–4 % (w/v) NaCl (0–1 %). The major fatty acids (>10 % of the total) were iso-C15 : 0, iso G-C15 : 1, iso-C17 : 0 3-OH and anteiso-C15 : 0. The predominant menaquinone was MK-6. The combined phylogenetic, physiological and chemotaxonomic data indicate that strain CW2-9T represents a novel species in the genus Tamlana , for which the name Tamlana fucoidanivorans sp. nov. is proposed. The type strain is CW2-9T (=CICC 24749T=KCTC 72389T).


2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 88-94 ◽  
Author(s):  
Kornelia Kosowski ◽  
Marie Schmidt ◽  
Rüdiger Pukall ◽  
Gerd Hause ◽  
Peter Kämpfer ◽  
...  

Two strains, 8-4-E12T and 8-4-E13T, were isolated from a biowaste composting reactor. Based on 16S rRNA gene sequences, both strains belong to the genus Bacillus . Strain 8-4-E12T was most closely related to the type strains of Bacillus shackletonii , B. acidicola , B. sporothermodurans and B. oleronius (96.4, 96.3, 96.0 and 95.6 % 16S rRNA gene similarity, respectively), whereas strain 8-4-E13T was most closely related to the type strain of Bacillus humi (96.5 % sequence similarity). Strains 8-4-E12T and 8-4-E13T shared 94 % 16S rRNA gene sequence similarity. The fatty acid profile of strain 8-4-E12T was dominated by saturated iso- and anteiso-branched fatty acids (iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0), and also contained considerable amounts of C16 : 0. The fatty acid profile of strain 8-4-E13T showed a predominance of iso-C15 : 0 (65 %), with smaller amounts of other saturated branched-chain fatty acids along with an unsaturated alcohol. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids. Additionally, strain 8-4-E12T contained an unknown lipid and strain 8-4-E13T two unknown (amino-)phospholipids. The diagnostic diamino acid found in the cell-wall peptidoglycan of 8-4-E12T and 8-4-E13T was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The results of physiological and biochemical tests also allowed phenotypic differentiation of the two strains from each other and from related Bacillus species. On the basis of their phylogenetic, phenotypic and chemotaxonomic properties, strains 8-4-E12T and 8-4-E13T represent novel species of the genus Bacillus , for which the names Bacillus pervagus sp. nov. (type strain 8-4-E12T = DSM 23947T = LMG 27601T) and Bacillus andreesenii sp. nov. (type strain 8-4-E13T = DSM 23948T = LMG 27602T) are proposed.


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3134-3139 ◽  
Author(s):  
Jung-Hye Choi ◽  
Kyung Min Lee ◽  
Myung-Ki Lee ◽  
Chang-Jun Cha ◽  
Geun-Bae Kim

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).


2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 839-843 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
...  

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped bacterial strain, designated DPG-28T, was isolated from seawater on the southern coast of Korea. Strain DPG-28T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DPG-28T formed a coherent cluster with members of the genera Marivita and Gaetbulicola , with which it exhibited sequence similarity values of 97.8–98.5 %. The DNA G+C content of strain DPG-28T was 65.1 mol%. The predominant ubiquinone of strain DPG-28T was ubiquinone-10 (Q-10), consistent with data for the genera Marivita and Gaetbulicola . The cellular fatty acid profiles of strain DPG-28T and the type strains of Marivita cryptomonadis , Marivita litorea and Gaetbulicola byunsanensis were essentially similar in that the common predominant fatty acid was C18 : 1ω7c. Major polar lipids found in strain DPG-28T and the type strains of M. cryptomonadis , M. litorea and G. byunsanensis were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. From these data, it is proposed that Gaetbulicola byunsanensis be reclassified as a member of the genus Marivita , for which the name Marivita byunsanensis comb. nov. is proposed, with the type strain SMK-114T ( = CCUG 57612T  = KCTC 22632T), and that strain DPG-28T be classified in the genus Marivita . Differential phenotypic properties and genetic distinctiveness of strain DPG-28T demonstrated that this strain is distinguishable from M. cryptomonadis , M. litorea and G. byunsanensis . On the basis of the data presented, strain DPG-28T is considered to represent a novel species of the genus Marivita , for which the name Marivita hallyeonensis sp. nov. is proposed. The type strain is DPG-28T ( = KCTC 23421T  = CCUG 60522T). An emended description of the genus Marivita is also provided.


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1509-1514 ◽  
Author(s):  
Sung-Min Won ◽  
Sooyeon Park ◽  
Ji-Min Park ◽  
Byung-Chan Kim ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9T, was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9T clustered with the type strain of Halocynthiibacter namhaensis , showing a highest sequence similarity of 97.3 %. It exhibited sequence similarity values of less than 95.6 % to the type strains of other species with validly published names. Strain BS-W9T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain BS-W9T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9T were distinguished from those of the type strains of H. namhaensis and other phylogenetically related genera. The DNA G+C content of strain BS-W9T was 53.2 mol% and its mean DNA–DNA relatedness value with H. namhaensis RA2-3T was 14 %. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9T is considered to represent a novel genus and species within the family Rhodobacteraceae , for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9T ( = KCTC 42348T = CECT 8726T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1297-1303 ◽  
Author(s):  
Keun Sik Baik ◽  
Han Na Choe ◽  
Seong Chan Park ◽  
Yeoung Min Hwang ◽  
Eun Mi Kim ◽  
...  

Two yellow-pigmented, Gram-reaction-negative strains, designated 01SU5-PT and 03SU3-PT, were isolated from the freshwater of Woopo wetland, Republic of Korea. Both strains were aerobic, non-motile and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Sphingopyxis , showing the highest level of sequence similarity with respect to Sphingopyxis witflariensis W-50T (95.4–95.7 %). The two novel isolates shared 99.4 % sequence similarity. DNA–DNA hybridization between the isolates and the type strain of S. witflariensis clearly suggested that strains 01SU5-PT and 03SU3-PT represent two separate novel species in the genus Sphingopyxis . The two strains displayed different fingerprints after PCR analysis using the repetitive primers BOX, ERIC and REP. Several phenotypic characteristics served to differentiate these two isolates from recognized members of the genus Sphingopyxis . The data from the polyphasic study presented here indicated that strains 01SU5-PT and 03SU3-PT should be classified as representing novel species in the genus Sphingopyxis , for which the names Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., respectively, are proposed. The type strain of Sphingopyxis rigui sp. nov. is 01SU5-PT ( = KCTC 23326T = JCM 17509T) and the type strain of Sphingopyxis wooponensis sp. nov. is 03SU3-PT ( = KCTC 23340T = JCM 17547T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 288-297 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vassilii I. Svetashev ◽  
Enevold Falsen

A group of five Gram-negative, aerobic, halotolerant, non-pigmented bacteria isolated from shallow sediment samples and invertebrate specimens collected from the Gulf of Alaska and the Sea of Japan was subjected to taxonomic study. On the basis of 16S rRNA gene sequence analysis, the novel isolates were affiliated to the genus Cobetia , sharing the highest sequence similarity of 99.3–99.9 % with Cobetia marina DSM 4741T. DNA–DNA hybridization experiments between and among the novel strains and C. marina DSM 4741T and Cobetia crustatorum JCM 15644T revealed that the five strains represent three separate genospecies, which could be differentiated in their morphological, physiological and biochemical characteristics. Halomonas halodurans NBRC 15607T was included in this study as it has recently been reported to exhibit high 16S rRNA gene sequence similarity to C. marina DSM 4741T, and it showed a high DNA relatedness value of 96 % with C. marina DSM 4741T, indicating that they belong to the same species. On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotypic characterization, three novel species are proposed, named Cobetia amphilecti sp. nov. (type strain KMM 1561T  = NRIC 0815T  = CCUG 49560T), Cobetia litoralis sp. nov. (type strain KMM 3880T  = NRIC 0814T  = CCUG 49563T) and Cobetia pacifica sp. nov. (type strain KMM 3879T  = NRIC 0813T  = CCUG 49562T). It is also proposed that Halomonas halodurans is a later heterotypic synonym of Cobetia marina , and emended descriptions of the genus Cobetia and the species Cobetia marina are provided.


Author(s):  
Peng Cao ◽  
Xi Xu ◽  
Chenxu Li ◽  
Liyuan Han ◽  
Wenhao Mu ◽  
...  

A novel actinobacterium, designated strain NEAU-AAG5T, was isolated from sandy soil collected from Niuwang island in Sanya, Hainan Province, PR China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-AAG5T belongs to the genus Actinomadura and shared highest sequence similarity with Actinomadura macra NBRC 14102T (98.8 %). Strain NEAU-AAG5T grows at 20–40 °C (optimum, 28 °C), pH 6–10 (optimum, pH 7) and has NaCl tolerance of 0–3 %. The menaquinones were identified as MK-9(H4) (4.2 %), MK-9(H6) (49.2 %) and MK-9(H8) (46.5 %). The major fatty acids were C16 : 0 (31.4 %), 10-methyl C18 : 0 (21.3 %) and C18 : 1  ω9c (15.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain NEAU-AAG5T based on whole genome sequences was 72.8 mol%. Digital DNA–DNA hybridization between strain NEAU-AAG5T and its closest phylogenetic neighbour, A. macra NBRC 14102T, resulted in similarity value of 28.0 % (<70 %). Additionally, the average nucleotide identity was 84.2 % for A. macra NBRC 14102T. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-AAG5T can be characterized to represent a novel species of the genus Actinomadura , for which the name Actinomadura litoris sp. nov. is proposed. The type strain is NEAU-AAG5T (=JCM 33456T=CCTCC AA 2019043T).


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