Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1126-1131 ◽  
Author(s):  
M. Madhaiyan ◽  
S. Poonguzhali ◽  
V. S. Saravanan ◽  
K. Hari ◽  
K.-C. Lee ◽  
...  

Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria , their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus Duganella , it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and Duganella radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 25-30 ◽  
Author(s):  
Libo Yu ◽  
Qiliang Lai ◽  
Zhiwei Yi ◽  
Limin Zhang ◽  
Ying Huang ◽  
...  

An aerobic, rod-shaped, Gram-positive, oxidase- and catalase-positive bacterial isolate, strain YLB-01T, was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Microbacterium and represented an evolutionary lineage that was distinct from recognized species of the genus Microbacterium . The isolate showed <97 % 16S rRNA gene sequence similarity with respect to the type strains of all of the members of the genus Microbacterium with validly published names. Cell-wall hydrolysate from the isolate contained the amino acids ornithine, alanine, glycine homoserine and glutamic acid, and the cell-wall sugars consisted of ribose, glucose and galactose. The main respiratory quinones were MK-8, 9, 10 and 11. The major cellular fatty acids were anteiso-C15 : 0 (38.5 %), anteiso-C17 : 0 (23.1 %) and C16 : 0 (18.9 %). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. The DNA G+C content of strain YLB-01T was 71 mol%. On the basis of the morphological, physiological and chemotaxonomic data and the results of comparative 16S rRNA gene sequence analysis, this isolate represents a novel species of the genus Microbacterium , for which the name Microbacterium sediminis sp. nov. is proposed. The type strain is YLB-01T ( = DSM 23767T = CCTCC AB2010363T = MCCC 1A06153T).


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1037-1041 ◽  
Author(s):  
Ling-Ling Yang ◽  
Tao Ao ◽  
Xing-Hong Wang ◽  
Jie He ◽  
Hans-Peter Klenk ◽  
...  

A Gram-positive and aerobic bacterium, designated strain YIM 49065T, was isolated from rhizospheric soil of Jatropha curcas in Yunnan, China. This isolate formed branched and fragmented mycelia containing ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major cellular fatty acid profile was characterized by iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The DNA G+C content was 69.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequence demonstrated that strain YIM 49065T was closely associated with Intrasporangium calvum DSM 43043T and Humihabitans oryzae KV-657T, exhibiting 98.8 % and 98.6 % 16S rRNA gene sequence similarities, respectively. Furthermore, DNA–DNA hybridizations among strains YIM 49065T, I. calvum DSM 43043T and H. oryzae DSM 22331T indicated that this isolate represented a novel species in the genus Intrasporangium . On the basis of these data, we proposed one novel species, Intrasporangium mesophilum sp. nov., for strain YIM 49065T ( = DSM 23217T  = CCTCC AA 209077T). Additionally, the comparison of biochemical and phylogenetic characters supported the reclassification of Humihabitans oryzae as a separate species within the genus Intrasporangium , Intrasporangium oryzae comb. nov. (type strain KV-657T  = JCM 15924T  = NBRC 101802T  = NRRL B-24470T).


2019 ◽  
Vol 69 (4) ◽  
pp. 957-963 ◽  
Author(s):  
Yong-Kun Xiao ◽  
Zheng-Fei Yan ◽  
Yoosung Kim ◽  
Hyun-Myung Lee ◽  
Huan Trinh ◽  
...  

A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium (THG-3.7T) was isolated from seawater. Growth occurred at 10–30 °C (optimum 25 °C), at pH 6–8 (optimum 7) and in the presence of 1–8 % (w/v) NaCl (optimum 4 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-3.7T were identified as Paraglaciecola mesophila DSM 15026T (95.3 % similarity), Glaciecola pallidula DSM 14239T (95.2 %), Paraglaciecola aquimarina KCTC 32108T (95.1 %), Paraglaciecola arctica KACC 14537T (94.9 %), Glaciecola nitratireducens KCTC 12276T (94.7 %) and Paraglaciecola psychrophila CGMCC 1.6130T (94.7 %). 16S rRNA gene sequence similarities among strain THG-3.7T and other species were lower than 94.7 %. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The quinone system was composed of Q-8. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain THG-3.7T was 47.9 mol%. On the basis of the data presented, strain THG-3.7T represents a novel species of the genus Glaciecola , for which the name Glaciecola amylolytica sp. nov. is proposed. The type strain is THG-3.7T (=KACC 19478T=CCTCC AB 2017258T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2150-2155 ◽  
Author(s):  
Revti Raichand ◽  
Siddhika Pareek ◽  
Nitin Kumar Singh ◽  
Shanmugam Mayilraj

A Gram-positive, motile, short rod-shaped, orange pigmented bacterium, designated strain IMTB-3094T, was isolated from a water sample collected from Tikkar Tal Lake, Haryana, and subjected to detailed polyphasic taxonomic analysis. Strain IMTB-3094T possessed most of the phenotypic and chemotaxonomic properties of the genus Exiguobacterium and, based on 16S rRNA gene sequence analysis, was assigned to this genus. Strain IMTB-3094T exhibited the highest 16S rRNA gene sequence similarity to Exiguobacterium mexicanum MTCC 7759T (99.5 %) followed by Exiguobacterium aurantiacum MTCC 6414T (99.1 %), Exiguobacterium aestuarii MTCC 7750T (98.0 %), Exiguobacterium profundum MTCC 10851T (98.0 %) and Exiguobacterium marinum MTCC 7751T (98.0 %). The G+C content of the genomic DNA of strain IMTB-3094T was 53.2 mol% and a DNA–DNA relatedness study confirmed that it represents a novel species. The major fatty acids of strain IMTB-3094T were iso-C17 : 0 (16.1 %), anteiso-C13 : 0 (19.0 %), iso-C13 : 0 (11.9 %), iso-C15 : 0 (9.8 %) and iso-C17 : 1 (12.7 %). The predominant quinones were MK-7 (55.0 %) and MK-6 (26.0 %) with minor amounts of MK-8 (12.0 %). Based on phenotypic, chemotaxonomic and phylogenetic analyses, strain IMTB-3094T represents a novel species of the genus Exiguobacterium , for which the name Exiguobacterium aquaticum sp. nov. is proposed. The type strain is IMTB-3094T ( = MTCC 10958T  = JCM 17977T).


2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2517-2521 ◽  
Author(s):  
Jie Li ◽  
Guo-Zhen Zhao ◽  
Li-Juan Long ◽  
Fa-Zuo Wang ◽  
Xin-Peng Tian ◽  
...  

In this study, two strains (SCSIO 10187T and SCSIO 10197) were isolated from a sediment sample collected from the South China Sea and characterized by using a polyphasic approach. Growth was observed at 15–35 °C (optimum 28 °C) and pH 5.0–8.0 (optimum pH 6.0). Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Rhodococcus . Phylogenetic analysis showed that the two strains clustered together and the 16S rRNA gene sequence similarities between them and other members of the genus Rhodococcus were 93.2–97.7 %. The menaquinone type was MK-8(H2). Major cellular fatty acids were C16 : 0, C18 : 1ω9c, C17 : 0, 10-methyl C18 : 0, C18 : 0, C19 : 0 and C17 : 1ω8c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C contents of strains SCSIO 10187T and SCSIO 10197 were 63.7 and 63.2 mol%, respectively. The combined genotypic and phenotypic data showed that the two strains represent a novel species of the genus Rhodococcus , for which the name Rhodococcus nanhaiensis is proposed; the type strain is SCSIO 10187T ( = DSM 45608T = CCTCC AB 2011024T), with SCSIO 10197 ( = DSM 45609 = CCTCC AB 2011025) as a reference strain.


2020 ◽  
Vol 70 (5) ◽  
pp. 3202-3209 ◽  
Author(s):  
Miri Park ◽  
Ilsuk Jung ◽  
Jaeho Song ◽  
Jang-Cheon Cho

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753T and IMCC26285T, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to Sphingorhabdus contaminans JC216T(98.7–98.8 %). The whole genome sequences of strains IMCC1753T and IMCC26285T were 3.5 and 2.9 Mbp in size with 56.6 and 55.5 mol% DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 82.2 and 25.8 %, respectively, indicating that they are separate species. The two strains showed ≤98.8 % 16S rRNA gene sequence similarities and ≤82.2 % ANI and ≤28.7 % dDDH values to closely related species of the genus Sphingorhabdus , indicating that the two strains each represent novel species. Major fatty acid constituents of strain IMCC1753T were C17 : 1  ω6c, C17 : 1  ω8c and summed features 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and 8 (C18 : 1  ω6c and/or C18 : 1  ω7c); those of strain IMCC26285T were summed features 3 and 8. The predominant isoprenoid quinone detected in both strains was ubiquinone-10 and the most abundant polyamine was spermidine. Both strains contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid as major polar lipids. On the basis of the phylogenetic and phenotypic characteristics, strains IMCC1753T and IMCC26285T were considered to represent two distinct novel species in the genus Sphingorhabdus , for which the names Sphingorhabdus lacus (IMCC1753T=KCTC 52480T=KACC 18985T=NBRC 112442T) and Sphingorhabdus profundilacus (IMCC26285T=KCTC 52479T=KACC 18986T=NBRC 112454T) are proposed, respectively.


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.


2020 ◽  
Vol 70 (4) ◽  
pp. 2732-2739 ◽  
Author(s):  
Yang Liu ◽  
Qiuhua Rao ◽  
Jochen Blom ◽  
Qiu Lin ◽  
Tuyan Luo

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagella, designated as MC042T, was isolated from the profound head ulcers of farmed Murray cod sampled from Zhejiang Province, China. Analysis of its 16S rRNA gene sequence and multilocus sequence analysis phylogeny showed that strain MC042T belonged to the genus Pseudomonas , showing the highest 16S rRNA gene sequence similarity to Pseudomonas juntendi BML3T (98.9 %), and less than 98.8 % similarity to other Pseudomonas species with validly published names. Whole-genome sequencing and phylogenetic reconstruction based on a core set of 1563 Pseudomonas genes further indicated that strain MC042T was most closely related to the clade formed by Pseudomonas protegens CHA0T and Pseudomonas saponiphila DSM 975T and distantly related to any of the validly published species of the genus Pseudomonas . Furthermore, strain MC042T could be distinguished from its closely related species of the genus Pseudomonas by its ability to assimilate maltose, d-xylose and melibiose, but not d-mannitol. The principal fatty acids were C16 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinone was Q-9. Polar lipids of strain MC042T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified glycolipids, an unidentified lipid, an unknown glycolipid and aminolipid. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain MC042T is considered to represent a novel species, for which the name Pseudomonas piscis sp. nov. is proposed. The type strain is MC042T (=KCTC 72033T=MCCC 1K03575T).


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1495-1500 ◽  
Author(s):  
Min Wu ◽  
Guiqin Yang ◽  
Zhen Yu ◽  
Li Zhuang ◽  
Yingqiang Jin ◽  
...  

Two Gram-stain-positive, rod-shaped and endospore-forming bacteria, designated WM-1T and WM-4, were isolated from a paddy soil and a forest soil, respectively, in South China. Comparative 16S rRNA gene sequence analyses showed that both strains were members of the genus Oceanobacillus and most closely related to Oceanobacillus chironomi LMG 23627T with pairwise sequence similarity of 96.0 %. The isolates contained menaquinone-7 (MK-7) as the respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0 as the major fatty acids (>10 %). Polar lipids consisted of a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The DNA G+C content was 38.6–39.2 mol%. The 16S rRNA gene sequence of strain WM-1T displayed 99.7 % similarity to that of strain WM-4, and DNA–DNA hybridization between the two strains showed a relatedness value of 91 %. Based on the results of this polyphasic study, strains WM-1T and WM-4 represent a novel species in the genus Oceanobacillus , for which the name Oceanobacillus luteolus sp. nov. is proposed. The type strain is WM-1T ( = KCTC 33119T = CGMCC 1.12406T).


2019 ◽  
Vol 69 (4) ◽  
pp. 1001-1008 ◽  
Author(s):  
Yuanyuan Tian ◽  
Chuanyu Han ◽  
Jiangmeihui Hu ◽  
Junwei Zhao ◽  
Chen Zhang ◽  
...  

A novel actinomycete, designated strain NEAU-TCZ24T, was isolated from soil and characterized using a polyphasic approach. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Cellulomonas and formed a stable clade with its closest relatives Cellulomonas terrae JCM 14899T (98.4 % 16S rRNA gene sequence similarity), Cellulomonas xylanilytica JCM 14281T (97.9 %) and Cellulomonas humilata JCM 11945T (97.7 %). The major menaquinones were identified as MK-9(H4) and MK-8(H4). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositolmannoside, a ninhydrin-positiveglycolipid, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15 : 0, C18 : 1ω9c, C16 : 0 and anteiso-C17 : 0. Moreover, morphological and chemotaxonomic properties of NEAU-TCZ24T also confirmed the affiliation of the isolate to the genus Cellulomonas . However, multilocus sequence analysis based on five other house-keeping genes (gyrB, rpoB, recA, relA and atpD), DNA–DNA relatedness, physiological and biochemical data indicated that NEAU-TCZ24T could be distinguished from its closest relatives. Therefore, it is proposed that NEAU-TCZ24T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas rhizosphaerae sp. nov. is proposed. The type strain is NEAU-TCZ24T (=CCTCC AA 2018042T=JCM 32383T).


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