scholarly journals Spongiibacterium pacificum sp. nov., isolated from seawater of South Pacific Gyre and emended description of the genus Spongiibacterium

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 154-158 ◽  
Author(s):  
Xin Gao ◽  
Zenghu Zhang ◽  
Xiaofeng Dai ◽  
Xiao-Hua Zhang

A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase-positive and yellow-pigmented rod-shaped bacterium, designated strain SW169T, was isolated from a surface seawater sample collected from the South Pacific Gyre (27° 55′ S 123° 10′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW169T belonged to the genus Spongiibacterium and showed the highest 16S rRNA gene sequence similarity with Spongiibacterium flavum A11T (95.9 %). It showed 16S rRNA gene sequence similarities of 93.2–94.8 % with members of the genera Croceitalea and Flagellimonas in the family Flavobacteriaceae . Optimal growth occurred in the presence of 3–4 % (w/v) NaCl, at pH 8.0 and at 28 °C. The DNA G+C content of strain SW169T was 43.3 mol%. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c,). The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. On the basis of the polyphasic analyses, strain SW169T is considered to represent a novel species of the genus Spongiibacterium , for which the name Spongiibacterium pacificum sp. nov. is proposed. The type strain is SW169T ( = JCM 18379T = LMG 26997T). An emended description of the genus Spongiibacterium is also provided.

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2865-2869 ◽  
Author(s):  
Jina Lee ◽  
Na-Ri Shin ◽  
Hae-Won Lee ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
...  

A Gram-negative, motile, facultatively anaerobic rod, designated A36T, was isolated from a dead ark clam found on the south coast of Korea. The isolate was catalase- and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain A36T was most closely related to Kistimonas asteriae KMD 001T, with which it shared 98.2 % 16S rRNA gene sequence similarity. Strain A36T grew optimally at 30–37 °C, with 1 % (w/v) NaCl and at pH 8.0. The major respiratory quinone was ubiquinone-9 (Q-9). The major polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 2-OH) and C16 : 0. The genomic DNA G+C content was 47.3 mol%. DNA–DNA relatedness between the isolate and K. asteriae JCM 15607T was <25±3 %. Strain A36T represents a novel species of the genus Kistimonas , for which the name Kistimonas scapharcae sp. nov. is proposed. The type strain is A36T ( = KACC 16204T  = JCM 17805T). An emended description of the genus Kistimonas is also provided.


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 513-517 ◽  
Author(s):  
Soo-Jin Kim ◽  
Ji-Young Moon ◽  
Jae-Hyung Ahn ◽  
Hang-Yeon Weon ◽  
Seung-Beom Hong ◽  
...  

A Gram-stain-negative, non-motile, aerobic rod, designated 8604S-37T, was isolated from an outdoor air sample collected in Suwon region, Republic of Korea. The isolate was catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain 8604S-37T was most closely related to Diaphorobacter nitroreducens NA10BT and Diaphorobacter oryzae RF3T, with which it shared 97.0 % 16S rRNA gene sequence similarity. Strain 8604S-37T grew at 10–37 °C (optimum 28 °C; no growth occurred at 4 or 40 °C) and pH 5–9 (optimum pH 7). The strain tolerated up to 3 % NaCl (w/v) (optimum 0 %). The only respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown aminolipid. The major fatty acids were C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C17 : 0 cyclo, and the predominant hydroxy fatty acid was C10 : 0 3-OH. Strain 8604S-37T exhibited less than 50 % DNA–DNA relatedness with Diaphorobacter nitroreducens KACC 13856T and Diaphorobacter oryzae KACC 16857T. The DNA G+C content was 65 mol%. Strain 8604S-37T represents a novel species of the genus Diaphorobacter , for which the name Diaphorobacter aerolatus sp. nov. is proposed. The type strain is 8604S-37T ( = KACC 16536T = NBRC 108926T). An emended description of the genus Diaphorobacter is also proposed.


2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2927-2933 ◽  
Author(s):  
G. S. N. Reddy ◽  
B. Poorna Manasa ◽  
Sanjay K. Singh ◽  
S. Shivaji

A Gram-stain-positive, aerobic, spore-forming, rod-shaped bacterium, PN2T, was isolated from a soil sample collected near the Pindari glacier. It contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 1ω7c alcohol as the predominant fatty acids, MK-7 as the major menaquinone and A4α type (l-Lys–d-Glu) peptidoglycan. Based on these characteristics, strain PN2T was assigned to the genus Paenisporosarcina . Phylogenetic analysis based on 16S rRNA gene sequence placed strain PN2T within the genus Paenisporosarcina and showed a sequence similarity of 98.5–99.0 % with members of this genus. Paenisporosarcina macmurdoensis CMS 21wT, Paenisporosarcina quisquiliarum SK 55T and Sporosarcina antarctica N-05T were identified as the most closely related species with 16S rRNA gene sequence similarities of 98.6 %, 99.0 % and 98.4 %, respectively. The values for DNA–DNA relatedness between strain PN2T and P. macmurdoensis , P. quisquiliarum and S. antarctica were below the 70 % threshold value (32.0 %, 42.0 % and 38.0 % respectively). In addition, strain PN2T exhibited a number of phenotypic differences from P. macmurdoensis , P. quisquiliarum and S. antarctica . Based on the cumulative differences, strain PN2T was identified as representing a novel species and the name Paenisporosarcina indica sp. nov. was proposed. The type strain of Paenisporosarcina indica sp. nov. is PN2T (LMG 23933T = JCM 15114T). Furthermore, based on the morphological and chemotaxonomic characteristics, the species Sporosarcina antarctica was reclassified as a species of the genus Paenisporosarcina and renamed Paenisporosarcina antarctica comb. nov. In addition, an emended description of the genus Paenisporosarcina is presented.


2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1155-1159 ◽  
Author(s):  
Xin Gao ◽  
Zenghu Zhang ◽  
Xiaofeng Dai ◽  
Xiao-Hua Zhang

A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive and rod-shaped yellow-pigmented bacterium, designated strain SW033T was isolated from a surface seawater sample collected from the South Pacific Gyre (GPS position: 26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program, expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW033T belonged to the genus Hyunsoonleella and showed the highest 16S rRNA gene sequence similarity with Hyunsoonleella jejuensis CNU004T (96.8 %). It showed 94.7–95.8 % 16S rRNA gene sequence similarity with respect to members of the genera Jejuia , Arenitalea and Algibacter in the family Flavobacteriaceae . Optimal growth occurred in the presence of 2–3 % (w/v) NaCl, at pH 8.0 and at 28 °C. The genomic DNA G+C content of strain SW033T was 36.1 mol%. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids. On the basis of the polyphasic analyses, strain SW033T is considered to represent a member of a novel species in the genus Hyunsoonleella , for which the name Hyunsoonleella pacifica sp. nov. is proposed. The type strain is SW033T ( = CGMCC 1.11009T = JCM 17860T).


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 887-893 ◽  
Author(s):  
Zhangran Chen ◽  
Luxi Yang ◽  
Yi Li ◽  
Qiliang Lai ◽  
Huajun Zhang ◽  
...  

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain KD51T, forming colonies coloured pink by carotenoid pigments, was isolated from aggregates of the alga Chlorella autotrophica collected from the coastal sea off the city of Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD51T was a member of the genus Cyclobacterium , forming a distinct lineage with Cyclobacterium lianum HY9T. The 16S rRNA gene sequence similarity between strain KD51T and the type strains of species of the genus Cyclobacterium ranged from 92.1 % to 95.2 %. Growth occurred at 4–40 °C (optimum, 28 °C), in the presence of 3–9 % NaCl (optimum, 3–5 %) and at pH 6–10 (optimum, pH 7.5). The dominant fatty acids (>20 %) of strain KD51T were iso-C15 : 0 (32.2 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c; 22.2 %). The DNA G+C content was 41.7 mol% and the only respiratory quinone was menaquinone-7. On the basis of phenotypic data and phylogenetic inference, strain KD51T represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium xiamenense sp. nov. is proposed. The type strain is KD51T ( = CGMCC 1.12432T = KCTC 32253T). An emended description of the genus Cyclobacterium is also proposed.


2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 977-983 ◽  
Author(s):  
Yong-Sik Oh ◽  
Dong-Hyun Roh

A Gram-staining-negative, non-motile, aerobic bacterium, designated strain A8T, was isolated from the beach soil of Muchangpo, Korea. Cells were rod-shaped (0.5–0.6×0.7–1.3 µm) and colonies were colourless, circular with entire edges and had a glistening surface. The isolate grew optimally at 25–35 °C and did not require NaCl for growth. Strain A8T could not assimilate acetate, dl-lactate, succinate, antipyrine or chloridazon, but weakly assimilated l-phenylalanine. Major fatty acids were summed feature 7 (comprising C18 : 1ω7c/ω9t/ω12t), C16 : 0 and summed feature 4 (comprising C16 : 1ω7c/ iso-C15 : 0 2-OH). The major isoprenoid quinone was ubiquinone-10 and the DNA G+C content was 72.3 mol%. Comparative 16S rRNA gene sequence studies showed that strain A8T belonged to the family Caulobacteraceae , class Alphaproteobacteria and was most closely related to type strains of members of the genus Phenylobacterium (95.7–97.1 % similarity). Signature nucleotides and phylogenetic analysis of the 16S rRNA gene sequence also suggested that strain A8T was affiliated with the genus Phenylobacterium . Low DNA–DNA relatedness values (3.0±1.8–11.5±3.2 %) indicated that strain A8T represented a distinct species that was separated from other type strains in the genus Phenylobacterium . On the basis of evidence from a polyphasic study, it is proposed that strain A8T ( = KACC 15042T  = LMG 25973T) represents the type strain of a novel species, Phenylobacterium muchangponense sp. nov. An emended description of the genus Phenylobacterium is also presented.


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1789-1794 ◽  
Author(s):  
MooChang Kook ◽  
YongJin Park ◽  
Tae-Hoo Yi

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterial strain, THG-DR3T, was isolated from soil of a pine grove in Jeju island, Republic of Korea. Strain THG-DR3T grew optimally at 20–25 °C, at pH 7.0–8.0 and in R2A broth without added NaCl. 16S rRNA gene sequence analysis indicated that strain THG-DR3T belongs to the genus Pedobacter . The closest relatives based on 16S rRNA gene sequence similarity were Pedobacter aquatilis AR107T (98.0 %), Pedobacter alluvionis NWER-II11T (97.7 %), Pedobacter borealis G-1T (97.7 %) and Pedobacter ginsengiterrae DCY49T (97.4 %). The G+C content of the genomic DNA of strain THG-DR3T was 47.5 mol%. Levels of DNA–DNA relatedness between strain THG-DR3T and its closest phylogenetic neighbours were below 44.7 %. The presence of menaquinone 7 and of iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids supported the affiliation of strain THG-DR3T to the genus Pedobacter . The polar lipids of strain THG-DR3T consisted of phosphatidylethanolamine, three unidentified aminophospholipids, five unidentified aminolipids and three unidentified lipids. The results of physiological and biochemical tests allowed the differentiation of strain THG-DR3T from recognized species of the genus Pedobacter . Strain THG-DR3T ( = KACC 17172T = JCM 18824T) is proposed as the type strain of a novel species of the genus Pedobacter , Pedobacter jejuensis sp. nov. An emended description of the genus Pedobacter is also proposed.


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).


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