scholarly journals Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium

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.

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.


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
Stefanie P. Glaeser ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, non-motile, non-spore-forming, coccus (strain Do 184T) was isolated from exhaust air of a turkey fattening plant on mannitol salt agar. The strain shared high 16S rRNA gene sequence similarity to the type strains of Jeotgalicoccus aerolatus (98.0%) followed by Jeotgalicoccus marinus (97.2%) and Jeotgalicoccus huakuii (97.1%). All other 16S rRNA gene sequence similarities to species of the genus Jeotgalicoccus were below 97%. The average nucleotide identities (ANI) between the Do 184T genome assembly and the ones of type strains of species of the genus Jeotgalicoccus were far below the 95% species delineation cutoff value, ranging from 79.47% ( J. marinus DSM 19772T) to 75.30% ( J. pinnipedialis CIP 107946T). The quinone system of Do 184T, the polar lipid profile, the polyamine pattern and the fatty acid profile were in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of Do 184T to this genus. Do 184T represents a novel species, for which the name Jeotgalicoccus meleagridis sp. nov. is proposed, with the type strain Do 184T (=LMG 31100T=CCM 8918T=CIP 111649T). In addition, data on genome sequences of Jeotgalicoccus halophilus C1-52T =CGMCC 1.8911T=NBRC 105788T and Jeotgalicoccus aerolatus MPA-33T=CCM 7679T=CCUG 57953T=DSM 22420T=CIP 111750T indicate that both isolates represent the same species. Pairwise ANI between the genomes of these two strains lead to similarities of 98.98–99.05 %. These results indicate that these strains represent members of the same species. Due to priority of publication it is proposed that Jeotgalicoccus halophilus is reclassified as Jeotgalicoccus aerolatus .


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3841-3847 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie Glaeser ◽  
Hans-Jürgen Busse ◽  
Tobias Eisenberg ◽  
Holger Scholz

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315T) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella – Ochrobactrum – Paenochrobactrum – Pseudochrobactrum group with 94.5–94.8 %, 94.3–96.1 %, 95.0–95.1 %, and 95.9–96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315T to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315T contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315T was clearly different from the genera Brucella , Ochrobactrum , Paenochrobactrum and Pseudochrobactrum . On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315T ( = CCM 8460T = LMG 27356T.) The taxonomic allocation of O. gallinifaecis , which grouped inconsistently together with strain B1315T on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum , remains to be clarified.


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.


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_5) ◽  
pp. 1559-1565 ◽  
Author(s):  
Radha Vaddavalli ◽  
Sneha Peddi ◽  
Srilekha Yadav Kothagauni ◽  
Zareena Begum ◽  
Bhagyanarayana Gaddam ◽  
...  

A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus Saccharopolyspora . The highest levels of 16S rRNA gene sequence similarity were found with Saccharopolyspora hirsuta subsp. kobensis JCM 9109T (98.71 %), Saccharopolyspora antimicrobica I05-00074T (98.69 %) and Saccharopolyspora jiangxiensis W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus Saccharopolyspora were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus Saccharopolyspora , for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2532-2537 ◽  
Author(s):  
Poonam Vashist ◽  
Yuichi Nogi ◽  
Sanjeev C. Ghadi ◽  
Pankaj Verma ◽  
Yogesh S. Shouche

A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13T, was isolated from the mangrove ecosystem of Goa, India. Strain DD-13T degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13T was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13T formed a coherent cluster with species of the genus Microbulbifer . Strain DD-13T exhibited 16S rRNA gene sequence similarity levels of 98.9–97.1 % with Microbulbifer hydrolyticus IRE-31T, Microbulbifer salipaludis JCM 11542T, Microbulbifer agarilyticus JAMB A3T, Microbulbifer celer KCTC 12973T and Microbulbifer elongatus DSM 6810T. However, the level of DNA–DNA relatedness between strain DD-13T and the five type strains of these species of the genus Microbulbifer were in the range of 26–33 %. Additionally, strain DD-13T demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer . Thus strain DD-13T represents a novel species of the genus Microbulbifer , for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13T ( = KCTC 23483T = JCM 17729T).


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.


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