scholarly journals Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum

2007 ◽  
Vol 57 (3) ◽  
pp. 588-593 ◽  
Author(s):  
Seo-Youn Jung ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

Two Gram-positive, non-motile, yellow-pigmented, slightly curved and rod-shaped bacterial strains, UMS-62T and UMS-101, were isolated from the rhizosphere of Allium victorialis var. platyphyllum, a variety of wild edible greens grown on Ulleung island, Korea. The taxonomic position of the strains was investigated by a polyphasic approach. Strains UMS-62T and UMS-101 grew optimally at 30 °C and at pH 6.5–7.5. The novel strains contained MK-11 and MK-12 as the predominant menaquinones and rhamnose, ribose and galactose as the major cell-wall sugars. The major cellular fatty acids (>10 % of the total fatty acids) were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C contents were 71.1–71.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strains UMS-62T and UMS-101 belong to the genus Agromyces. Strains UMS-62T and UMS-101 showed a 16S rRNA gene sequence similarity value of 99.9 % and a mean DNA–DNA relatedness level of 91.1 %. Similarity values between the 16S rRNA gene sequences of the two novel strains and the type strains of recognized Agromyces species ranged from 95.2 to 99.1 %. The levels of DNA–DNA relatedness between the two novel strains and the type strains of five phylogenetically related Agromyces species were in the range of 13.4 to 54.2 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain UMS-62T (=KCTC 19181T=JCM 13584T) and strain UMS-101 are classified as representing a novel species in the genus Agromyces, for which the name Agromyces allii sp. nov. is proposed.

2007 ◽  
Vol 57 (10) ◽  
pp. 2284-2288 ◽  
Author(s):  
Seo-Youn Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

Two Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1 ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).


2006 ◽  
Vol 56 (3) ◽  
pp. 613-617 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh

Two Gram-negative, rod-shaped bacterial strains, KSL-102T and KSL-110, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by use of a polyphasic study. The two strains grew optimally at pH 7·0–8·0 and 30 °C without NaCl. They contained Q-10 as the predominant ubiquinone. The major fatty acids were C18 : 1 ω7c and C16 : 0 on trypticase soy agar, but 11-methyl C18 : 1 ω7c was also a major component when the two strains were cultivated on LMG medium no. 221. Their DNA G+C contents were 68·4–68·7 mol%. Strains KSL-102T and KSL-110 exhibited three nucleotide differences in their 16S rRNA gene sequences and a mean DNA–DNA relatedness value of 85 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the two strains fell within the evolutionary radiation encompassed by the genus Brevundimonas. Levels of 16S rRNA gene sequence similarity between the two strains and the type strains of recognized Brevundimonas species ranged from 96·3 to 98·4 %. DNA–DNA relatedness levels between the two strains and recognized Brevundimonas species were 8–21 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-102T and KSL-110 were classified in the genus Brevundimonas as members of a novel species, for which the name Brevundimonas kwangchunensis sp. nov. is proposed. The type strain is KSL-102T (=KCTC 12380T=DSM 17033T).


2005 ◽  
Vol 55 (4) ◽  
pp. 1611-1614 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh

Three Gram-positive, rod- or coccoid-shaped bacterial strains, KSL-2T, KSL-5 and KSL-6, were isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomical analysis. These isolates grew optimally at pH 9·0 and 30 °C. They were characterized chemotaxonomically as having cell wall peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. The DNA G+C content of the isolates was 73–74 mol%. Strains KSL-2T, KSL-5 and KSL-6 were identical in their 16S rRNA gene sequences and exhibited DNA–DNA relatedness values of 88–93 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the three isolates fell within the evolutionary radiation encompassed by the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species ranged from 93·6 % (with Nocardioides albus) to 97·2 % (with Nocardioides aquiterrae). DNA–DNA relatedness levels between the three isolates and N. aquiterrae CJ-14T were 8–15 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-2T, KSL-5 and KSL-6 were classified in the genus Nocardioides as members of a novel species for which the name Nocardioides kribbensis sp. nov. is proposed, with KSL-2T (=KCTC 19038T=DSM 16314T) as the type strain.


2004 ◽  
Vol 54 (4) ◽  
pp. 1177-1184 ◽  
Author(s):  
Irene Wagner-Döbler ◽  
Holger Rheims ◽  
Andreas Felske ◽  
Aymen El-Ghezal ◽  
Dirk Flade-Schröder ◽  
...  

A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97·4 % sequence similarity to Sulfitobacter mediterraneus and 96·5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1–7 % sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25–30 °C. The DNA base composition (G+C content) is 60·1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1ω7c, 18 : 0, 16 : 1ω7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7 %) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1ω7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).


2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh

Two Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.


2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2662-2668 ◽  
Author(s):  
Rosa Margesin ◽  
Cathrin Spröer ◽  
De-Chao Zhang ◽  
Hans-Jürgen Busse

The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12T and Cr4-35T, were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12T and Cr4-35T were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas . Although the 16S rRNA gene sequences of strains Cr4-12T and Cr4-35T were very similar (98.7 % sequence similarity), hybridizations indicated a DNA–DNA relatedness value of only 26.9 % between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12T and Cr4-35T showed 16S rRNA gene sequence similarities of 96.4–98.5 % and 96.5–98.4 %, respectively. Based on the phenotypic and phylogenetic evidence and DNA–DNA relatedness data, strains Cr4-12T and Cr4-35T represent two novel species within the genus Polaromonas , for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12T ( = DSM 24062T  = LMG 26049T  = KACC 15089T) and that of Polaromonas cryoconiti sp. nov. is Cr4-35T ( = DSM 24248T  = LMG 26050T  = KACC 15090T).


2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4873-4879 ◽  
Author(s):  
Sooyeon Park ◽  
Sona Kim ◽  
Chul-Hyung Kang ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, motile, aerobic and rod-shaped bacterium, designated HJM-18T, was isolated from the place where the ocean and a freshwater lake meet at Hwajinpo, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HJM-18T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain HJM-18T belonged to the genus Marinobacter. Strain HJM-18T exhibited 16S rRNA gene sequence similarity values of 97.05–98.22 % to the type strains of Marinobacter algicola, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter salarius, Marinobacter salsuginis, Marinobacter guineae and Marinobacter gudaonensis and of 93.21–96.98 % to the type strains of the other species of the genus Marinobacter. Strain HJM-18T contained Q-9 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω9c as the major fatty acids. The major polar lipids detected in strain HJM-18T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminophospholipid. The DNA G+C content was 58 mol% and the mean DNA–DNA relatedness values with the type strains of the seven phylogenetically related species of the genus Marinobacter were 10–27 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain HJM-18T is separated from recognized species of the genus Marinobacter. On the basis of the data presented, strain HJM-18T represents a novel species of the genus Marinobacter, for which the name Marinobacter confluentis sp. nov. is proposed. The type strain is HJM-18T ( = KCTC 42705T = NBRC 111223T).


2005 ◽  
Vol 55 (4) ◽  
pp. 1635-1639 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh

Two Gram-negative, rod-shaped, non-motile bacterial strains, MSS-170T and MSS-171, were isolated from sea water of a marine solar saltern of the Yellow Sea, Korea, and characterized by using a polyphasic taxonomic approach. The two isolates grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. They were characterized chemotaxonomically as having MK-7 as the predominant menaquinone and major amounts of fatty acids iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of each of the two strains was 42 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the evolutionary radiation enclosed by the genus Algoriphagus. Strains MSS-170T and MSS-171 had identical 16S rRNA gene sequences and exhibited a mean DNA–DNA relatedness level of 93 %. The two strains exhibited 16S rRNA gene sequence similarity levels of 96·4–98·9 % with respect to the type strains of recognized Algoriphagus species. DNA–DNA relatedness levels between the two strains and the type strains of six Algoriphagus species were less than 35 %. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains MSS-170T and MSS-171 were classified in the genus Algoriphagus as members of a novel species, for which the name Algoriphagus locisalis sp. nov. is proposed. The type strain is MSS-170T (=KCTC 12310T=JCM 12597T).


2011 ◽  
Vol 61 (7) ◽  
pp. 1572-1578 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vasily I. Svetashev ◽  
Valery V. Mikhailov

Two Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3T (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7–95.1 and 95.8–95.2 %), Phaeobacter (95.0–94.2 and 95.1–94.2 %) and Thalassobius (96.3–94.8 and 96.2–94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018T were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018T were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018T represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018T ( = NRIC 0784T  = JCM 16874T).


2011 ◽  
Vol 61 (7) ◽  
pp. 1511-1514 ◽  
Author(s):  
Yochan Joung ◽  
Sung-Heun Cho ◽  
Haneul Kim ◽  
Seung Bum Kim ◽  
Kiseong Joh

A non-motile, red-pigmented bacterium, designated strain HMD1010T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010T formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C16 : 1ω5c (21.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %), iso-C15 : 0 (14.5 %) and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010T ( = KCTC 22745T  = CECT 7546T).


Sign in / Sign up

Export Citation Format

Share Document