scholarly journals Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea

2004 ◽  
Vol 54 (6) ◽  
pp. 2231-2235 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Unsaturated Fatty Acids ◽  
Sea Water ◽  
East Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
The 16S Rrna Gene

Two Gram-negative, motile, non-spore-forming, bacteriochlorophyll a-containing slightly halophilic strains, SW-132T and SW-158, were isolated from sea water of the East Sea in Korea, and subjected to a polyphasic taxonomic study. The two isolates were characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and major amounts of unsaturated fatty acids C18 : 1 ω7c and C17 : 1 ω6c. The DNA G+C contents of the two strains were in the range 66·8–65·9 mol%. The 16S rRNA gene sequences of strains SW-132T and SW-158 were 99·9 % (1 nt difference) similar and their mean level of DNA–DNA relatedness was 86 %. The 16S rRNA gene sequence analysis showed that strains SW-132T and SW-158 are phylogenetically closely related to Porphyrobacter species and Erythromicrobium ramosum. Similarities between the 16S rRNA gene sequences of strains SW-132T and SW-158 and the type strains of Porphyrobacter species and E. ramosum ranged from 97·8 to 99·0 %. DNA–DNA relatedness data indicated that strains SW-132T and SW-158 are members of a genomic species that is separate from the four Porphyrobacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains SW-132T (=KCTC 12229T=DSM 16220T) and SW-158 (=KCTC 12230) are classified as a novel Porphyrobacter species, for which the name Porphyrobacter donghaensis sp. nov. is proposed.

scholarly journals Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo

2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

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.

Rheinheimera aquimaris sp. nov., isolated from seawater of the East Sea in Korea

2007 ◽  
Vol 57 (7) ◽  
pp. 1386-1390 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soon Ei Park ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
East Sea ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Dna Relatedness

Two Gram-negative, motile, non-spore-forming bacterial strains, SW-353T and SW-369, were isolated from seawater from the East Sea, Korea, and their taxonomic positions were investigated by means of a polyphasic study. Strains SW-353T and SW-369 grew optimally at 30–37 °C and pH 7.0–8.0. Strains SW-353T and SW-369 contained Q-8 as the predominant ubiquinone and contained C16 : 0, C18 : 1 ω7c and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C contents were 50.1 and 50.5 mol%. Strains SW-353T and SW-369 exhibited no differences in their 16S rRNA gene sequences and showed a mean DNA–DNA relatedness level of 91 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-353T and SW-369 belong to the genus Rheinheimera. Similarity values between the 16S rRNA gene sequences of the two isolates and the type strains of the recognized Rheinheimera species were in the range 96.6–97.9 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strains SW-353T and SW-369 differ from the recognized Rheinheimera species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strains SW-353T and SW-369 represent a novel species of the genus Rheinheimera, for which the name Rheinheimera aquimaris sp. nov. is proposed. The type strain is SW-353T (=KCTC 12840T=JCM 14331T).

scholarly journals Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea

2004 ◽  
Vol 54 (6) ◽  
pp. 1981-1985 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sea Water ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains

Three Gram-negative, non-motile, non-spore-forming, slightly halophilic rods (strains SW-110T, SW-116 and SW-140) were isolated from sea water of a tidal flat of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. The three isolates did not produce bacteriochlorophyll a and were characterized chemotaxonomically by having ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. The DNA G+C content of the three isolates was between 62·2 and 62·9 mol%. Strains SW-110T, SW-116 and SW-140 showed no difference in their 16S rRNA gene sequences, and their mean level of DNA–DNA relatedness was 94·8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that the three strains form a distinct phylogenetic lineage within the cluster comprising Erythrobacter species. Similarities between the 16S rRNA gene sequences of strains SW-110T, SW-116 and SW-140 and the type strains of Erythrobacter species ranged from 98·4 % (with Erythrobacter longus) to 97·7 % (with Erythrobacter flavus). Levels of DNA–DNA relatedness between strains SW-110T, SW-116 and SW-140 and the type strains of all recognized Erythrobacter species were in the range 5·3–12·7 %. On the basis of polyphasic taxonomic data, strains SW-110T, SW-116 and SW-140 were classified as a novel Erythrobacter species, for which the name Erythrobacter aquimaris sp. nov. is proposed. The type strain is SW-110T (=KCCM 41818T=JCM 12189T).

scholarly journals Nitratireductor aquimarinus sp. nov., isolated from a culture of the diatom Skeletonema costatum, and emended description of the genus Nitratireductor

2011 ◽  
Vol 61 (11) ◽  
pp. 2676-2681 ◽  
Author(s):  
Gwang Il Jang ◽  
Chung Yeon Hwang ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Skeletonema Costatum ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
The 16S Rrna Gene

Two Gram-negative-staining, aerobic bacterial strains, designated CL-SC21T and CL-SC22, were isolated from a culture of the diatom Skeletonema costatum (Korean Marine Microalgae Culture Center, KMMCC strain B-396) established from the East Sea, Korea. The two novel strains shared 99.9 % 16S rRNA gene sequence similarity. Analysis of the 16S rRNA gene sequences showed an affiliation with the genus Nitratireductor, with the strains sharing 96.5–97.5 % similarity with the type strains of recognized species of the genus Nitratireductor and being most closely related to Nitratireductor aquibiodomus NL21T. Phylogenetic analyses of the 16S rRNA gene sequences showed that strain CL-SC21T together with strain CL-SC22 belonged to the genus Nitratireductor and formed a robust clade among closely related Nitratireductor species. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid, an unidentified phospholipid and five unidentified lipids. Ubiquinone 10 was the major quinone. The major cellular fatty acids of strains CL-SC21T and CL-SC22 were C18 : 1ω7c (70.6–72.3 %) and C19 : 0ω8c cyclo (10.9–11.8 %). The genomic DNA G+C contents of strains CL-SC21T and CL-SC22 were 56.7 and 57.1 mol%, respectively. The level of DNA–DNA relatedness between strains CL-SC21T and CL-SC22 was 86 % (reciprocal 91 %), indicating that the two isolates represented a single species. However, levels of DNA–DNA relatedness between N. aquibiodomus NL21T and strains CL-SC21T and CL-SC22 were 28 % (reciprocal 45 %) and 25 % (reciprocal 50 %), respectively. Phylogenetic analysis and the results of biochemical tests showed that strains CL-SC21T and CL-SC22 were different from all recognized species of the genus Nitratireductor. Thus, strains CL-SC21T and CL-SC22 represent a novel species of the genus Nitratireductor, for which the name Nitratireductor aquimarinus sp. nov. is proposed. The type strain is CL-SC21T ( = KCCM 90090T = JCM 17288T).

scholarly journals Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

scholarly journals Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow’s milk

2012 ◽  
Vol 62 (2) ◽  
pp. 322-329 ◽  
Author(s):  
William J. Wolfgang ◽  
An Coorevits ◽  
Jocelyn A. Cole ◽  
Paul De Vos ◽  
Michelle C. Dickinson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New York State ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clinical Specimens ◽  
The 16S Rrna Gene

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T  = DSM 23544T  = CCUG 59649T  = LMG 26022T) is proposed.

scholarly journals ‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1890-1899 ◽  
Author(s):  
Nigel A. Harrison ◽  
Robert E. Davis ◽  
Carlos Oropeza ◽  
Ericka E. Helmick ◽  
María Narváez ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cocos Nucifera ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Lethal Yellowing ◽  
The 16S Rrna Gene

In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus Phytoplasma ’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus Phytoplasma ’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.

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