scholarly journals A novel subgroup 16SrVII-D phytoplasma identified in association with erigeron witches' broom

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2761-2765 ◽  
Author(s):  
Daniela Flôres ◽  
Ana Paula de Oliveira Amaral Mello ◽  
Thays Benites Camargo Pereira ◽  
Jorge Alberto Marques Rezende ◽  
Ivan Paulo Bedendo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rrna Gene ◽  
Phytoplasma Strain ◽  
Total Dna ◽  
Virtual Rflp ◽  
The 16S Rrna Gene

Erigeron sp. plants showing symptoms of witches' broom and stunting were found near orchards of passion fruit in São Paulo state, Brazil. These symptoms were indicative of infection by phytoplasmas. Thus, the aim of this study was to detect and identify possible phytoplasmas associated with diseased plants. Total DNA was extracted from symptomatic and asymptomatic plants and used in nested PCR conducted with the primer pairs P1/Tint and R16F2n/16R2. Amplification of genomic fragments of 1.2 kb from the 16S rRNA gene confirmed the presence of phytoplasma in all symptomatic samples. The sequence identity scores between the 16S rRNA gene of the phytoplasma strain identified in the current study and those of previously reported ‘Candidatus Phytoplasma fraxini’-related strains ranged from 98 % to 99 % indicating the phytoplasma to be a strain affiliated with ‘Candidatus Phytoplasma fraxini’. The results from a phylogenetic analysis and virtual RFLP analysis of the 16S rRNA gene sequence with 17 restriction enzymes revealed that the phytoplasma strain belongs to the ash yellows phytoplasma group (16SrVII); the similarity coefficient of RFLP patterns further suggested that the phytoplasma represents a novel subgroup, designated 16SrVII-D. The representative of this new subgroup was named EboWB phytoplasma (Erigeron bonariensis Witches' Broom).

scholarly journals Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis

2010 ◽  
Vol 60 (4) ◽  
pp. 938-943 ◽  
Author(s):  
Eun Ju Choi ◽  
Hak Cheol Kwon ◽  
Young Chang Sohn ◽  
Hyun Ok Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Asterias Amurensis ◽  
Light Yellow ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel marine bacterium, strain KMD 001T, was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001T was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001T represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001T is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001T shows similarities of approximately 91.8–94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001T is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. Strain KMD 001T should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001T (=KCCM 90076T =JCM 15607T).

Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga–Flavobacterium–Bacteroides group bacterium from an Hawaiian hypersaline lake

2004 ◽  
Vol 54 (3) ◽  
pp. 935-940 ◽  
Author(s):  
Stuart P. Donachie ◽  
John P. Bowman ◽  
Maqsudul Alam
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Tetradecanoic Acid ◽  
Antarctic Sea Ice ◽  
The 16S Rrna Gene

A Gram-negative bacterium designated LA1T was isolated from water collected in hypersaline Lake Laysan on Laysan Island in the Northwestern Hawaiian Islands. Cells occurred singly as fine rods to short filaments. Growth in 50 % strength marine broth occurred optimally when the medium contained 7·5–10 % (w/v) NaCl. The major fatty acids in LA1T grown at 15 and 30 °C were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. The nucleotide sequence of the 16S rRNA gene showed that LA1T belonged in the Cytophaga–Flavobacterium–Bacteroides (CFB) group in the domain Bacteria. The closest described neighbour in terms of 16S rRNA gene sequence identity was Psychroflexus torquis ACAM 623T (94·4 % over 1423 bases), an obligate psychrophile from Antarctic sea-ice. The G+C content of 35·0 mol% was consistent with this affiliation. Phenotypic and genotypic analyses, including DNA hybridization, indicated that LA1T could be assigned to the genus Psychroflexus but, based on significant differences, including growth at 43 °C, it constitutes a novel species, Psychroflexus tropicus sp. nov., for which LA1T (=ATCC BAA-734T=DSM 15496T) is the type strain.

scholarly journals Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India

2006 ◽  
Vol 56 (12) ◽  
pp. 2765-2770 ◽  
Author(s):  
Preeti Chaturvedi ◽  
S. Shivaji
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Rrna Gene Sequence ◽  
Alkaliphilic Bacterium ◽  
The 16S Rrna Gene

Strain HHS 31T, a Gram-positive, motile, rod-shaped, non-spore-forming, alkaliphilic bacterium, was isolated from the melt water of a glacier. Phenotypic and chemotaxonomic characteristics indicate that strain HHS 31T is related to species of the genus Exiguobacterium. The 16S rRNA gene sequence similarities between HHS 31T and strains of known species confirm that it is closely related to members of the genus Exiguobacterium (93–99 %) and that it exhibits >97 % similarity with Exiguobacterium acetylicum DSM 20416T (98.9 %), Exiguobacterium antarcticum DSM 14480T (98.0 %), Exiguobacterium oxidotolerans JCM 12280T (97.9 %) and Exiguobacterium undae DSM 14481T (97.4 %). Phylogenetic analysis based on the 16S rRNA gene sequence further confirms the affiliation of HHS 31T with the genus Exiguobacterium. However, the levels of DNA–DNA relatedness between HHS 31T and E. oxidotolerans JCM 12280T, E. acetylicum DSM 20416T, E. undae DSM 14481T and E. antarcticum DSM 14480T are 50, 63, 67 and 28 %, respectively. Strain HHS 31T also differs from these four closely related species in terms of a number of phenotypic traits. The phenotypic, chemotaxonomic and phylogenetic data suggest that HHS 31T merits the status of a novel species, for which the name Exiguobacterium indicum sp. nov. is proposed. The type strain is HHS 31T (=LMG 23471T=IAM 15368T).

scholarly journals Classification and phylogeny of the cyanobiont Anabaena azollae Strasburger: an answered question?

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1830-1840 ◽  
Author(s):  
Ana L. Pereira ◽  
Vitor Vasconcelos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Rflp Analysis ◽  
Future Research ◽  
Rrna Gene ◽  
Anabaena Azollae ◽  
Content Type ◽  
Link Type

The symbiosis Azolla–Anabaena azollae, with a worldwide distribution in pantropical and temperate regions, is one of the most studied, because of its potential application as a biofertilizer, especially in rice fields, but also as an animal food and in phytoremediation. The cyanobiont is a filamentous, heterocystic cyanobacterium that inhabits the foliar cavities of the pteridophyte and the indusium on the megasporocarp (female reproductive structure). The classification and phylogeny of the cyanobiont is very controversial: from its morphology, it has been named Nostoc azollae, Anabaena azollae, Anabaena variabilis status azollae and recently Trichormus azollae, but, from its 16S rRNA gene sequence, it has been assigned to Nostoc and/or Anabaena , and from its phycocyanin gene sequence, it has been assigned as non-Nostoc and non-Anabaena. The literature also points to a possible co-evolution between the cyanobiont and the Azolla host, since dendrograms and phylogenetic trees of fatty acids, short tandemly repeated repetitive (STRR) analysis and restriction fragment length polymorphism (RFLP) analysis of nif genes and the 16S rRNA gene give a two-cluster association that matches the two-section ranking of the host (Azolla). Another controversy surrounds the possible existence of more than one genus or more than one species strain. The use of freshly isolated or cultured cyanobionts is an additional problem, since their morphology and protein profiles are different. This review gives an overview of how morphological, chemical and genetic analyses influence the classification and phylogeny of the cyanobiont and future research.

scholarly journals RFLP analysis of a PCR-amplified fragment of the 16S rRNA gene as a tool to identify Enterococcus strains

2009 ◽  
Vol 104 (7) ◽  
pp. 1003-1008 ◽  
Author(s):  
EMD Scheidegger ◽  
SAP Fracalanzza ◽  
LM Teixeira ◽  
P Cardarelli-Leite
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils

2005 ◽  
Vol 55 (5) ◽  
pp. 1985-1989 ◽  
Author(s):  
Angel Valverde ◽  
Encarna Velázquez ◽  
Félix Fernández-Santos ◽  
Nieves Vizcaíno ◽  
Raúl Rivas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Trifolium Pratense ◽  
Lupinus Albus ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

Bacterial strain PETP02T was isolated from nodules of Trifolium pratense growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene sequence showed that this strain represents a member of the genus Phyllobacterium. However, divergence found with the 16S rRNA gene sequence of the single recognized species of this genus, Phyllobacterium myrsinacearum, indicated that strain PETP02T belongs to a different species. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium trifolii sp. nov. is proposed. The type strain is PETP02T (=LMG 22712T=CECT 7015T). This strain was strictly aerobic and used several carbohydrates as carbon source. It was not able to reduce nitrate. Aesculin hydrolysis was negative. It did not produce urease, arginine dihydrolase, gelatinase or β-galactosidase. The DNA G+C content was 56·4 mol%. The nodD gene of this strain showed a sequence closely related to those of strains able to nodulate Lupinus. Infectivity tests showed that this strain is able to produce nodules in both Trifolium repens and Lupinus albus.

scholarly journals Salinisphaera dokdonensis sp. nov., isolated from surface seawater

2010 ◽  
Vol 60 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Gi Duk Bae ◽  
Chung Yeon Hwang ◽  
Hye Min Kim ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).

Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 208-211 ◽  
Author(s):  
Lourdes Martínez-Aguilar ◽  
Jesús Caballero-Mellado ◽  
Paulina Estrada-de los Santos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T  = DSM 15562T  = CIP 108892T).

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