scholarly journals 'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

2020 ◽  
Author(s):  
Kiran Kirdat ◽  
Bhavesh Tiwarekar ◽  
Vipool Thorat ◽  
Shivaji Sathe ◽  
Yogesh Shouche ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Phytoplasma Strain ◽  
White Leaf

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

Yonghaparkia Aerolata sp. nov., a Novel Member of the Genus Yonghaparkia, Isolated From Electronic Waste Associated Bioaerosols

2021 ◽  
Author(s):  
Yimin Pan ◽  
Qiaoqiao Ren ◽  
Lingyun Chen ◽  
Yunxia Jiang ◽  
Jiguo Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Electronic Waste ◽  
Draft Genome ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Actinomycete Strain

Abstract A Gram-positive, non-motile, non-spore-forming and short rod-shaped actinomycete strain, designated GA224T, was isolated from an electronic waste associated bioaerosols. The isolate is facultatively anaerobic, which is able to grow at 25–40 ℃ (optimum 37 ℃) and pH 6.5–8.5 (optimum 8.0). The diamino acid in the cell wall of strain GA224T is 2,4-diaminobutyric acid (DAB), while major menaquinone is MK-12. The polar lipid profile is composed of diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unidentified lipid. The major cellular fatty acid is anteiso-C15:0 and iso-C16:0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GA224T fell within the genus Yonghaparkia, the highest 16S rRNA gene sequence similarity values (98.60%) being obtained with respect to Yonghaparkia alkaliphile KSL-113T. The draft genome of strain GA224T comprised 2,495,189 bp with a G+C content of 72.17 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain GA224T and phylogenetically related Yonghaparkia species were lower than 95% and 70%, respectively. Based on the phenotypic, chemotaxonomic and genomic data, strain GA224T represents a novel species, for which the name Yonghaparkia aerolata sp. nov. is proposed, with GA224T as the type strain (= GDMCC 1.2165T = JCM 34462T).

scholarly journals Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7

2012 ◽  
Vol 194 (18) ◽  
pp. 5147-5148 ◽  
Author(s):  
Steven D. Brown ◽  
Mircea Podar ◽  
Dawn M. Klingeman ◽  
Courtney M. Johnson ◽  
Zamin K. Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Sequence ◽  
Type Strain ◽  
Draft Genome ◽  
Contaminated Site ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Genome Sequences ◽  
Content Type

ABSTRACTPelosinus fermentans16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of theP. fermentanstype strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.

scholarly journals Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

2011 ◽  
Vol 61 (11) ◽  
pp. 2582-2588 ◽  
Author(s):  
Fang Wang ◽  
En Tao Wang ◽  
Li Juan Wu ◽  
Xin Hua Sui ◽  
Ying Li ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7T (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570T (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA–DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T m). The type strain of R. vallis sp. nov. is CCBAU 65647T ( = LMG 25295T  = HAMBI 3073T), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

scholarly journals ‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects

2004 ◽  
Vol 54 (4) ◽  
pp. 1243-1255 ◽  
Author(s):  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Additional Species ◽  
White Leaf

The trivial name ‘phytoplasma’ has been adopted to collectively name wall-less, non-helical prokaryotes that colonize plant phloem and insects, which were formerly known as mycoplasma-like organisms. Although phytoplasmas have not yet been cultivated in vitro, phylogenetic analyses based on various conserved genes have shown that they represent a distinct, monophyletic clade within the class Mollicutes. It is proposed here to accommodate phytoplasmas within the novel genus ‘Candidatus (Ca.) Phytoplasma’. Given the diversity within ‘Ca. Phytoplasma’, several subtaxa are needed to accommodate organisms that share <97·5 % similarity among their 16S rRNA gene sequences. This report describes the properties of ‘Ca. Phytoplasma’, a taxon that includes the species ‘Ca. Phytoplasma aurantifolia’ (the prokaryote associated with witches'-broom disease of small-fruited acid lime), ‘Ca. Phytoplasma australiense’ (associated with Australian grapevine yellows), ‘Ca. Phytoplasma fraxini’ (associated with ash yellows), ‘Ca. Phytoplasma japonicum’ (associated with Japanese hydrangea phyllody), ‘Ca. Phytoplasma brasiliense’ (associated with hibiscus witches'-broom in Brazil), ‘Ca. Phytoplasma castaneae’ (associated with chestnut witches'-broom in Korea), ‘Ca. Phytoplasma asteris' (associated with aster yellows), ‘Ca. Phytoplasma mali’ (associated with apple proliferation), ‘Ca. Phytoplasma phoenicium’ (associated with almond lethal disease), ‘Ca. Phytoplasma trifolii’ (associated with clover proliferation), ‘Ca. Phytoplasma cynodontis' (associated with Bermuda grass white leaf), ‘Ca. Phytoplasma ziziphi’ (associated with jujube witches'-broom), ‘Ca. Phytoplasma oryzae’ (associated with rice yellow dwarf) and six species-level taxa for which the Candidatus species designation has not yet been formally proposed (for the phytoplasmas associated with X-disease of peach, grapevine flavescence dorée, Central American coconut lethal yellows, Tanzanian lethal decline of coconut, Nigerian lethal decline of coconut and loofah witches'-broom, respectively). Additional species are needed to accommodate organisms that, despite their 16S rRNA gene sequence being >97·5 % similar to those of other ‘Ca. Phytoplasma’ species, are characterized by distinctive biological, phytopathological and genetic properties. These include ‘Ca. Phytoplasma pyri’ (associated with pear decline), ‘Ca. Phytoplasma prunorum’ (associated with European stone fruit yellows), ‘Ca. Phytoplasma spartii’ (associated with spartium witches'-broom), ‘Ca. Phytoplasma rhamni’ (associated with buckthorn witches'-broom), ‘Ca. Phytoplasma allocasuarinae’ (associated with allocasuarina yellows), ‘Ca. Phytoplasma ulmi’ (associated with elm yellows) and an additional taxon for the stolbur phytoplasma. Conversely, some organisms, despite their 16S rRNA gene sequence being <97·5 % similar to that of any other ‘Ca. Phytoplasma’ species, are not presently described as Candidatus species, due to their poor overall characterization.

scholarly journals High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis

2020 ◽  
Vol 9 (31) ◽  
Author(s):  
Yui Sato ◽  
Juliane Wippler ◽  
Cecilia Wentrup ◽  
Tanja Woyke ◽  
Nicole Dubilier ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Species ◽  
Draft Genome ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Link Type

ABSTRACT Here, we present two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm Olavius algarvensis. Their 16S rRNA gene sequences share 98% identity with Delta3 endosymbionts of related host species Olavius ilvae (GenBank accession no. AJ620501) and Inanidrilus exumae (GenBank accession no. FM202060), for which no symbiont genomes are available.

scholarly journals Rhizobium tubonense sp. nov., isolated from root nodules of Oxytropis glabra

2011 ◽  
Vol 61 (3) ◽  
pp. 512-517 ◽  
Author(s):  
Rong Juan Zhang ◽  
Bao Chao Hou ◽  
En Tao Wang ◽  
Ying Li ◽  
Xiao Xia Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Physiological Tests

Four rhizobial strains, designated CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049, isolated from root nodules of Oxytropis glabra grown in Tibet, China, were previously defined, using amplified 16S rRNA gene restriction analysis, as a novel group within the genus Rhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. The 16S rRNA gene analysis showed that the four isolates formed a distinct phylogenetic lineage in the genus Rhizobium. The isolates showed highest sequence similarity (97.8 %) to Rhizobium indigoferae CCBAU 71042T. Phenotypic and physiological tests, DNA–DNA hybridization, phylogenetic analyses of housekeeping genes recA, atpD and glnII and fatty acid profiles also indicated that these four strains constitute a novel group distinct from recognized species of the genus Rhizobium. Based on this evidence, strains CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049 represent a novel species in the genus Rhizobium, for which the name Rhizobium tubonense sp. nov. is proposed. The type strain is CCBAU 85046T (=LMG 25225T =HAMBI 3066T) and its DNA G+C content is 59.52 mol% (T m). Strain CCBAU 85046T could form effective nodules on plant species Vigna unguiculata and Medicago sativa but not on its host of origin Oxytropis glabra.

Streptococcus troglodytidis sp. nov., isolated from a foot abscess of a chimpanzee (Pan troglodytes)

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 449-453 ◽  
Author(s):  
Michael Zhang ◽  
Lifang Yan ◽  
Guan Zhu ◽  
Michael Holifield ◽  
Donna Todd ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pan Troglodytes ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Positive Staining ◽  
Content Type ◽  
Link Type

A facultative anaerobic, non-motile, non-spore-forming, Gram-positive-staining, coccus-shaped bacterium was isolated from an abscess on the right foot of a chimpanzee (Pan troglodytes). The colonies were β-haemolytic. Catalase and oxidase activities were negative. The Lancefield group B antigen was expressed. On the basis of morphological and biochemical characteristics, the bacterium was tentatively identified as a streptococcal species. 16S rRNA gene sequence analysis indicated that the bacterium shared 96.7 %, 96.4 %, 96.1 %, 95.8 % and 95.7 % sequence similarities with Streptococcus gordonii , S. cristatus , S. intermedius , S. anginosus and S. constellatus , respectively. Phylogenetic analyses based on the sequences of the 16S rRNA gene and housekeeping genes encoding d-alanine : d-alanine ligase (ddl), the β-subunit of RNA polymerase (rpoB) and manganese-dependent superoxide dismutase (sodA) revealed that the bacterium represented a novel species closely related to, albeit different from, S. gordonii , S. cristatus and the anginosus streptococci. The name Streptococcus troglodytidis sp. nov. is proposed. The type strain is M09-11185T ( = ATCC BAA-2337T = KCTC 33006T).

scholarly journals Rufibacter hautae sp. nov., a red-pigmented bacterium from freshwater lake sediment, and proposal of Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber

2020 ◽  
Vol 70 (11) ◽  
pp. 5950-5957 ◽  
Author(s):  
Jia Zhou ◽  
Wen-Wen Ma ◽  
Jian-Hang Qu ◽  
Hai-Feng Li ◽  
Bang-Bang Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A taxonomic identification using a polyphasic approach was performed on strain NBS58-1T, which was isolated from the interfacial sediment of Taihu Lake in China. Strain NBS58-1T was Gram-stain-negative, aerobic, non-spore-forming and catalase-positive. Phylogenetic analyses based on 16S rRNA gene and three housekeeping genes (rpoB, gyrB and dnaK) sequences supported the position that strain NBS58-1T should be classified within the genus Rufibacter . The 16S rRNA gene sequence of strain NBS58-1T possessed the highest similarity to Rufibacter sediminis H-1T (96.60 %), followed by Rufibacter glacialis MDT1-10-3T (96.17 %). And the ANI value between strain NBS58-1T and R. glacialis MDT1-10-3T was 79.3 %. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids comprised iso-C15 : 0 and summed feature 3. Phosphatidylethanolamine, two unidentified phospholipids and four unidentified lipids were the main polar lipids. The genomic DNA G+C content was 51.3 mol%. Based on phenotypic features and phylogenetic position, a novel species with the name Rufibacter hautae sp. nov. is proposed. The type strain is NBS58-1T=(KACC 21309T=MCCC 1K04037T). We also proposed Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber .

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

2005 ◽  
Vol 55 (3) ◽  
pp. 1167-1170 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

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