Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks

Parasitology ◽  
2018 ◽  
Vol 145 (14) ◽  
pp. 1969-1978 ◽  
Author(s):  
M. Buysse ◽  
O. Duron
Keyword(s):  
Tick Species ◽  
Phylogenetic Analyses ◽  
High Specificity ◽  
Housekeeping Genes ◽  
Limited Range ◽  
Evolutionary Strategies ◽  
Rrna Gene ◽  
Typing Method ◽  
History Of ◽  
Horizontal Transfers

AbstractCandidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria–tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.

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.

scholarly journals Bacterial Canker Disease on Populus × euramericana Caused by Lonsdalea populi in Serbia

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1080
Author(s):  
Milica Zlatković ◽  
Imola Tenorio-Baigorria ◽  
Tamás Lakatos ◽  
Tímea Tóth ◽  
András Koltay ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Test Chamber ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Bacterial Canker ◽  
Canker Disease ◽  
Populus Euramericana ◽  
First Report ◽  
Eastern Cottonwood

Populus × euramericana (Dode) Guinier clone (cl.) “I-214” is a fast-growing interspecific hybrid between Eastern cottonwood (P. deltoides Bartr. ex Marsh) and European black poplar (Populus nigra L.). Populus × euramericana was introduced into Serbia in the 1950s and has become one of the most widely grown poplar species. In September 2019, cankers were observed on stems and branches of P. × euramericana cl. “I-214” trees in a two-year-old poplar plantation in the province of Vojvodina, Serbia. The canker tissue was soft and watery, and a colorless fluid that smelled rotten flowed from the cracks in the bark, suggesting possible bacterial disease. After two weeks, diseased trees experienced crown die-back and oozing of foamy, odorous exudates and this study aimed to identify the causal agent of the disease. Canker margins and exudates were collected from 20 symptomatic trees. The associated bacterium was isolated and identified using biochemical characteristics, phylogenetic analyses based on 16S rRNA gene sequences, and multilocus sequence analyses (MLSA) based on partial sequencing of three housekeeping genes (gyrB, infB, and atpD). The pathogen was identified as Lonsdalea populi. Pathogenicity tests were conducted on rooted cuttings of P. × euramericana cl. “I-214” in an environmental test chamber and demonstrated that the isolated bacterial strain was able to reproduce symptoms of softened, water-soaked cankers and exudation. To the best of our knowledge, this is the first report of L. populi causing bacterial canker disease on P. × euramericana cl. “I-214” in Serbia and in southeastern Europe (SEE). It is also the first report of a bacterial disease on hybrid poplars, including P. × euramericana in this country and in SEE. If the disease spreads into new areas, selection for L. populi resistance may need to be integrated into future poplar breeding programs.

scholarly journals Bradyrhizobium ingae sp. nov., isolated from effective nodules of Inga laurina grown in Cerrado soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3395-3401 ◽  
Author(s):  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Luc F. M. Rouws ◽  
Eliane N. C. Farias ◽  
Marco A. O. dos Santos ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Slow Growth Rate ◽  
Link Type ◽  
Commercial Inoculant

Root-nodule bacteria were isolated from Inga laurina (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250T, BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus Bradyrhizobium . Phylogenetic analyses of sequences of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T to be the closest type strain (97.4 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C16 : 0 and summed feature 8 (C18 : 1ω6c/C18 : 1ω7c)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus Bradyrhizobium . Results from DNA–DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus Bradyrhizobium with validly published names. Sequences of symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped together with those of B. iriomotense EK05T and Bradyrhizobium sp. strains BR 6610 (used as a commercial inoculant for Inga marginata in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name Bradyrhizobium ingae sp. nov. is proposed. The type strain is BR 10250T ( = HAMBI 3600T).

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 Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa

2020 ◽  
Vol 70 (3) ◽  
pp. 1720-1728 ◽  
Author(s):  
Anusha Rai ◽  
Smita N ◽  
Suresh G ◽  
Shabbir A ◽  
Deepshikha G ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Western Ghats Of India

A Gram-stain-negative, non-motile, coccoid-shaped, catalase- and oxidase-positive, non-denitrifying, neutrophilic bacterium designated as strain JC501T was isolated from an epiphytic rhizosphere of an orchid, Aerides maculosa, growing in the Western Ghats of India. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain JC501T belonged to the genus Paracoccus and had the highest levels of sequence identity with Paracoccus marinus KKL-A5T (98.9 %), Paracoccus contaminans WPAn02T (97.3 %) and other members of the genus Paracoccus (<97.3 %). Strain JC501T produced indole-3 acetic acid and other indole derivatives from tryptophan. The dominant respiratory quinone was Q-10 and the major fatty acid was C18 : 1ω7c/C18 : 1ω6c, with significant quantities of C18 : 1ω9c, C17 : 0 and C16 : 0. The polar lipids of strain JC501T comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, two unidentified aminolipids, two unidentified lipids and four unidentified phospholipids. The genome of strain JC501T was 3.3 Mbp with G+C content of 69.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of eight housekeeping genes. Based on the results of phylogenetic analyses, low (<85.9 %) average nucleotide identity, digital DNA–DNA hybridization (<29.8 %), chemotaxonomic analysis and physiological properties, strain JC501T could not be classified into any of the recognized species of the genus Paracoccus . Strain JC501T represents a novel species, for which the name Paracoccus aeridis sp. nov. is proposed. The type strain is JC501T (=LMG 30532T=NBRC 113644T).

scholarly journals Gimesia chilikensis sp. nov., a haloalkali-tolerant planctomycete isolated from Chilika lagoon and emended description of the genus Gimesia

2020 ◽  
Vol 70 (6) ◽  
pp. 3647-3655 ◽  
Author(s):  
Dhanesh Kumar ◽  
Kumar Gaurav ◽  
Sreya PK ◽  
Shabbir A. ◽  
Jagadeeshwari Uppada ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Nitrogen Sources ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Chilika Lagoon ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, non-motile, salt- and alkali-tolerant, pear to oval shaped, rosette-forming, white coloured, bacterium, designated as strain JC646T, was isolated from a sediment sample collected from Chilika lagoon, India. Strain JC646T reproduced through budding, grew well at up to pH 9.0 and tolerated up to 7 % NaCl. Strain JC 646T utilized α-d-glucose, fumarate, lactose, sucrose, fructose, d-galactose, mannose, maltose and d-xylose as carbon sources. Peptone, l-isoleucine, l-serine, l-lysine, l-glutamic acid, l-aspartic acid, dl-threonine and l-glycine were used by the strain as nitrogen sources for growth. The respiratory quinone was MK6. Major fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The polar lipids of strain JC646T comprised phosphatidyl-dimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified amino lipid and two unidentified lipids. Strain JC646T had highest (97.3 %) 16S rRNA gene sequence identity to the only species of the genus Gimesia , Gimesia maris DSM 8797T. The genome of strain JC646T was 7.64 Mbp with a DNA G+C content of 53.2 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 housekeeping genes. Based on phylogenetic analyses, digital DNA–DNA hybridization (19.0 %), genome average nucleotide identity (74.5 %) and average amino acid identity/percentageof conserved proteins (77 %) results, chemotaxonomic characteristics, and differential physiological properties, strain JC646T is recognized as representing a new species of the genus Gimesia , for which we propose the name Gimesia chilikensis sp. nov. The type strain is JC646T (=KCTC 72175T=NBRC 113881T).

scholarly journals Yersinia pekkanenii sp. nov.

2011 ◽  
Vol 61 (10) ◽  
pp. 2363-2367 ◽  
Author(s):  
Anna Murros-Kontiainen ◽  
Per Johansson ◽  
Taina Niskanen ◽  
Maria Fredriksson-Ahomaa ◽  
Hannu Korkeala ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Yersinia Pseudotuberculosis ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Taxonomic Approach ◽  
Phenotypic Tests ◽  
Encoding Genes ◽  
The 16S Rrna Gene

The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA–DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA–DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7.1KOH2T ( = DSM 22769T  = LMG 25369T).

scholarly journals Halomonas vilamensis sp. nov., isolated from high-altitude Andean lakes

2011 ◽  
Vol 61 (5) ◽  
pp. 1211-1217 ◽  
Author(s):  
Rodolfo Javier Menes ◽  
Claudia Elizabeth Viera ◽  
María Eugenia Farías ◽  
Manfredo J. Seufferheld
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Limited Range ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (SV325T) was isolated from the sediment of a hypersaline lake located 4600 m above sea level (Laguna Vilama, Argentina). Strain SV325T formed cream to pink colonies, was motile and moderately halophilic, and tolerated NaCl concentrations of 1–25 % (w/v) with an optimum of 5–10 % (w/v). Growth occurred at 5–40 °C (optimum around 30 °C) and at pH 5.0–10.0 (optimum 7.0–8.0). The bacterium did not produce exopolysaccharides and stained positively for intracellular polyphosphate granules but not for poly-β-hydroxyalkanoates. It produced catalase and oxidase, reduced nitrate to nitrite, hydrolysed gelatin, did not produce acids from sugars and utilized a limited range of substrates as carbon and energy sources: acetate, caproate, fumarate, dl-β-hydroxybutyrate, malate, maleate, malonate and succinate. The predominant ubiquinones were Q-9 (92.5 %) and Q-8 (7.5 %), the major fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C17 : 0 cyclo and C16 : 1ω7c/iso-C15:0 2-OH, and the DNA G+C content was 55.0 mol%. Phylogenetic analyses based on the 16S rRNA gene indicated that strain SV325T belongs to the genus Halomonas in the class Gammaproteobacteria. Physiological and biochemical tests allowed phenotypic differentiation of strain SV325T from closely related species with validly published names. We therefore propose a novel species, Halomonas vilamensis sp. nov., with type strain SV325T ( = DSM 21020T  = LMG 24332T).

scholarly journals Vibrio atlanticus sp. nov. and Vibrio artabrorum sp. nov., isolated from the clams Ruditapes philippinarum and Ruditapes decussatus

2011 ◽  
Vol 61 (10) ◽  
pp. 2406-2411 ◽  
Author(s):  
Ana L. Diéguez ◽  
Roxana Beaz-Hidalgo ◽  
Ilse Cleenwerck ◽  
Sabela Balboa ◽  
Paul de Vos ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Ruditapes Philippinarum ◽  
Rrna Gene ◽  
Ruditapes Decussatus ◽  
Well Differentiated ◽  
Type Strains

Facultatively anaerobic marine bacteria isolated from cultured clams, Ruditapes decussatus and Ruditapes philippinarum, were previously investigated using amplified fragment length polymorphism (AFLP) and 16S rRNA gene sequence analyses. The isolates formed two AFLP clusters and belonged to the genus Vibrio, more precisely to the Splendidus clade. In this study, phylogenetic analyses based on sequences of the housekeeping genes rpoA, rpoD, pyrH, atpA and recA supported their inclusion in that clade forming two well differentiated groups with respect to the rest of the species within the clade, and confirmed that they formed two groups, separated from the rest of the species of the clade. DNA–DNA hybridization demonstrated that the isolates constitute two novel species of the genus Vibrio, which can be phenotypically differentiated from their closest relatives. The names Vibrio atlanticus sp. nov. and Vibrio artabrorum sp. nov. are proposed, with Vb 11.11T ( = CECT 7223T  = LMG 24300T) and Vb 11.8T ( = CECT 7226T  = LMG 23865T) as the type strains, respectively.

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.

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