scholarly journals Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade

2018 ◽  
Vol 200 (15) ◽  
Author(s):  
Huei-Mien Ke ◽  
Dang Liu ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi ◽  
Henryk Urbanczyk ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Analyses ◽  
Gene Gain ◽  
Marine Animals ◽  
Evolutionary Mechanisms ◽  
Closely Related Species ◽  
Content Type ◽  
Comparative Analyses ◽  
Ecological Diversification ◽  
Study Results

ABSTRACT The mechanism of bacterial speciation remains a topic of tremendous interest. To understand the ecological and evolutionary mechanisms of speciation in Vibrio bacteria, we analyzed the genomic dissimilarities between three closely related species in the so-called Harveyi clade of the genus Vibrio, V. campbellii, V. jasicida, and V. hyugaensis. The analysis focused on strains isolated from diverse geographic locations over a long period of time. The results of phylogenetic analyses and calculations of average nucleotide identity (ANI) supported the classification of V. jasicida and V. hyugaensis into two species. These analyses also identified two well-supported clades in V. campbellii; however, strains from both clades were classified as members of the same species. Comparative analyses of the complete genome sequences of representative strains from the three species identified higher syntenic coverage between genomes of V. jasicida and V. hyugaensis than that between the genomes from the two V. campbellii clades. The results from comparative analyses of gene content between bacteria from the three species did not support the hypothesis that gene gain and/or loss contributed to their speciation. We also did not find support for the hypothesis that ecological diversification toward associations with marine animals contributed to the speciation of V. jasicida and V. hyugaensis. Overall, based on the results obtained in this study, we propose that speciation in Harveyi clade species is a result of stochastic diversification of local populations, which was influenced by multiple evolutionary processes, followed by extinction events. IMPORTANCE To investigate the mechanisms underlying speciation in the genus Vibrio, we provided a well-assembled reference of genomes and performed systematic genomic comparisons among three evolutionarily closely related species. We resolved taxonomic ambiguities and identified genomic features separating the three species. Based on the study results, we propose a hypothesis explaining how species in the Harveyi clade of Vibrio bacteria diversified.

scholarly journals Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1913-1919 ◽  
Author(s):  
Luis Collado ◽  
Ronald Jara ◽  
Susana González
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Wild Bird ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Study Results

Two Gram-stain-negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter . This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0 %; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T ( = CECT 8410T = LMG 27920T).

scholarly journals Phallus haitangensis, a new species of stinkhorn from Yunnan Province, China

Phytotaxa ◽  
2016 ◽  
Vol 280 (2) ◽  
pp. 116 ◽  
Author(s):  
HUILI LI ◽  
XUELAN MA ◽  
PETER E. MORTIMER ◽  
SAMANTHA C. KARUNARATHNA ◽  
JIANCHU XU ◽  
...  
Keyword(s):  
New Species ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Yunnan Province ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequence ◽  
Closely Related Species ◽  
Line Drawings ◽  
A New Species

Four specimens of Phallus were collected during surveys in a Pinus armandii forest in Baoshan, Yunnan Province, China. Macro- and micro-characteristics, together with Internal Transcribed Spacer (ITS) sequence data, showed that the four specimens belong to a new species, here named Phallus haitangensis. The ITS phylogenetic analyses, morphological descriptions, color photographs, and line drawings are provided, and compared with closely related species in the genus.

Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.)

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3030-3035 ◽  
Author(s):  
Eu Jin Chung ◽  
Tae Soon Park ◽  
Che Ok Jeon ◽  
Young Ryun Chung
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Oryza Sativa L ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel bacterial strain, YC7001T, was isolated from the rhizosphere soil of rice collected at Jinju, Korea, and was characterized using a polyphasic approach. Cells of strain YC7001T were Gram-negative-staining, yellow-pigmented, rod-shaped, aerobic, heterotrophic and non-motile. Strain YC7001T grew optimally at 25–30 °C, pH 5.0–8.0 and degraded gelatin, cellulose and chitin. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC7001T belonged to the genus Chitinophaga in the family Chitinophagaceae . The most closely related species were Chitinophaga sancti NBRC 15057T (96.9 %), Chitinophaga ginsengisoli Gsoil 052T (95.9 %), Chitinophaga pinensis DSM 2588T (95.7 %), Chitinophaga filiformis IFO 15056T (95.7 %) and Chitinophaga niabensis JS13-10T (95.0 %). The DNA–DNA relatedness value of strain YC7001T with C. sancti NBRC 15057T was 15.2±0.6 %. Strain YC7001T contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The major fatty acids of strain YC7001T were C15 : 0 iso, C16 : 1ω5c and C17 : 0 iso 3-OH. The polar lipids were phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total genomic DNA G+C content was 41.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain YC7001T represents a novel species of the genus Chitinophaga , in the family Chitinophagaceae , for which the name Chitinophaga oryziterrae sp. nov. is proposed. The type strain is YC7001T ( = KACC 14533T = JCM 16595T).

scholarly journals Morphology of the suspensorial, jaw, and opercle musculature of Beloniformes and related species (Teleostei: Acanthopterygii), with a special reference to the m. adductor mandibulae complex

2014 ◽  
Author(s):  
Ingmar Werneburg
Keyword(s):  
Related Species ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Closely Related Species ◽  
Jaw Bones ◽  
Morphological Findings ◽  
Lower Jaw ◽  
Flying Fishes ◽  
Reduced Mobility ◽  
Jaw Musculature

The taxon Beloniformes represents a heterogeneous group of teleost fishes that show an extraordinary diversity of jaw morphology. I present new anatomical descriptions of the jaw musculature in six selected beloniforms and four closely related species. A reduction of the external jaw adductor (A1) and a changed morphology of the intramandibular musculature were found in many Beloniformes. This might be correlated with the progressively reduced mobility of the upper and lower jaw bones. The needlefishes and sauries, which are characterised by extremely elongated and stiffened jaws, show several derived characters, which in combination enable the capture of fish at high velocity. The ricefishes are characterised by several derived and many plesiomorphic characters that make broad scale comparisons difficult. Soft tissue characters are highly diverse among hemiramphids and flying fishes reflecting the uncertainty about their phylogenetic position and interrelationship. The morphological findings presented herein may help to interpret future phylogenetic analyses using cranial musculature in Beloniformes.

scholarly journals Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type Strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956

2019 ◽  
Vol 8 (26) ◽  
Author(s):  
Masako Takashima ◽  
Ri-ichiroh Manabe ◽  
Moriya Ohkuma
Keyword(s):  
Related Species ◽  
Draft Genome ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Phylloplane Yeasts ◽  
Type Strains ◽  
Plant Microbiome

We report the draft genome sequences of type strains for Dioszegia crocea and its closely related species Dioszegia aurantiaca, which should improve our understanding of the epiphytic phylloplane yeasts. These data will also have implications for the plant microbiome, since Dioszegia is considered a microbial “hub” taxon.

scholarly journals Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1906-1912 ◽  
Author(s):  
Natasha R. Mavengere ◽  
Allan G. Ellis ◽  
Johannes J. Le Roux
Keyword(s):  
South African ◽  
Type Strain ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Associated Species

During a study to investigate the diversity of rhizobia associated with native legumes in South Africa’s Cape Floristic Region, a Gram-negative bacterium designated VG1CT was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1CT belongs to the genus Burkholderia , with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5 % and 98 %, respectively). The DNA G+C content of strain VG1CT was 60.1 mol%, and DNA–DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70 %. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1CT represents a novel rhizosphere-associated species in the genus Burkholderia , for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1CT ( = DSM 27239T = LMG 27731T).

scholarly journals Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
M. Andreína Pacheco ◽  
Esha R. Kadakia ◽  
Zainab Chaudhary ◽  
Douglas J. Perkins ◽  
Julia Kelley ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Related Species ◽  
Population Expansion ◽  
Population Level ◽  
Parasite Clearance ◽  
Recent Common Ancestor ◽  
Closely Related Species ◽  
Content Type ◽  
Time Of Divergence ◽  
Generation Sequencing

ABSTRACT Mutations in the Plasmodium falciparum k13 (Pfk13) gene are linked to delayed parasite clearance in response to artemisinin-based combination therapies (ACTs) in Southeast Asia. To explore the evolutionary rate and constraints acting on this gene, k13 orthologs from species sharing a recent common ancestor with P. falciparum and Plasmodium vivax were analyzed. These comparative studies were followed by genetic polymorphism analyses within P. falciparum using 982 complete Pfk13 sequences from public databases and new data obtained by next-generation sequencing from African and Haitian isolates. Although k13 orthologs evolve at heterogeneous rates, the gene was conserved across the genus, with only synonymous substitutions being found at residues where mutations linked to the delayed parasite clearance phenotype have been reported. This suggests that those residues were under constraint from undergoing nonsynonymous changes during evolution of the genus. No fixed nonsynonymous differences were found between Pfk13 and its orthologs in closely related species found in African apes. This indicates that all nonsynonymous substitutions currently found in Pfk13 are younger than the time of divergence between P. falciparum and its closely related species. At the population level, no mutations linked to delayed parasite clearance were found in our samples from Africa and Haiti. However, there is a high number of single Pfk13 mutations segregating in P. falciparum populations, and two predominant alleles are distributed worldwide. This pattern is discussed in terms of how changes in the efficacy of natural selection, affected by population expansion, may have allowed for the emergence of mutations tolerant to ACTs.

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

scholarly journals Bacillus invictae sp. nov., isolated from a health product

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3867-3876 ◽  
Author(s):  
Raquel Branquinho ◽  
Clara Sousa ◽  
Hugo Osório ◽  
Luís Meirinhos-Soares ◽  
João Lopes ◽  
...  
Keyword(s):  
Related Species ◽  
Acid Production ◽  
Type Species ◽  
Rrna Gene ◽  
Spectroscopic Techniques ◽  
Health Product ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-positive, rod-shaped, endospore-forming Bacillus isolate, Bi.FFUP1 T, recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of Bacillus pumilus , Bacillus safensis , Bacillus altitudinis and Bacillus xiamenensis , the phenotypically and genotypically most closely related species. Acid production from cellobiose, d-glucose and d-mannose and absence of acid production from d-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and l-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.FFUP1 T comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.FFUP1 T showed ≥99 % 16S rRNA gene sequence similarity to B. safensis FO-036bT, B. pumilus (7061T and SAFR-032), B. altitudinis 41KF2bT and B. xiamenensis HYC-10T. Differences in strain Bi.FFUP1 T gyrB and rpoB sequences in comparison with the most closely related species and DNA–DNA hybridization experiments with Bi.FFUP1 T and B. pumilus ATCC 7061T, B. safensis FO-036bT, B. altitudinis 41KF2bT and B. xiamenensis HYC-10T gave relatedness values of 39.6 % (reciprocal 38.0 %), 49.9 % (reciprocal 42.9 %), 61.9 % (reciprocal 52.2 %) and 61.7 % (reciprocal 49.2 %), respectively, supported the delineation of strain Bi.FFUP1 T as a representative of a novel species of the genus Bacillus , for which the name Bacillus invictae sp. nov. is proposed, with strain Bi.FFUP1 T ( = DSM 26896T = CCUG 64113T) as the type strain.

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