Species reassignment of Geotrichum bryndzae, Geotrichum phurueaensis, Geotrichum silvicola and Geotrichum vulgare based on phylogenetic analyses and mating compatibility

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3072-3080 ◽  
Author(s):  
Marizeth Groenewald ◽  
Teresa Coutinho ◽  
Maudy Th. Smith ◽  
J. P. van der Walt
Keyword(s):  
South African ◽  
Phylogenetic Analyses ◽  
Culture Collection ◽  
Rrna Gene ◽  
Yeast Culture ◽  
Centraalbureau Voor ◽  
Dna Reassociation ◽  
Nucleotide Divergence ◽  
26S Rrna

The present classification of Galactomyces and its anamorph, Geotrichum, is based on various studies that used morphology, ecology, biochemistry, DNA–DNA reassociation comparisons and gene sequencing. In this study, the identities of strains of the Centraalbureau voor Schimmelcultures yeast culture collection, as well as seven strains from South Africa, were examined by analyses of the nucleotide divergence in the internal transcribed spacer regions of the nuclear rRNA gene (nrRNA) operon, the D1/D2 domains of the 26S rRNA gene and partial actin gene sequences as well as compatibility studies. The South African strains were assigned to species in the genus Galactomyces. The phylogenetic analyses and mating studies revealed that Geotrichum silvicola and Geotrichum bryndzae are synonyms of Galactomyces candidus and that Geotrichum vulgare is a synonym of Galactomyces pseudocandidus.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Comprehensive Picture ◽  
Host Parasite

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.

Sulfobacillus thermotolerans sp. nov., a thermotolerant, chemolithotrophic bacterium

2006 ◽  
Vol 56 (5) ◽  
pp. 1039-1042 ◽  
Author(s):  
Tat'yana I. Bogdanova ◽  
Iraida A. Tsaplina ◽  
Tamara F. Kondrat'eva ◽  
Vitalii I. Duda ◽  
Natalya E. Suzina ◽  
...  
Keyword(s):  
Ferrous Iron ◽  
Phylogenetic Analyses ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Physiological Properties ◽  
Dna Reassociation ◽  
Bacterium Strain ◽  
Ph Range ◽  
High Degree

A thermotolerant, Gram-positive, aerobic, endospore-forming, acidophilic bacterium (strain Kr1T) was isolated from the pulp of a gold-containing sulfide concentrate processed at 40 °C in a gold-recovery plant (Siberia). Cells of strain Kr1T were straight to slightly curved rods, 0.8–1.2 μm in diameter and 1.5–4.5 μm in length. Strain Kr1T formed spherical and oval, refractile, subterminally located endospores. The temperature range for growth was 20–60 °C, with an optimum at 40 °C. The pH range for growth on medium containing ferrous iron was 1.2–2.4, with an optimum at pH 2.0; the pH range for growth on medium containing S0 was 2.0–5.0, with an optimum at pH 2.5. Strain Kr1T was mixotrophic, oxidizing ferrous iron, S0, tetrathionate or sulfide minerals as energy sources in the presence of 0.02 % yeast extract or other organic substrates. The G+C content of the DNA of strain Kr1T was 48.2±0.5 mol%. Strain Kr1T showed a low level of DNA–DNA reassociation with the known Sulfobacillus species (11–44 %). 16S rRNA gene sequence analysis revealed that Kr1T formed a separate phylogenetic group with a high degree of similarity between the nucleotide sequences (98.3–99.6 %) and 100 % bootstrap support within the phylogenetic Sulfobacillus cluster. On the basis of its physiological properties and the results of phylogenetic analyses, strain Kr1T can be affiliated to a novel species of the genus Sulfobacillus, for which the name Sulfobacillus thermotolerans sp. nov. is proposed. The type strain is Kr1T (=VKM B-2339T=DSM 17362T).

scholarly journals Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria)

2005 ◽  
Vol 55 (1) ◽  
pp. 11-26 ◽  
Author(s):  
Pirjo Rajaniemi ◽  
Pavel Hrouzek ◽  
Klára Kaštovská ◽  
Raphaël Willame ◽  
Anne Rantala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Morphological Changes ◽  
Phylogenetic Analyses ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
Morphological Studies

The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.

Chachezhania sediminis sp. nov., isolated from marine sediment

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Jihye Baek ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung-Sook Lee ◽  
Ampaitip Sukhoom ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Republic

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain (CAU 1508T) was isolated from marine sediment collected in the Republic of Korea. Growth was observed at 10–45 °C (optimum, 30 °C), pH 4.0–11.0 (optimum, pH 6.0–8.0) and with 0–8.0 % (w/v) NaCl (optimum, 2–4 %). The isolate formed a monophyletic clade in the phylogenetic analyses using 16S rRNA gene and whole-genome sequences, exhibiting the highest similarity to Chachezhania antarctica SM1703T (96.5 %), and representing a distinct branch within the genus Chachezhania (family Rhodobacteraceae ). Its whole genome sequence was 5.59 Mb long, with a G+C content of 65.7 mol% and 2183 predicted genes belonging to six functional categories. The average nucleotide identity and digital DNA–DNA hybridization values between CAU 1508T and C. antarctica SM1703T were 79.1 and 22.2 %, respectively. The predominant cellular fatty acids were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminophospholipid. The sole isoprenoid quinone was ubiquinone 10. Phenotypic phylogenetic properties supported the classification of CAU 1508T as representing a novel species of the genus Chachezhania , with the proposed name Chachezhania sediminis sp. nov. The type strain is CAU 1508T (=KCTC 62999T=NBRC 113697T).

scholarly journals Re-examination of strains formerly assigned to Hyphopichia burtonii, the phylogeny of the genus Hyphopichia, and the description of Hyphopichia pseudoburtonii sp. nov.

2010 ◽  
Vol 60 (11) ◽  
pp. 2675-2680 ◽  
Author(s):  
Marizeth Groenewald ◽  
Maudy Th. Smith
Keyword(s):  
Internal Transcribed Spacer ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Phylogenetic Groups ◽  
D2 Domain ◽  
Nucleotide Divergence ◽  
26S Rrna

On the basis of the nucleotide divergence in the internal transcribed spacer (ITS) domain of the rRNA gene and the D1/D2 domain of the 26S rRNA gene, species of the genus Hyphopichia can be divided into different phylogenetic groups. In this study, three distinct phylogenetic clusters as well as a novel species, Hyphopichia pseudoburtonii sp. nov. with type strain CBS 2455T (=JCM 16346T), are introduced. Mating studies indicate that strains belonging to Hyphopichia pseudoburtonii are heterothallic.

scholarly journals Cryptococcus mujuensis sp. nov. and Cryptococcus cuniculi sp. nov., basidiomycetous yeasts isolated from wild rabbit faeces

2006 ◽  
Vol 56 (9) ◽  
pp. 2241-2244 ◽  
Author(s):  
Kee-Sun Shin ◽  
Hee-Mock Oh ◽  
Yong-Ha Park ◽  
Kang Hyun Lee ◽  
Haryoung Poo ◽  
...  
Keyword(s):  
Type Strain ◽  
Yeast Species ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
Wild Rabbit ◽  
Faecal Pellets ◽  
Phenotypic Differences ◽  
Taxonomic Methods ◽  
26S Rrna

Two previously undescribed anamorphic yeasts, strains T-11T and T-26T, recovered from wild rabbit faecal pellets collected in Muju, Korea, were identified using phenotypic and molecular taxonomic methods. The isolates were characterized by the proliferation of budding cells, positive diazonium blue B and urease reactions, the presence of Q-10 as the major ubiquinone, the presence of xylose in whole-cell hydrolysates and the inability to ferment sugars. Phylogenetic analyses based on 26S rRNA gene partial sequences revealed that strain T-11T was located in the Bulleromyces clade and was related to Sirobasidium intermedium, Tremella exigua, Cryptococcus cellulolyticus and Bullera pseudoalba. Strain T-26T was located in the Mesenterica clade and was closely related to Cryptococcus sp. F6 and Cryptococcus heveanensis CBS 8976. Sequence divergence values of more than 4 % from other described Cryptococcus species, together with the phenotypic differences, showed that the isolated yeasts represent previously unrecognized members of this genus. Therefore, two novel yeast species are proposed: Cryptococcus mujuensis sp. nov., with strain T-11T (=KCTC 17231T=CBS 10308T) as the type strain, and Cryptococcus cuniculi sp. nov., with strain T-26T (=KCTC 17232T=CBS 10309T) as the type strain.

scholarly journals Leucosporidium drummii sp. nov., a member of the Microbotryomycetes isolated from soil

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 728-734 ◽  
Author(s):  
A. M. Yurkov ◽  
A. M. Schäfer ◽  
D. Begerow
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Rrna Gene ◽  
Grassland Soil ◽  
Core Group ◽  
The Core ◽  
26S Rrna ◽  
Phenotypic Tests

Two strains of a novel teleomorphic basidiomycete were isolated from grassland soil. Standard phenotypic tests and phylogenetic analyses of 26S rRNA gene (D1/D2 domains) and ITS region sequences showed that the species belongs to the core group of the genus Leucosporidium. A novel species, Leucosporidium drummii sp. nov., is proposed to accommodate the two strains, with SEG-3-2-AY220T ( = CBS 11562T = MUCL 52878T) as the type strain. In addition, phylogenetic analysis revealed great genetic variability in the Leucosporidium scottii complex.

scholarly journals Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore

2010 ◽  
Vol 60 (5) ◽  
pp. 1224-1235 ◽  
Author(s):  
Marek Eliáš ◽  
Yvonne Němcová ◽  
Pavel Škaloud ◽  
Jiří Neustupa ◽  
Veronika Kaufnerová ◽  
...  
Keyword(s):  
Cell Wall ◽  
Green Alga ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Culture Conditions ◽  
Culture Collection ◽  
Its2 Region ◽  
Rrna Gene ◽  
Cell Periphery ◽  
Algal Flora

The algal flora of subaerial habitats in the tropics remains largely unexplored, despite the fact that it potentially encompasses a wealth of new evolutionary diversity. Here we present a detailed morphological and molecular characterization of an autosporic coccoid green alga isolated from decaying wood in a natural forest in Singapore. Depending on culture conditions, this alga formed globular to irregularly oval solitary cells. Autosporulation was the only mode of reproduction observed. The cell periphery was filled with numerous vacuoles, and a single parietal chloroplast contained a conspicuous pyrenoid surrounded by a bipartite starch envelope. The cell wall was composed of a thick inner layer and a thin trilaminar outer layer, and the cell surface was ornamented with a few delicate ribs. Phylogenetic analyses of 18S rRNA gene sequences placed our strain in the family Scenedesmaceae (Sphaeropleales, Chlorophyceae) as a strongly supported sister branch of the genus Desmodesmus. Analyses of an alternative phylogenetic marker widely used for the Scenedesmaceae, the ITS2 region, confirmed that the strain is distinct from any scenedesmacean alga sequenced to date, but is related to the genus Desmodesmus, despite lacking the defining phenotypic features of Desmodesmus (cell wall with four sporopolleninic layers ornamented with peculiar submicroscopic structures). Collectively, our results establish that we identified a novel, previously undocumented, evolutionary lineage of scenedesmacean algae necessitating its description as a new species in a new genus. We propose it be named Hylodesmus singaporensis gen. et sp. nov. A cryopreserved holotype specimen has been deposited into the Culture Collection of Algae of Charles University in Prague, Czech Republic (CAUP) as CAUP C-H8001.

scholarly journals Bacillus qingdaonensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China

2007 ◽  
Vol 57 (5) ◽  
pp. 1143-1147 ◽  
Author(s):  
Qian-fu Wang ◽  
Wei Li ◽  
Yan-li Liu ◽  
Hai-hua Cao ◽  
Zhao Li ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Sea Salt ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Positive Bacterium ◽  
Salt Sample ◽  
Dna Reassociation ◽  
Isoprenoid Quinones

A moderately haloalkaliphilic, Gram-positive bacterium, designated as strain CM1T, was isolated from a crude sea-salt sample collected near Qingdao in eastern China. Strain CM1T was found to grow optimally at 37 °C and pH 9.0. It was shown to be aerobic, rod-shaped and capable of growth at salinities of 2.5–20 % (w/v) NaCl (optimum, 12 %). The genomic DNA G+C content was about 48 mol%. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 and the major isoprenoid quinones were MK-7(H2) and MK-6(H2). Phylogenetic analyses based on 16S rRNA gene sequences revealed that CM1T is a member of the genus Bacillus and has less than 95.2 % gene sequence similarity to the most closely related strain, Bacillus salarius BH169T. Its DNA–DNA reassociation value with respect to B. salarius BH169T was 35.4 %. On the basis of phenotypic and molecular properties, strain CM1T represents a novel Bacillus species, for which the name Bacillus qingdaonensis sp. nov. is proposed. The type strain is CM1T (=CGMCC 1.6134T=JCM 14087T).

scholarly journals Pedobacter terrae sp. nov., isolated from soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2462-2466 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Dna Relatedness ◽  
The Family ◽  
Type Strains

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 °C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5 % NaCl. Strain DS-57T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57T exhibited levels of DNA–DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA–DNA relatedness data, were sufficient to allow the classification of strain DS-57T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57T (=KCTC 12762T=DSM 17933T).

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