The Phylogeny of Species of the Genus Saccharomycopsis Schiönning (Saccharomycetaceae) Based on the Partial Sequences of 18S and 26S Ribosomal RNAs

Eight strains of Saccharomycopsis species were examined for their partial base sequences of 18S and 26S rRNAs. The base sequences on the fingerprint segment showed three kinds of ACUAU, UCUAU, and AUAU. In the partial base sequences (positions 1451–1618, 168 bases) of 18S rRNA, all the strains of Saccharomycopsis species examined had 1–0 base difference except for the strains of Saccharomycopsis fibuligera (base differences, 5–4). In the partial base sequences on the positions 1611–1835 region (225 bases) of 26S rRNA, however, S’copsis vini had 15–11 base differences. The other species had 7–2 base differences. In the partial base sequences on the positions 493–622 region (130 bases) of 26S rRNA, the calculated percent similarities were 62–77. Discussion was made phylogenetically and taxonomically, especially on the separation of S’copsis fibuligera (≡ Endomyces fibuliger) from the genus Saccharomycopsis.     

The Phylogenetic Relationships of the Saturn-shaped Ascospore-forming Species of the Genus Williopsis Zender and Related Genera Based on the Partial Sequences of 18S and 26S Ribosomal RNAs (Saccharomycetaceae): The Proposal of Komagataea Gen. Nov.

The partial base sequences of 18S and 26S rRNAs of strains of Williopsis and Saturnospora species were analyzed. In the three regions partially sequenced, the higher base differences were observed in the strains examined of the three species, W. californica, W. mucosa, and W. pratensis, compared with those of W. saturnus var. saturnus (type species of genus Williopsis), W. beijerinckii, W. mrakii, W. saturnus var. subsufficiens, W. suaveolens, P. membranaefaciens (type species of genus Pichia), C. matritensis (type species of genus Citeromyces), and S’spora dispora (type species of genus Saturnospora): the percent similarities were 52–82 in positions 493–622, 130 bases, of 26S rRNA, and the number of base differences was 28–6 in positions 1611–1835, 225 bases, of 26S rRNA, and the number of base differences was 25–4 in positions 1451–1618, 168 bases, of 18S rRNA. In the 18S rRNA partial base sequencings, W. mucosa had an identical base sequence with P. anomala (≡ H. anomala, type species of genus Hansenula). Based on the sequence data obtained, the taxonomic positions of the three Williopsis species mentioned above are discussed. The genus Zygowilliopsis Kudriavzev was postulated to be retained and emended, and a new genus, Komagataea was proposed for W. pratensis with a new combination, Komagataea pratensis.     

Inhibition of Protein Synthesis by Antiviral Protein from Yucca recurvifolia Leaves

We analyzed 18S and 26S rRNA partial base sequences [positions 1451–1618 (168 bases) of 18S rRNA and positions 1611–1835 (225 bases) and 493–622 (130 bases) of 26S rRNA] of a total of three strains of Pichia jadinii and Candida utilis. The three strains had identical base sequences with the type strain of P. jadinii (IFO 0987) in the 18S rRNA partial base sequencings. In the 26S rRNA partial base sequencings, there were partial base sequences similar to each other (1–0 base difference and 87–95 percent similarities). The sequence data obtained are discussed taxonomically and phylogenetically, especially in connection with Williopsis saturnus, the type species of the genus Williopsis ZENDER.     

The Phylogeny of Acetic Acid Bacteria Based on the Partial Sequences of 16S Ribosomal RNA: The Elevation of the Subgenus Gluconoacetobacter to the Generic Level

Thirty-six strains of acetic acid bacteria classified in the genera Acetobacter, Gluconobacter, and Acidomonas were examined for their partial base sequences in positions 1220 through 1375, 156 bases, of 16S rRNA. The strains of the Q₁₀-equipped Gluconobacter species examined were divided into two subgroups, which included the type strains of Gluconobacter oxydans, the type species of the genus Gluconobacter, and of a second species, Gluconobacter cerinus, respectively. The base differences numbered four between the two type strains. The strains of the Q₉-equipped species examined classified in the type subgenus Acetobacter of the genus Acetobacter were not very distant phylogenetically from those of the genus Gluconobacter. The calculated number of base differences was 9–6 between the type strains of G. oxydans and G. cerinus and the type strains of Acetobacter aceti and Acetobacter pasteurianus. In contrast, the strains of the Q₁₀-equipped species examined classified in the subgenus Gluconoacetobacter of the genus Acetobacter were very distant phylogenetically from those of the Acetobacter and Gluconobacter species mentioned above. The number of base differences was calculated to be 14-8. Furthermore, the strains of the methanol-assimilating, Q₁₀-equipped species of the genus Acidomonas examined were located in phylogenetically isolated positions. The type strain of Acidomonas methanolica (≡ Acetobacter methanolicus), the type species of the genus Acidomonas, had 16–9 base differences. The data obtained here indicated that the members of the subgenus Gluconoacetobacter of the genus Acetobacter can be distinguished at the generic level. The new genus Gluconoacetobacter was proposed with the type species, Gluconoacetobacter liquefaciens, in recognition of the genus Acidomonas along with the genera Acetobacter and Gluconobacter in the classification of the acetic acid bacteria.     

Phylogenetic Relationships of Species of the Genus Kluyveromyces van der Walt (Saccharomycetaceae) Deduced from the Partial Sequences of 18S and 26S Ribosomal RNAs

In order to clarify the phylogenetic relationships of the species classified in the genus Kluyveromyces (Saccharomycetaceae), three partial base sequences of 18S and 26S rRNAs of eighteen strains were determined. The regions determined of the strains corresponded to positions 1451 through 1618 (168 bases) of 18S rRNA and to positions 1611 through 1835 (225 bases) and 493 through 622 (130 bases) of a strain (IFO 2376) of Saccharomyces cerevisiae. The analyses of the partial base sequences suggested that the genus Kluyveromyces is phylogenetically heterogeneous, ranging from the strains that are quite close to the strain of S. cerevisiae to the strains that are distinct enough to be classified in genera separate from the genus Saccharomyces. From our sequence data, we concluded that the extent of the genus Kluyveromyces should be restricted to only one species, K. polysporus, the type species of the genus. Kluyveromyces phaffii was also distinct enough to deserve another genus. Kluyveromyces cellobiovorus was not close to any of the strains of Kluyveromyces species examined, and should be excluded from the genus. Most of the strains of the species examined were fairly close to the strain of S. cerevisiae.     

The phylogenetic relationships ofEeniella nana Smith,Batenburg-van der Vegte et Scheffers based on the partial sequences of 18S and 26S ribosomal RNAs (Candidaceae)

Summary Two strains ofEeniella nana were examined for their partial base sequences of 18S and 26S rRNAs. In the partial base sequences of 18S rRNA (prositions 1451 through 1618, 168 bases) the strains ofE. nana have five, five, four and eleven base differences with those ofDekkera bruxellensis (type species).D. anomala (andBrettanomyces anomalus),D. naardenensis andD. custersiana, respectively. In the 26S rRNA partial base sequencings (positions 1611 through 1835, 225 bases and positions 493 through 622, 130 bases) the base differences were 46, 43, 34 and 40 and the percent similarities were 53–54, 51–54, 56–57 and 51–53, respectively. The sequence data obtained are discussed phylogenetically and taxonomically, especially on retention of the generic nameEeniella.This paper is dedicated to Professor Herman Jan Phaff in honor of his 50 years of active research which still continues.Significance of the coenzyme Q system in the classification of yeasts and yeast-like organisms. Part LVIII. For part LVII, see ref. [20].     

Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.     

Phylogenetic relationships among species of the genus Issatchenkia Kudriavzev

The phylogenetic relatedness of Issatchenkia spp. was estimated from partial rRNA sequences in two regions of the large subunit and one region of the small subunit. I. terricola was the most divergent species of the genus, differing from other members by 18% nucleotide differences in the highly variable 25S-635 region. These data indicate Issatchenkia to be the most divergent ascomycetous yeast genus presently known.     

The Phylogenetic Relationship of the Conidium-forming Anamorphic Yeast Genera Sterigmatomyces,Kurtzmanomyces, Tsuchiyaea and Fellomyces,and the Teleomorphic Yeast Genus Sterigmatosporidium on the Basis of the Partial Sequences of 18S and 26S Ribosomal Ribonucleic Acids

The eleven strains of conidium-forming yeasts classified in the basidiomycetous anamorphic genera Sterigmatomyces, Kurtzmanomyces, Tsuchiyaea and Fellomyces, and the teleomorphic genus Sterigmatosporidium were examined as to the partial sequences of 18S rRNA and 26S rRNA. The positions determined (in Saccharomyces cerevisiae) were 1451 through 1618 of 18S rRNA, and 1618 through 1835 and 470 through 626 of 26S rRNA. The partial sequence determination of positions 470 through 626 of 26S rRNA indicated that T. wingfieldii should be included in the group comprised of Fellomyces and Sterigmatosporidium species. However, the genera Sterigmatomyces, Kurtzmanomyces, Tsuchiyaea and Fellomyces constituted their own separate clusters as to the partial sequences of positions 1451 through 1618 of 18S rRNA and 1618 through 1835 of 26S rRNA. The classification of the conidium-forming yeasts in the four basidiomycetous anamorphic genera mentioned above was proved to be reasonable from the phylogenetic point of view.     

16S rRNA gene sequence analyses and inter- and intrageneric relationships of Xanthomonas species and Stenotrophomonas maltophilia

The nearly complete, PCR-amplified, 16S rRNA gene sequences have been determined from the representative type strains of eight xanthomonad phena, including six validly described species of the genus Xanthomonas and Stenotrophomonas maltophilia. Pairwise sequence comparisons and phylogenetic analysis demonstrated that the xanthomonads comprise a monophyletic lineage within the γ-subclass of the Proteobacteria. Although the genus Xanthomonas was observed to comprise a cluster of very closely related species, the observed species-specific primary sequence differences were confirmed through sequencing additional strains belonging to the respective species.     

Genetic Identification of Members of the Genus Corynebacterium at Genus and Species Levels with 16S rDNA-Targeted Probes

16S rRNA gene-targeted probes were designed for the identification of corynebacteria at the genus and species levels. The genus-specific probe hybridized all clinically important members of the genus Corynebacterium and could distinguish them from other coryneform bacteria and phylogenetically related high G + C% gram-positive bacteria, including Actinomyces, Rhodococcus, Gordona, Nocardia, Streptomyces, Brevibacterium and Mycobacterium. The species-specific probes for C. jeikeium and C. diphtheriae could differentiate these two species from other members of this genus. The probes were used to select corynebacteria among gram-positive clinical isolates which had been tentatively identified as corynebacteria by biochemical tests. We screened 59 strains with the genus-specific probe; 51 strains hybridized to the genus-specific probe, 8 did not. Of the 51 strains that hybridized to the genus-specific probe, 1 hybridized to the C. diphtheriae species probe and 13 hybridized to the C. jeikeium species probe. The 8 strains that did not hybridize to the genus probe were further characterized by analyzing cell wall diaminopimelic acid and partial 16S rRNA sequencing. The results indicated that these strains were distributed in the genera Arthrobacter and Brevibacterium.     

Stenomitos terricola sp. nov. (Leptolyngbyaceae,Cyanobacteria) from the moist soil of Mt. Gwanggyo,Republic of Korea

Stenomitos terricola FBCC-A190 was collected from soils around the trees of Mt. Gwanggyo, located in Yeongtong-gu, Suwon-si, Gyeonggi-do. S. terricola FBCC-A190 is a thin and simple filament with a cell length that is longer than its width. It has a thin and firm sheath, exhibiting a blue-green color. Species belonging to genus Stenomitos is semi-cryptic species with slight morphological differences from each other. They were confirmed as Stenomitos species by analysis using 16S rRNA and 16S–23S ITS. A monophyletic cluster was formed with the previously reported genus Stenomitos, with 16S rRNA gene sequences sharing similarities of 95.9–97.9% except for S. pantisii TAU-MAC 4318. In addition, 16S–23S ITS gene sequencing showed tRNA^Ala, tRNA^Ile and V2, similar to the previously reported genus Stenomitos. From these results, Stenomitos terricola sp. nov. was proposed as a new species belonging to genus Stenomitos.     

Igniting taxonomic curiosity: The amazing story of Amazonocrinis with the description of a new genus Ahomia gen. nov. and novel species of Ahomia,Amazonocrinis, and Dendronalium from the biodiversity-rich northeast region of India

Five cyanobacterial strains exhibiting Nostoc-like morphology were sampled from the biodiversity hotspots of the northeast region of India and characterized using a polyphasic approach. Molecular and phylogenetic analysis using the 16S rRNA gene indicated that the strains belonged to the genera Amazonocrinis and Dendronalium. In the present investigation, the 16S rRNA gene phylogeny clearly demarcated two separate clades of Amazonocrinis. The strain MEG8-PS clustered along with Amazonocrinis nigriterrae CENA67, which is the type strain of the genus. The other three strains ASM11-PS, RAN-4C-PS, and NP-KLS-5A-PS clustered in a different clade that was phylogenetically distinct from the Amazonocrinis sensu stricto clade. Interestingly, while the 16S rRNA gene phylogeny exhibited two separate clusters, the 16S–23S ITS region analysis did not provide strong support for the phylogenetic observation. Subsequent analyses raised questions regarding the resolving power of the 16S–23S ITS region at the genera level and the associated complexities in cyanobacterial taxonomy. Through this study, we describe a novel genus Ahomia to accommodate the members clustering outside the Amazonocrinis sensu stricto clade. In addition, we describe five novel species, Ahomia kamrupensis, Ahomia purpurea, Ahomia soli, Amazonocrinis meghalayensis, and Dendronalium spirale, in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN). Apart from further enriching the genera Amazonocrinis and Dendronalium, the current study helps to resolve the taxonomic complexities revolving around the genus Amazonocrinis and aims to attract researchers to the continued exploration of the tropical and subtropical cyanobacteria for interesting taxa and lineages.     

Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus

Aim:  To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP‐ and BOX‐polymerase chain reaction) were also used. Methods and Results:  rpoB DNA (458 bp) were amplified from 21 Geobacillus‐ and Bacillus type strains, producing different BOX‐ and REP‐PCR profiles, in addition to 11 thermophilic isolates of Geobacillus and Bacillus species from a Santorini volcano habitat. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The results demonstrated between 90–100% (16S rRNA) and 74–100% (rpoB) similarity among examined bacteria. Conclusion:  BOX‐ and REP‐PCR can be applied for molecular typing within Geobacillus genus. rpoB sequence similarity analysis permits a more accurate discrimination of the species within the Geobacillus genus than the more commonly used 16S rRNA. Significance and Impact of the Study:  The obtained results suggested that rpoB sequence similarity analysis is a powerful tool for discrimination between species within the ecologically and industrially important strains of Geobacillus genus.     

Description of two new species of Nostoc (Nostocales,Cyanobacteria) from central Mexico,using morphological,ecological, and molecular attributes

The present study describes two new Nostoc species, N. montejanii and N. tlalocii, based on a polyphasic approach that combines morphological, ecological, and genetic characteristics. The five investigated populations, including those from newly collected material from central Mexico, were observed to possess morphological features characteristic of the Nostoc genus. Results showed that both new species are strictly associated with running water, and they show clear differences in their habitat preferences. The 16S rRNA gene sequences of the five strains displayed between 98% and 99% similarity to the genus Nostoc sensu stricto. The 16S rRNA gene phylogenetic analyses inferred using Bayesian inference, maximum likelihood, and parsimony methods, placed these five strains in two separate clades distinct from other Nostoc species. The secondary structures of the 16S–23S internal transcribed spacer rRNA region in the two new species showed >10.5% dissimilarities in the operons when compared with other Nostoc species. In addition, clear morphological differences were observed between the two Mexican species, including the color of the colonies (black in N. montejanii and green in N. tlalocii), the size of the cells (greater in N. montejanii), and the number of polyphosphate granules present in the cells (one in N. montejanii and up to four in N. tlalocii).     

Characterization of freshwater benthic biofilm‐forming Hydrocoryne (Cyanobacteria) isolates from Antarctica

The aims of this work were to study cyanobacterial isolates resembling the genus Hydrocoryne using a combination of morphology and phylogeny of 16S rRNA and nifH sequences and to investigate genes involved in cyanotoxin and protease inhibitor production. Four new cyanobacterial strains, isolated from biofilm samples collected from King George Island, Antarctica, were studied. In terms of morphology, these new strains share traits similar to true Anabaena morphotypes (benthic ones), whereas phylogenetic analysis of their 16S rRNA gene sequences grouped them with the sequence of the type species Hydrocoryne spongiosa (H. Schwabe ex Bornet and Flahault 1886–1888), but not with sequences of the type species from the genus Anabaena. This cluster is the sister group of Anabaena morphotypes isolated only from the Gulf of Finland. In addition, this cluster is related to two other clusters formed by sequences of Anabaena isolated from different sites. Partial nifH genes were sequenced from two strains and the phylogenetic tree revealed that the Antarctic nifH sequences clustered with sequences from Anabaena. Furthermore, two strains were tested, using PCR with specific primers, for the presence of genes involved in cyanotoxins (microcystin and saxitoxin) and protease inhibitor (aeruginosin, and cyanopeptolin). Only cyanopeptolin was amplified using PCR. These four Hydrocoryne strains are the first to be isolated and sequenced from Antarctica, which improves our knowledge on this poorly defined cyanobacterial genus.     

Unusual intragenomic and interspecific variability of <Emphasis Type="Italic">Geobacillus</Emphasis> 16S-23S rRNA internal transcribed spacers

The aim of this study was to evaluate the inter-and intraspecific as well as intragenomic variability of Geobacillus 16S–23S rRNA internal transcribed spacers without tRNA genes and to compare these sequences with sequences bearing tRNA genes. In this study the structural analysis was performed in a unique way because the length and the sequence of the structural blocks were adjusted to fit the structure of 16S–23S rRNA internal transcribed spacers of five different Geobacillus species. Our study demonstrated the mosaic-like structure of 16S–23S rRNA internal transcribed spacers in Geobacillus. Some characteristics of these spacers of geobacilli were not previously reported for other bacteria: unusually short conserved sequence in the 5′ end region, some identical conserved blocks in both 5′ and 3′ regions of 16S–23S rRNA internal transcribed spacers, the same sequence blocks in both 16S–23S and 23S–5S rRNA intergenic spacers. Our study demonstrated quite uniform arrangement of the sequence blocks in Geobacillus thermodenitrificans. This species diverged early in the phylogenetic tree of the genus Geobacillus. For the phylogenetically recent species Geobacillus kaustophilus and Geobacillus lituanicus the low inter-and intraspecific, but high intragenomic variability, as a consequence of recent phylogenetic events, was established.     

Molecular methods of analysing bacterial diversity: the case of Rhizobia

The distribution of rhizobia, bacteria which nodulate the roots of leguminous plants, was surveyed for 91 species of the familyLeguminosae. A total of 117 strains of rhizobia were isolated, and 28 strains were obtained from culture collections. The sample total of 145 strains was discriminated by rapid ribosomal RNA (rRNA) sequencing. The partial sequences (157 bases from position (inEscherichia coli) 1220 to 1377 from 5 end) of 16S rRNA revealed the presence of 16 groups in these rhizobia. Further, DNA-DNA homology studies suggested that the differences of the 16 groups were enough to justify establishing at least 16 species.     

Heterogeneity of the Nucleotide Sequences of the 16S rRNA Genes of the Type Strain of Desulfotomaculum kuznetsovii

Two copies of the 16S rRNA gene, rrnAand rrnB, of the type strain 17^Tof the thermophilic sulfate-reducing bacterium Desulfotomaculum kuznetsoviiwere cloned and completely sequenced. The comparison of the determined sequences revealed considerable heterogeneity (8.3%) of the two genes, rrnAand rrnB.The main differences were associated with superlong inserts located in the variable 5"- and 3"-terminal regions of the 16S rRNA genes. Comparative analysis that involved analogous genes from the phylogenetically closest representatives of the genus Desulfotomaculumshowed that disregard of the heterogeneity of the two gene copies distorts the position of the bacterium studied in the phylogenetic tree.     

Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil

Tropical forests have a high diversity of plant species; are they associated with a correspondingly rich microbial flora? We addressed this question by examining the symbiotic rhizobium bacteria that nodulate a diverse pool of forest legume species in Brazil. The 44 strains studied had been isolated from 29 legume tree species representing 13 tribes including all three subfamilies of the Leguminosae, and were chosen to represent major groups from a larger sample that had previously been characterized by SDS–PAGE of total proteins. Partial 16S rRNA gene sequence was determined, corresponding to positions 44–303 in the Escherichia coli sequence. Fifteen sequences were found, including six novel ones. However, all but one of them could be assigned to a genus because they grouped closely with sequences from previously described rhizobial species. Fast-growing strains had sequences similar to Rhizobium spp., Sinorhizobium spp. or Mesorhizobium spp., while the slow-growing strains had sequences similar to Bradyrhizobium spp. One strain with an intermediate growth rate had a unique sequence which indicated that the strain might belong to the genus Azorhizobium. Although the strains showed a variety of sequences, it was surprising that these strains isolated from taxonomically very diverse host plants in previously unexplored environments were mostly very similar to strains described previously, largely from agricultural systems.