- Volume 47, Issue 2, 1997

Phenotypic studies, as well as the reaction of Paenibacillus durum genomic DNA with a 16S ribosomal DNA (sequence of variable regions V1 to V4)-based Paenibacillus azotofixans-specific PCR system and oligonucleotide probe, the presence of sequences homologous to Klebsiella pneumoniae nifKDH in both P. durum and P. azotofixans, and the results of DNA-DNA hybridization experiments performed with the P. durum and P. azotofixans type strains and one additional P. durum strain, showed that these two species form a homogeneous group. In addition, evidence was found for the presence of nif genes in P. durum, and P. durum was shown to fix atmospheric nitrogen. Therefore, the names P. durum and P. azotofixans should be considered synonyms. As P. durum was capable of fixing nitrogen and fixation without inhibition by nitrate is a major characteristic of the group, we propose that P. durum be included in the species P. azotofixans.

Reexamination of the morphological, cultural, and physiological characteristics of Streptomyces spitsbergensis Wieczorek et al. 1993 revealed that this organism belongs to the whorl-forming streptomycetes, and DNA-DNA hybridization data confirmed that S. spitsbergensis is a later subjective synonym of Streptomyces baldaccii (Farina and Locci 1966) Witt and Stackebrandt 1991.

Randomly amplified polymorphic DNA (RAPD) fingerprinting of 14 laboratory strains of leptospiral serovars (serovars australis, autumnalis, ballum, bataviae, canicola, grippotyphosa, hardjoprajitno, hebdomadis, icterohaemorrhagiae, javanica, pomona, pyrogenes, panama, and tarassovi) was carried out by using a pair of primers. Each serovar had a unique and distinct fingerprint pattern. DNAs of other bacterial species, including Escherichia coli, Pasteurella multocida, Salmonella spp., Pseudomonas spp., and Klebsiella spp., did not show any amplification. RAPD fingerprinting was found to be a rapid and sensitive method for serovar identification when it was compared to DNA restriction enzyme analysis, which produced a larger number of bands that made it more difficult to compare serovars.

“Pseudomonas azotocolligans” ATCC 12417T (T = type strain), which was described as a diazotrophic bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this strain clusters phylogenetically with species of the genus Sphingomonas and represents a new species. The results of investigations of the fatty acid patterns, polar lipid profiles, and quinone system supported this placement. The substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of any previously described species of the genus Sphingomonas. The new name Sphingomonas trueperi is proposed on the basis of these results and previously published data for the G+C content of the genomic DNA and the polyamine pattern.

The word Nostoch was invented by the 15th century scientist, philosopher, and alchemist Aureolus Philippus Theophrastus Bombastus von Hohenheim (Paracelsus) to describe the gelatinous colonies of the ubiquitous terrestrial cyanobacterium Nostoc commune. It is proposed that Nostoch is a play on two words, an Old English word and a German word, which both describe that part of the human anatomy intimately associated with extracellular polysaccharide; Nost hryl and Nasenloch = Nostoch.

The names Acetobacter xylinum, Acetobacter xylinum subsp. sucrofermentans, Acetobacter xylinum subsp. xylinum. Caedibacter caryophila, Campylobacter cryaerophila, Fibrobacter succinogenes subsp. elongata, Iodobacter fluviatile, and Rhodobacter blastica are revised in accordance with Rule 12c or Rule 13b of the International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 revision.

Large restriction fragment (macrorestriction) patterns resolved by pulsed-field gel electrophoresis (PFGE) were used to calculate the genomic similarity within and among five members of the genus Chromatium with closely related phenotypes: C. minutissimum, C. vinosum, C. gracile, C. salexigens, and C. tepidum. PFGE allowed the study of the genomic organizations of these organisms. The results reveal a high level of homogeneity among the strains of C. vinosum analyzed. Moreover, there seems to be a close genetic relationship between C. vinosum and C. minutissimum.

A cresol-assimilating yeast strain of a previously undescribed species belonging to the genus Rhodotorula was isolated from soil. The new strain differs from the previously described species of the genus in its pattern of assimilation of carbon and nitrogen compounds, G+C content, and low levels of DNA-DNA-homology. The new species Rhodotorula cresolica is described. The type strain is CBS 7998.

We describe Candida aquaetextoris, a new yeast species isolated from sludge that accumulates at the main wastewater treatment facility which processes discharges from textile factories located in the Prato metropolitan district, northern Tuscany, Italy. This yeast degrades 4-(1-nonyl)phenol, a toxic intermediate originating from the microbial attack of nonylphenol polyethoxylates, which are nonionic surfactants largely used in leather and textile industries. In the investigation we employed conventional and molecular taxonomy techniques to compare the new isolate to strains of physiologically similar species, such as Candida maltosa and Candida tropicalis, as well as strains of quite phenotypically different species, such as Candida haemulonii. The results demonstrate that the yeast which we identified represents a separate taxon. The type strain of C. aquaetextoris is strain Lmar1, which has been deposited in the Industrial Yeast Collection of the Division of Applied Microbiology, Department of Plant Biology, University of Perugia, Perugia, Italy, as strain DBVPG 6732.

Allozyme electrophoresis was used to characterize 39 isolates belonging to the wild yeast species Saccharomyces paradoxus for variation at nine enzyme loci. The data revealed significant genetic differentiation between isolates from two geographically distinct regions, one including continental Europe and the other including the Russian Far East and Japan. The results are consistent with previous observations indicating that there is partial reproductive isolation between isolates collected from these regions, and they suggest the possibility that these two populations represent an early stage in speciation.

Clinical isolates of Candida guilliermondii that were investigated by isoenzyme and randomly amplified polymorphic DNA analyses represented two distinct species. The two species were distinguished on the basis of delayed fermentation of galactose. The larger group of isolates was closely related to the anamorph C. guilliermondii ATCC 6260T (T = type strain) and its teleomorph, Yamadazyma (= Pichia) guilliermondii ATCC 46036T. The remaining group, whose members fermented galactose, was very similar to Candida fermentati CBS 2022, which had for many years been placed in synonymy with C. guilliermondii. Three additional groups were represented by individual strains; these strains included C. guilliermondii var. soya ATCC 20216, which was found to represent Yamadazyma ohmeri. The type strain of Y. guilliermondii is redefined.

Pulsed-field gel elecrophoresis (PFGE), randomly amplified polymorhic DNA (RAPD) analysis, serotype, and killer toxin sensitivity patterns of a wide range of saprobic, clinical, and veterinary isolates of both varieties of Cryptococcus neoformans were examined. C. neoformans var. neoformans and C. neoformans var. gattii differed in chromosomal makeup, RAPD patterns, and killer sensitivity patterns. These result suggest that there are two separate species rather than two varieties. No clear genetic or phenotypic differences were observed among the clinical, saprobic, and verterianary isolates within each taxon. The serotypes differed substantially in their RAPD characteristics. Geographical clustering was observed among the isolates of C. neoformans var. gattii, but not among the isolates of C. neoformans var. neoformans. The isolates of each taxon that originated from resteted geographical areas often had identical or similar karyotpes and RAPD patterns, suggesting that clonal reproduction had occurred. The combination of PFGE and RAPD analysis allowed us to distinguish almost all isoltes. This combination of techniques is recommended for further research on epidemiological, ecological, and population issues.

A phylogenetic investigation of the ascomycetous yeast genus Saccharomyces was performed by using 18S rRNA gene sequence analysis. Comparative sequence analysis showed that the genus is phylogenetically very heterogeneous. Saccharomyces species were found to be phylogenetically interdispersed with members of other ascomycetous genera (e.g., the genera Kluyveromyces, Torulaspora, and Zygosaccharomyces). The four species of the Saccharomyces sensu stricto complex (viz., Saccharomyces bayanus, Saccharomyces cerevisiae, Saccharomyces paradoxus, and Saccharomyces pastorianus) were found to be phylogenetically closely related to one another, displaying exceptionally high levels of sequence similarity (>99.9%). These four species formed a natural group that was quite separate from the other Saccharomyces and non-Saccharomyces species examined. Saccharomyces exiguus and its anamorph, Candida holmii, were found to be genealogically almost identical and, along with Saccharomyces barnettii. formed a stable group closely related to, but nevertheless distinct from, Kluyveromyces africanus, Kluyveromyces lodderae, Saccharomyces rosinii, Saccharomyces spencerorum, and Saccharomyces sp. strain CBS 7662T (T = type strain). Saccharomyces spencerorum and Kluyveromyces lodderae displayed a particularly close genealogical affinity with each other, as did Saccharomyces castellii and Saccharomyces dairensis. Similarly, Saccharomyces servazzii, Saccharomyces unisporus, and Saccharomyces sp. strain CBS 6904 were found to be genotypically highly related and to form a phylogenetically distinct lineage. The recently reinstated species Saccharomyces transvaalensis was found to form a distinct lineage and displayed no specific association with any other Saccharomyces or non-Saccharomyces species. Saccharomyces kluyveri formed a very loose association with a group which included Kluyveromyces thermotolerans, Kluyveromyces waltii, Zygosaccharomyces cidri, and Zygosaccharomyces fermentati. Saccharomyces sp. strain CBS 6334T, on the other hand, displayed no specific association with any of the other Saccharomyces spp. studied, although a neighbor-joining analysis did reveal that this strain exhibited a loose phylogenetic affinity with Kluyveromyces polysporus and Kluyveromyces yarrowii. On the basis of the phylogenetic findings, two new Saccharomyces species, Saccharomyces kunashirensis (with type strain CBS 7662) and Saccharomyces martiniae (with type strain CBS 6334), are described.