Legionella bozemanii sp. nov. andLegionella dumoffii sp. nov.: Classification of two additional species ofLegionella associated with human pneumonia

Deoxyribonucleic acid (DNA) relatedness was used to distinguish strains ofLegionella-like organisms (LLO) fromLegionella pneumophila. Two of these LLO strains, WIGA and MI 15, showed sufficient DNA relatedness to one another to be classified in the same species. The nameLegionella bozemanii species nova is proposed for this new species. The type strain ofL. bozemanii is WIGA (=ATCC 33217) Two other LLO strains, NY 23 and Tex-KL, were shown to represent a new species. The nameLegionella dumoffii species nova is proposed for this species. The type strain ofL. dumoffii is NY 23 (=ATCC 33279). These two species joinL. pneumophila andL. micdadei in the genusLegionella.     

Identification of Actinomycetes Producing Phospholipase D with High Transphosphatidylation Activity

Previously we isolated six actinomycetes strains, 9-4, 10-1, 10-2, 10-3, 10-6, and 21-4, that produce phospholipase D (PLD) with high transphosphatidylation activity. In this study, we identified these strains, and the PLD activities were compared with those of reference strains. 16S rDNA sequences and DNA–DNA hybridization tests indicated taxonomic affiliations of strain 9-6 with Streptomyces senoensis, strains 10-1 and 10-6 with S. vinaceus, and strains 10-2 and 10-3 with S. racemochromogenes. Strain 21-4, though identified as a Streptomyces sp., could not be identified with any known species. Meanwhile, most of the culture supernatants of reference strains demonstrated no or very weak PLD activity, while those of our strains exhibited significantly higher activity. All of the strains in this study were identified as Streptomyces species. The PLD activity of our strains exceeded most of the reference Streptomyces strains. The findings in this study imply that the Streptomyces strains, although they are members of the same species, can produce different quantities of PLD enzyme.     

Pyrolysis-gas-liquid chromatography of fungi: Observations on variability among nine Penicillium species of the section asymmetrica,subsection fasciculata

Mathematical expressions of variability or similarity based on data from pyrolysis-gas-liquid chromatograms were calculated for each combination among three strains of each of nine fasciculatePenicillium spp. The mean similarity for eight of these species clustered around 41 but the similarity forP. cyclopium was 58. Within each of the nine species, exceptP. urticae, at least one combination of strains had a similarity of 51 or greater. Similarities were also calculated for 576 possible combinations among 27 strains used in this study. These data indicate that certain strains of these nine penicillia may be more closely related to strains of other fasciculate species than they are to strains within their own species. This agrees with previous observations on variability and intergradation in the subsection Fasciculata.     

Discrimination of species and strains of basidiomycete genusCoprinus by random amplified polymorphic DNA (RAPD) analysis

All five examined strains ofCoprinus cinereus could be clearly discriminated from the strains of five otherCoprinus species by RAPD patterns with 12 of 13 primers. Also one specimen of unknownCoprinus strain was identified to beC. cinereus by this method. The RAPD patterns were similar among the strains in the same species; many common DNA fragments were recognized as well as some strain-specific DNA fragments. Thus all seven strains ofC. cinereus and all four strains ofC. angulatus examined could be distinguished individually. Diakryotic strains showed the combined RAPD patterns of the two monokaryotic strains constituting the dikaryon. The combined RAPD markers observed in the dikaryons were segregated in their basidiospore progeny. All 18 randomly picked progeny showed different combinations of RAPD markers from the parental strains.     

Temperature resistant Nocardia biovarieties in Tucumán,Argentina?

Eighty-six regional strains of the pathogenic Nocardia species isolated from soil and human mycetoma were tested for their response to different incubation temperatures and for their tolerance to different temperatures. The aim was to assess whether growth temperature and tolerance to elevated temperatures are valuable criteria for the differentiation of pathogenic species of local strains based on the results obtained from a large number of strains. The results showed that 75.34% of all N. brasiliensis isolates from both sources grew at a temperature higher than 37 °C. 20% of the mycetoma strains and 11.32% of those from soil grew at 45 °C. 98.1% of N. brasiliensis from soil and 55.0% of the mycetoma strains tolerated 50 °C for 8 h and many isolates from both sources endured this temperature for an even longer time and tolerated yet higher temperatures. Both properties (growth temperature and temperature tolerance) are used to identify N. asteroides complex (N. farcinica) and N. otitidiscaviarum, and according to our results they are not suitable to differentiate regional strains of this species. The N. asteroides strains assayed showed an ability to grow at and tolerate elevated temperatures superior to those belonging to the other species. Although adaptation of local N. asteroides and N. otitidiscaviarum strains to temperature is important, it is more significant for N. brasiliensis, because this species is predominant in the Tucumán soil and responsible for the major number of diseases in the area.This revised version was published online in October 2005 with corrections to the Cover Date.     

Distribution and analysis of plasmids inStreptococcus thermophilus

Summary In a survey of 35 strains ofStreptococcus thermophilus, 13 strains were found to harbor plasmid DNA. Most of these strains contained plasmid species varying in size from 2.2 to 7.15 kilobases. Only three strains had more than one plasmid species. Each of the nine distinct types of plasmid DNAs identified had two or more unique recognition sites for restriction endonucleases. The characteristics of the indigenous cryptic plasmids ofS. thermophilus may allow their development as cloning vectors useful in the genetic engineering of this species and other streptococci that are important in food production     

Cold-adapted yeasts from Antarctica and the Italian Alps—description of three novel species: Mrakia robertii sp. nov., Mrakia blollopis sp. nov. and Mrakiella niccombsii sp. nov.

Worldwide glaciers are annually retreating due to global overheating and this phenomenon determines the potential lost of microbial diversity represented by psychrophilic microbial population sharing these peculiar habitats. In this context, yeast strains, all unable to grow above 20°C, consisting of 42 strains from Antarctic soil and 14 strains isolated from Alpine Glacier, were isolated and grouped together based on similar morphological and physiological characteristics. Sequences of the D1/D2 and ITS regions of the ribosomal DNA confirmed the previous analyses and demonstrated that the strains belong to unknown species. Three new species are proposed: Mrakia robertii sp. nov. (type strain CBS 8912), Mrakia blollopis sp. nov. (type strain CBS 8921) and a related anamorphic species Mrakiella niccombsii sp. nov. (type strain CBS 8917). Phylogenetic analysis of the ITS region revealed that the new proposed species were closely related to each other within the Mrakia clade in the order Cystofilobasidiales, class Tremellomycetes. The Mrakia clade now contains 8 sub-clades. Teliospores were observed in all strains except CBS 8918 and for the Mrakiella niccombsii strains.     

Similarities of genome deoxyribonucleic acids ofPseudomonas strains isolated from meat

A total of 29Pseudomonas strains from meat and 14 reference strains of differentPseudomonas species were studied by DNA-DNA hybridization. Of the field strains, 15 were phenotypically similar toP. fragi; the others represented a new group described by Molin and Ternström [4], phenotypically related toP. fragi and the fluorescent pseudomonads; 12 strains of this phenotype formed one major DNA-relatedness group; the type strain ofP. fragi together with nine field strains formed another group. The remaining eight meat isolates could not be assigned to either of the two groups. The intergroup relatedness and the relatedness of both groups to the fluorescent pseudomonads was about 50%. Hybridization data indicate that the phenotype of Molin and Ternström deserves species rank and that this tentative species andP. fragi belong to the group of fluorescent pseudomonads.     

Isoenzyme and Total Protein Analysis by Agarose Isoelectric Focusing, and Taxonomy of the Genus Acanthamoeba

Thirty axenically grown reference strains belonging to 15 different Acanthamoeba spp. were investigated for isoenzyme patterns by agarose isoelectric focusing in the pH range 3–10. Zymograms of acid phosphatase, leucine amino peptidase, malate dehydrogenase, propionyl esterase, glucose phosphate isomerase, phosphoglucomutase, and alcohol dehydrogenase were compared. The same strains were also analyzed for protein patterns separated by agarose isoelectric focusing in a pH gradient of 5–8. The results suggested changes in taxonomy within morphology group II of Pussard & Pons. Acanthamoeba paradivionensis becomes a synonym of A. divionensis. Although this species seems to be related to A. rhysodes, it could not be concluded that the species names are synonyms since the type strain of A. rhysodes was not available for comparison. In the subgroup A. polyphaga–A. quina–A. lugdunensis, A. lugdunensis becomes the species name for pathogenic strains of this subroup, A. quina for the nonpathogenic strains, while A. polyphaga is the species name for an atypical strain. Two strains of A. castellanii showed different zymograms from strain Neff of this species, but related protein patterns. In group III, A. pustulosa is found to be a synonym of A. palestinensis, while one strain of A. lenticulata is also found to belong to the A. palestinensis species. All other species names in both morphology groups could be retained as valuable, on the basis of the techniques used. Group I was not investigated, as axenic cultures could not be obtained.     

The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses

Sequences of the 16S rRNA gene were determined from all type strains of the recognized Ectothiorhodospira species and from a number of additional strains. For the first time, these data resolve the phylogenetic relationships of the Ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain affiliation. Two major groups that are recognized as separate genera were clearly established. The extremely halophilic species were removed from the genus Ectothiorhodospira and reassigned to the new genus Halorhodospira gen. nov., to recognize that the most halophilic eubacteria are species of this genus. These species are Halorhodospira halophila comb. nov., Halorhodospira halochloris comb. nov., and Halorhodospira abdelmalekii comb. nov. Among the slightly halophilic Ectothiorhodospira species, the classification of strains belonging to Ectothiorhodospira mobilis and Ectothiorhodospira shaposhnikovii was improved. Several strains that were tentatively identified as Ectothiorhodospira mobilis form a separate cluster on the basis of their 16S rDNA sequences and are recognized as two new species: Ectothiorhodospira haloalkaliphila sp. nov., which includes the most alkaliphilic strains originating from strongly alkaline soda lakes, and Ectothiorhodospira marina, describing isolates from the marine environment. Received: 12 October 1995 / Accepted: 1 December 1995     

微小杆菌属(Exiguobacterium)细菌的能量代谢途径分析

【目的】微小杆菌属(Exiguobacterium)细菌广泛分布于海洋及非海洋环境中,具有多种代谢途径以适应复杂多样的生境。本研究从能量代谢途径角度出发,探究该属菌株对不同生境的适应能力。【方法】从美国国家生物科技数据中心(National Center for Biotechnology Information, NCBI)数据库中获取146个Exiguobacterium属菌株的基因组,查找并统计光营养、厌氧呼吸和底物代谢等多种能量代谢途径的关键蛋白或关键酶基因在各菌株基因组中的分布,包括光营养型的视紫红质基因、厌氧呼吸营养型的钼辅因子合成蛋白基因,以及底物代谢营养型中乙醛酸分流途径的异柠檬酸裂解酶及苹果酸合酶基因等。根据对应的氨基酸序列构建视紫红质、MoaC和异柠檬酸裂解酶的系统发育树,分析不同能量代谢途径在该属菌株进化过程中的保守性,推测其对于该属菌株的重要性。【结果】Exiguobacterium属中50%的种具有视紫红质基因,其中分离自非海洋生境的菌株更趋向于含有视紫红质基因。本研究所统计的全部非海洋生境菌株中,含有视紫红质基因的菌株占比约为70%,而在海洋生境菌株中该比例...     

DNA-DNA hybridization of Rhodopseudomonas capsulata,Rhodopseudomonas sphaeroides and Rhodopseudomonas sulfidophila strains

The genetic relatedness of 21 Rhodopseudomonas strains has been studied by means of DNA-DNA hybridization. All strains included in the study belonged to the subgroup of the genus Rhodopseudomonas which is characterized by a short-rod to coccus morphology, a vesicular intracytoplasmic membrane system and carotenoids of the spheroidene group. Mol percentages guanine + cytosine ranged from 64 to 73, most strains having values between 68 and 72. With few exceptions, the hybridization data obtained were in agreement with the subdivision in three (or possibly four) species on the basis of classical taxonomy. Strain SCJ, formerly considered to be a somewhat atypical R. capsulata strain, is most probably a R. sphaeroides strain and two out of seven strains that were received as R. sulfidophila did not fit in this species on the basis of the hybridization data. The results also showed that two undesignated strains that were previously thought to be related to R. capsulata (Hansen et al. 1975) cannot be assigned to this species and may be representatives of another species. The seven strains that required approximately 2.5% NaCl in the medium and that had been designated R. sulfidophila were found to synthesize far higher levels of bacteriochlorophyll during fully aerobic growth in the dark than the purple bacteria studied thus far.Abbreviations GC guanosine + cytosine - SSC standard saline citrate buffer     

Host range ofFrankia endophytes

Summary Cross-inoculation experiments with 10 pure cultured strains and 17 host species were carried out. The 10 strains were isolated from the root nodules on actinorhizal trees ranging in 9 species, 5 genera and 4 families. The host species belong to 5 genera. The pure cultured strains fromAlnus are of strong ability to infect different species of the same genus. The seedlings inoculated with these strains are able to nodulate normally. These strains can also infect and nodulate the seedlings ofMyrica californica, but not the seedlings of Elaeagnus, Casuarina andMyrica rubra. The pure cultured strains from Elaeagnus can infect and nodulate the host species in the same genus and family with an exception ofE. viridis vardelavayi, which can be only poorly nodulated by a few strains from Elaeagnus. The strains from Elaeagnus cannot infect the seedlings of Alnus andMyrica rubra. The results presented here suggest thatFrankia endophytes can be divided into two groups: Alnus group and Elaeagnus group.     

A Taxonomic Study of Strains Received as “Mycobacterium” rhodochrous

A taxonomic study was carried out on 20 strains received as “Mycobacterium” rhodochrous. These strains were exceedingly similar to the strains of the genus Gordona recently proposed by the present author. Out of the 20 strains studied, 10 strains, including two strains previously named Rhodococcus rhodochrous, formed one cluster and were considered to belong to a species of the genus Gordona. The species has been named Gordona rhodochroa (Zopf; Overbeck; Gordon et Mihm) Tsukamura comb. nov. Two strains were considered to belong to the species Gordona rubra. One of the two had initially been named Mycobacterium rubropertinctum. It was considered from the facts that the specific epithet for the species should be “rubropertinta” and the name Gordona rubra be changed to Gordona rubropertincta. The other strains seemed to belong to some other species. In conclusion, the species “Mycobacterium” rhodochrous appears to be divided into several species of the genus Gordona.     

Serological characteristics within the genus Desulfovibrio

Antisera were prepared against one strain each of Desulfovibrio desulfuricans, D. vulgaris and D. salexigens. The antisera were tested for cross reactivity against 36 heterologous Desulfovibrio strains by both agglutination titration and by double immunodiffusion precipitin plates.Generally no cross-reaction was demonstrated by agglutination even between heterologous strains of the same species, suggesting that the surface antigens of Desulfovibrio are highly specific. In immunodiffusion plates a single apparently genus-specific surface antigen could be shown to be present in all but two of the strains tested. Although other common precipitin bands showed the presence of some antigens common between heterologous strains these appeared to be randomly distributed among the strains tested, with the exception of one band shown to be generally specific to strains of D. salexigens. With this exception no other precipitin band could be shown to be consistently specific to any other species, nor consistently common to more than one species.     

Plasmid RFLP profiling and DNA homology inThermus isolated from hot springs of different geographical areas

Thirty-four strains belonging to various species of the genus Thermus (T. aquaticus, "T. thermophilus," "T. brockianus," T. scotoductus, and genomic species 2) isolated from hot springs of different geographical areas were examined for plasmid content and restriction fragment length polymorphism (RFLP) of plasmid DNAs. The four strains of the numerical taxonomy cluster E of genomic species 2 did not harbor plasmid DNA. Overall examination of the HindIII-RFLP profiling of plasmid DNA showed considerable variability between and within genomic species, with the exception of presumed clonal isolates. In spite of this heterogeneity, HindIII plasmid digests within a numerical taxonomic cluster gave a subset of restriction fragments of similar or identical length. Strains belonging to genomic species 2 or unclassified isolates from S. Pedro do Sul that harbored plasmid DNA (7 of the 14 strains studied) exhibited strong DNA homology between plasmid regions. No homologous sequences to these plasmid regions were found in chromosomal DNA from strains isolated from S. Pedro do Sul in which no plasmids were detected. The strains belonging to T. scotoductus formed two plasmid DNA homology groups, as estimated by probing with a plasmid fragment that coincided with the two numerical taxonomy clusters proposed previously. Among the other species, homology of plasmid regions was also found between some strains. Strong homology was also found between plasmid regions from some strains of different taxonomic groups, isolated from the same and from different sources, suggesting that these sequences are highly conserved in plasmids present in Thermus. For plasmid-containing strains, results of plasmid RFLP profiling/DNA homology appear promising for the typing of Thermus at the level of biotypes or of individual strains, namely, for monitoring the diversity and frequency of isolates from a particular hot spring. Received: 24 October 1994 / Accepted: 6 March 1995     

Torulaspora indica a novel yeast species isolated from coal mine soils

Four yeast strains (APSS 805, APSS 806, APSS 815 and AP-18) belonging to a novel Torulaspora species were isolated from coal mine soils of Singareni in Andhra Pradesh state, India. Another strain (PBA-22) was isolated from agricultural field soil from Gujarat state, India. The vegetative cells of all these strains were round, haploid and produced asci by conjugation between independent cells or mother cell and bud, with rough ascospores, suggesting their possible relation to ascomycetous yeast genus Torulaspora. Phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and Internal Transcribed Spacer (ITS) regions revealed that, among the five strains, three viz. APSS 805, APSS 806 and APSS 815 have identical sequences. The other two strains (AP-18 and PBA-22) differed from the other three strains in less than 1% nucleotide substitutions in the combined D1/D2 domain and ITS sequences, indicating that all of them (five strains) may belong to the same species. These five strains were closely related to Torulaspora globosa, but showed more than 3–7% sequence divergence from T. globosa and all other species in the genus Torulaspora in the combined sequence analysis of D1/D2 domain and ITS region of rRNA gene. In addition, these strains also showed distinct microsatellite finger-printing pattern from related species and differed in several physiological responses suggesting that these strains belong to a novel species of Torulaspora. We propose to name these strains as Torulaspora indica sp. nov., and designate APSS 805^T = MTCC 9772 ^T = CBS 12408 ^T as the type strain of this novel species. The Mycobank number of the novel species is MB 563738.     

Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China

In the present study, a total of 154 bacterial strains isolated from nodules of eighteen Vicia species mainly grown in the temperate Chinese provinces were characterized by ARDRA, ITS PCR–RFLP, BOX-PCR, sequencing of 16S rDNA, nodC, nifH, atpD and glnII, and nodulation tests. The results demonstrated that most of the R. leguminosarum strains were effective microsymbionts of the wild Vicia species, while genomic species related to Rhizobium gallicum, Mesorhizobium huakuii, Ensifer meliloti and Bradyrhizobium spp. were symbiotic bacteria occasionally nodulating with Vicia species. In addition, fourteen strains related to Agrobacterium, Phyllobacterium, Ensifer, Shinella and R. tropici, as well as 22 strains of R. leguminosarum might be nodule endophytes without symbiotic genes. Diverse symbiotic gene lineages were found among the test strains and a strong association was found among the symbiotic gene types and genomic species, indicating the absence of lateral gene transfer. These results greatly enlarged the rhizobial spectrum of Vicia species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.