Jutta Burghardt

Phylogenetic Analysis of the Genus Desulfotomaculum: Evidence for the Misclassification of Desulfotomaculum guttoideum and Description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov.

Almost complete 16S ribosomal DNA (rDNA) sequences were determined for the type strains of nine species belonging to the genus Desulfotomaculum and for seven strains described as strains of this genus. The sequences were compared with previously published 16S rDNA and rRNA sequences of the type strains of the other species of the genus. The majority of the species form a phylogenetically coherent cluster within the Clostridium-Bacillus subphylum of gram-positive bacteria. The cluster consists of phylogenetically well-separated lineages containing (i) Desulfotomaculum nigrificans, Desulfotomaculum aeronauticum, and Desulfotomaculum ruminis, (ii) Desulfotomaculum geothermicum, Desulfotomaculum thermosapovorans, and Desulfotomaculum sapomandens, (iii) Desulfotomaculum kuznetsovii, Desulfotomaculum australicum, and Desulfotomaculum thermocisternum, (iv) Desulfotomaculum thermobenzoicum and Desulfotomaculum thermoacetoxidans, and (v) Desulfotomaculum acetoxidans. Some as-yet-undescribed Desulfotomaculum strains are phylogenetically well-separated from strains of the described species. Desulfotomaculum guttoideum shares extremely high 16S rDNA similarity with certain Clostridium species (e.g., Clostridium sphenoides and Clostridium celerecrescens) and is most likely a misidentified species. Desulfotomaculum orientis represents a new genus which branches most closely to the genus Desulfitobacterium. The name Desulfosporosinus orientis gen. nov., comb. nov., is proposed for this taxon.

A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.

Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of alpha-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 17741T (the type strain of P. denitrificans), LMD 22.21T, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 413T) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb. nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.

Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species

SUMMARY: 16S rDNA analysis was performed on 32 strains of 26 species of the genera Rhodococcus and Nocardia in order to investigate the phylogenetic structure of these genera within the radiation of other mycolic-acid-containing genera such as Corynebacterium, Dietzia, Gordona, Mycobacterium and Tsukamurella. The genus Rhodococcus shows a complex structure, consisting of six phylogenetically equidistant lineages. The genus Nocardia does not appear to be a sister taxon of Rhodococcus but branches off from within the radiation of Rhodococcus; thus its species can be considered to be derived from a Rhodococcus ancestor. The main known phenotypic feature that separates Nocardia species from those of Rhodococcus appears to be the presence of a cyclic component in menaquinone of the MK-8(H4) type.

Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia)

Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T.

A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.

The taxonomic position of a yellow-pigmented group of bacteria, isolated from the phyllosphere of grasses was investigated. Results obtained from restriction analysis of amplified 16S rDNA with seven endonucleases (CfoI, HaeIII, AluI, HinfI, MspI, Sau3A and ScrFI) showed identical restriction patterns for each enzyme of all isolates studied, which suggests that all strains belong to the same species. The grass isolates displayed the characteristics of the genus Pseudomonas. They were Gram-negative, aerobic and rod-shaped with polar flagella. Isolates were catalase-positive and oxidase-negative, and unable to oxidize or ferment glucose with the production of acid. The isolates did not reduce nitrate to nitrite but were able to utilize a wide range of compounds individually as a sole carbon source, with preference being given to the utilization of monosaccharides. The disaccharides tested were not utilized as substrates. The DNA base compositions of the tested strains ranged from 60 to 61 mol% G+C. The major isoprenoid quinone of each was ubiquinone Q-9 and hydroxy fatty acids were represented by 3-hydroxydodecanoic acid and 2-hydroxydodecanoic acid. Comparison of 16S rDNA sequences showed that the bacteria were members of the genus Pseudomonas, with similarity values between 91.5 and 97.7%. DNA-DNA hybridization studies with closely related neighbours revealed a low level of homology (< 27%), indicating that the isolates represent an individual species. On the basis of phenotypic and phylogenetic analyses a new species, Pseudomonas graminis sp. nov. (type strain DSM 11363T), is proposed.

Characterization and Identification of Two Vibrio Species Indigenous to the Intestine of Fish in Cold Sea Water; Description of Vibrio iliopiscarius sp. nov.

Summary The taxonomic identity of two groups of bacteria from the intestinal microbial flora of fish in sea water previously called “Gut vibrios” were investigated. A number of strains were tested with respect to morphology, motility, nutrient requirements, salinity and temperature optima and ranges, susceptibility to antibacterials, pathogenicity, guanine-plus-cytosine contents of their deoxyribonucleic acid, DNA-DNA similarities and 16S ribosomal RNA (16S rRNA) sequences. It was confirmed that both groups of bacteria belong to the genus Vibrio . The first group appears to represent a Vibrio species not previously described. We propose the name Vibrio iliopiscarius sp. nov. for this new species. Strains of the other bacterial group were identified as strains of V. salmonicida . These “intestinal strains” of V. salmonicida differ from the previously described pathogenic strains with respect to biochemical and serological characteristics. The importance of the cold-water vibriosis bacterium, V. salmonicida , as part of the indigenous flora of fish is discussed.

Psychromonas antarcticus gen. nov., sp. nov., A new aerotolerant anaerobic, halophilic psychrophile isolated from pond sediment of the McMurdo ice shelf, antarctica

Abstract A gram-negative, rod- to oval-shaped, aerotolerant anaerobic bacterium was isolated from an anaerobic enrichment inoculated with sediment taken from below the cyanobacterial mat of a high-salinity pond near Bratina Island on the McMurdo Ice Shelf, Antarctica. The organism was positive for terminal oxidase and catalase and was motile by means of a polar flagellum. Optimal growth of anaerobic cultures occurred at 12° C, at pH 6.5, and at an NaCl concentration of 3% (w/v). Of a variety of polysaccharides tested, only starch and glycogen supported growth. No growth was observed on cellulosic substrates and xylan, and the organism was unable to attack esculin. Monosaccharides and disaccharides, including the cyanobacterial cell-wall constituent N-acetyl glucosamine, were fermented. Per 100 mol of hexose, the following products (in mol) were formed: acetate, 60; formate, 130; ethanol, 56; lactate, 73; CO2, 15; and butyrate, 2. Propionate, ethanol, n-propanol, n-butanol and succinate were not detectable in the culture medium (< 1 mol per 100 mol of monomer). Hydrogen was not detected in the head space (detection limit < 10–5 atm). Growth yields in aerobic static liquid cultures were slightly higher than those in anaerobic culture, and fermentation favoured acetate at the expense of electron sink products. Growth was inhibited in aerobic shaking cultures, and the organism did not utilize nitrate or sulfate as electron acceptors. The G+C content of the DNA from the bacterium was 42.8 mol%. A phylogenetic analysis indicated that the organism is a member of the γ-subgroup of Proteobacteria, but that it is distinct from other members of this group based on the sequence of its 16S rRNA gene, mol% G+C, morphology, and physiological and biochemical characteristics. It is designated as a new genus and species; the type strain is star-1 (DSM 10704).

Phylogenetic evidence for the taxonomic heterogeneity of Photorhabdus luminescens.

The sequences of the 16S rRNA gene of 40 strains of bacterial symbionts isolated from the nematodes Heterorhabditis spp. and seven bacterial symbionts of the nematodes Steinernema spp. which were isolated from different geographical areas, as well as the type strain of Xenorhabdus japonicus, were determined and compared to each other and to the sequences of several reference strains of members of the Enterobacteriaceae. The data confirmed the separate status of the two genera of symbionts of entomopathogenic rhabditid nematodes. The symbionts of Heterorhabditis spp. clustered with the type strain of Photorhabdus luminescens, while the symbionts of Steinernema spp. grouped with Xenorhabdus species. X. japonicus clustered with the other Xenorhabdus species. Phylogenetic analysis of 15 almost complete 16S ribosomal DNA (rDNA) sequences of the Heterorhabditis symbionts indicated that there were several subclusters. The properties correlated with these subclusters are not yet apparent, although there may be some geographical and ecological correlations. For example, among the nematode-symbiotic bacteria, the members of subclusters I and III are from southeastern and midwestern North America, respectively, while the members of subclusters II and IV are primarily from Europe and Australia, respectively. The nonsymbiotic strains of P. luminescens form a highly homologous subcluster by themselves. The results of DNA-DNA hybridization studies performed with a few selected strains of five of the 16S rDNA subclusters support the existence of several genospecies within P. luminescens.

Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica

Abstract A gram-positive, motile, rod-shaped, strictly anaerobic bacterium was isolated from an enrichment initiated with sediment taken from below the cyanobacterial mat of a low-salinity pond on the McMurdo Ice Shelf, Antarctica. The organism grew optimally at 12° C, at pH 6.5, and at an NaCl concentration of < 0.5% (w/v). It survived freeze-thawing at low salt concentrations, but not exposure to temperatures over 25° C for more than 20 h or short-term exposure to temperatures > 50° C. Out of a variety of polysaccharides tested as growth substrates, only xylan supported growth. The organism also grew on a variety of mono- and disaccharides including the cyanobacterial cell wall constituent, N-acetyl glucosamine. Fermentation products on a mol product per 100 mol of hexose monomer fermented basis were: acetate, 72; formate, 72; butyrate, 55; hydrogen, 114; and CO2, 100. Not detectable in the culture medium (< 2 mol per 100 mol of monomer) were lactate, propionate, ethanol, n-propanol, n-butanol, and succinate. The G+C content of the DNA from the bacterium was 33 mol%, and a phylogenetic analysis indicated that it grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. It differed from other species of this genus with regard to growth temperature optimum, substrate range, and fermentation pattern, and is therefore designated as a new species of Clostridium for which the name Clostridium vincentii is proposed. The type strain is lac-1 (DSM 10228).

Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus strain HSR as members of Bacillus thermoleovorans

Summary An aerobic, endospore forming thermophilic microorganism was isolated from a soil sample in Jordan. The cells stained Gram-positive and the cylindrical spores are terminal and wider than the mother cell. Growth occurs at temperature values between 45 °C and 70 °C, with an optimum at 55°C. The optimum pH for growth is 7.0. The G + C content of the DNA is 50.4 mol% and the sequence analysis of the 16S rDNA shows that the new isolate is phylogenetically closely related to the members of the Bacillus rRNA Group 5. DNA-DNA hybridization studies revealed a high similarity between the new isolate and the thermophilic species of the above mentioned group. A number of thermophilic Bacillus species are combined on the basis of DNA-DNA hybridization data.