A phylogeny of the genus Nocardia deduced from the analysis of small-subunit ribosomal DNA sequences, including transfer of Nocardia amarae to the genus Gordona as Gordona amarae comb. nov.

Abstract According to phylogenetic analyses of nearly complete small-subunit ribosomal DNA sequences, the genus Nocardia should not comprise the two species Nocardia petroleophila and Nocardia amarae. N. amarae should be reassigned to the genus Gordona as Gordona amarae . All of the other Nocardia species form a monophyletic unit, closely related to species of the genus Rhodococcus . It is proposed to revive the name 'CMN' to comprise the genera Corynebacterium, Tsukamurella, Mycobacterium, Gordona, Rhodococcus and Nocardia that form a well identified and monophyletic unit. They are all characterized by a cell wall chemotype IV with mycolic acids.     

Free mycolic acids as criteria in the classification of Gordona and the 'rhodochrous' complex.

The methyl esters of free mycolic acids from representative strains of Gordona bronchialis, G. rubra, G. terrae and Nocardia kirovani each gave, on mass spectroscopy, homologous series of anhydromycolic esters containing from one to four double bonds with the main components of the parent mycolic acids centered on 56, 58, 62 or 64 carbon atoms (total range from C52 to C66). The mycolic acids from the Gordona strains, with chain lengths centered around C60, form a group intermediate in size between nocardomycolic acids (centered around C50) and mycolie different from those of the 'rhodochrous' complex which have anhydromycolates ranging from C34 to C50. Gordonae are thus more closely related in their mycolic acid composition to Nocardia than to Mycobacterium but can be distinguished from each of these genera.     

Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization

Twenty different strains of Pseudomonas, Mycobacterium, Gordona, Sphingomonas, Rhodococcus and Xanthomonas which degrade polycyclic aromatic hydrocarbons (PAH) were characterized in respect to genes encoding degradation enzymes for PAH. Genomic DNA from these strains was hybridized with a fragment of ndoB, coding for the large iron sulfur protein (ISP alpha) of the naphthalene dioxygenase from Pseudomonas putida PaW736 (NCIB 9816). A group of seven naphthalene-degrading Pseudomonas strains showed strong hybridization with the ndoB probe, and five Gordona, Mycobacterium, Rhodococcus and Pseudomonas strains able to degrade higher molecular weight PAH showed weaker hybridization signals. Using a polymerase chain reaction (PCR) approach, seven naphthalene-degrading Pseudomonas strains showed a PCR fragment of the expected size with ndoB-specific primers and additionally ten strains of Gordona, Mycobacterium, Pseudomonas, Sphingomonas and Xanthomonas able to degrade higher molecular weight PAH were detected with degenerate primer-pools specific for the ISP alpha [2Fe-2S]-Rieske center of diverse aromatic hydrocarbon dioxygenases. This suggests a molecular relationship between genes coding for PAH catabolism in various PAH-degrading bacterial taxa, which could be used to evaluate the PAH-degradation potential of mixed populations.     

Electrophoretic heterogeneity of ribosomal protein AT-L30 among actinomycete genera.

The ribosomal proteins from 17 type strains of species belonging to various actinomycete genera were compared by two-dimensional polyacrylamide gel electrophoresis. I detected a striking variability among certain ribosomal proteins (designated AT-L30 proteins) with respect to electrophoretic mobility in the first dimension. In contrast, such variability was not observed among ribosomal L30 proteins from other bacteria, such as Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, and Staphylococcus aureus. Although actinomycete AT-L30 proteins from different taxa exhibited considerable heterogeneity in electrophoretic mobility, within each genus the proteins had a specific mobility characteristic. On the basis of this observation, the ribosomal AT-L30 proteins from 11 type strains of species belonging to the mycolic acid-containing genera Nocardia, Rhodococcus, Gordona, and Tsukamurella were analyzed. The relative electrophoretic mobilities of AT-L30 protein preparations from these strains, as determined by two-dimensional gel electrophoresis, revealed that the genera Nocardia, Rhodococcus, Gordona, and Tsukamurella can be sharply separated from each other. My results are consistent with the previously discussed view that each of these genera merits separate genus status.     

Transfer of Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona amarae comb. nov.

The taxonomic status of Nocardia amarae strains was examined using chemical, microbiological and nucleic acid sequencing methods. It was evident from the results of this and previous studies that Nocardia amarae has properties that are at variance with its classification in the genus Nocardia but consistent with its transfer to the genus Gordona . It is proposed that Nocardia amarae Lechevalier and Lechevalier 1974 be transferred to the genus Gordona as Gordona amarae comb. nov.     

Nutritional physiology of type isolates of currently accepted species ofExophiala andPhaeococcomyces

Nutritional physiological and tolerance tests were performed for all type strains of species currently classified in the black yeast generaExophiala andPhaeococcomyces, including some additional type strains of taxa recently reidentified asExophiala species. Most describedExophiala species can be distinguished by physiological characters.Exophiala jeanselmei with its varieties, andE. castellanii should all be retained as separate taxa. The pairs of strainsMycotorula schawii/Exophiala dermatitidis, Hormodendrum negronii/Exophiala jeanselmei var.lecaniicorni andSporotrichum gougerotii/Torula bergeri were found to be conspecific. Phenetic analyses of physiological data support the identity ofPhaeococcomyces exophialae as a yeast-like synanamorph ofExophiala spinifera. The taxonomic positions of the generaNadsoniella, Phaeoannellomyces andWangiella are discussed. The generaExophiala andPhaeococcomyces are unrelated.     

Numerical classification of some Rhodococci, Corynebacteria and related organisms

Nineteen strains of Corynebacterium sensu stricto, 23 received as Corynebacterium equi or Rhodococcus equi, marker cultures of Arthrobacter, Brevibacterium, Bacterionema matruchotii, Cellulomonas flavigena, Kurthia zopfii, Listeria denitrificans, Microbacterium lacticum, Rhodococcus rubropertinctus and 88 representatives of Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon were the subject of numerical phenetic analyses using 92 characters. The data were examined using the simple matching (SSM) and Jaccard (SJ) coefficients and clustering was achieved using the average linkage algorithm. With a single exception, strains containing meso-diaminopimelic acid, arabinose, galactose and mycolic acids were recovered in five aggregate clusters corresponding to Corynebacterium sensu stricto, Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon. Most of the Corynebacterium (Rhodococcus) equi strains formed a good taxospecies which included the type strain of Corynebacterium hoagii. The numerical data, and the results of earlier chemical and genetical studies, also provide sufficient evidence for the transfer of Bacterionema matruchotii to Corynebacterium sensu stricto as Corynebacterium matruchotii comb.nov. and for the recognition of Rhodococcus globerulus sp.nov. for some strains previously classified as Rhodococcus rubropertinctus (Hefferan) Goodfellow & Alderson. The classification of the remaining marker strains correlates well with other major developments in coryneform taxonomy.     

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.     

Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems.

Foaming in activated sludge systems is characterized by the formation of a thick, chocolate brown-colored scum that floats on the surface of aeration basins and secondary clarifiers. These viscous foams have been associated with the presence of filamentous mycolic acid-containing actinomycetes. To aid in evaluating the microbial representation in foam, we developed and characterized group-, genus-, and species-specific oligonucleotide probes targeting the small subunit rRNA of the Mycobacterium complex, Gordona spp., and Gordona (Nocardia) amarae, respectively. The use of a universal base analog, 5-nitroindole, in oligonucleotide probe design was evaluated by comparing the characteristics of two different versions of the Mycobacterium complex probe. The temperature of dissociation of each probe was determined. Probe specificity studies with a diverse collection of 67 target and nontarget rRNAs demonstrated the specificity of the probes to the target groups. Whole-cell hybridizations with fluorescein- and rhodamine-labeled probes were performed with pure cultures of various members of the Mycobacterium complex as well as with environmental samples from a full-scale activated sludge plant which experienced foaming. Quantitative membrane hybridizations with activated sludge and anaerobic digester foam showed that 15.0 to 18.3% of the total small-subunit rRNAs could be attributed to members of the Mycobacterium complex, of which a vast majority consisted of Gordona rRNA. Several G. amarae strains made up only a very small percentage of the Gordona strains present. We demonstrated that group-specific rRNA probes are useful tools for the in situ monitoring and identification of filamentous bacteria in activated sludge systems.     

Cell envelope architectures of leprosy-derived corynebacteria,Mycobacterium leprae,and related organisms: a comparative study

Cell-envelope architectures of three strains of leprosy-derived corynebacteria (LDC) named Kim, FPSA, and 43LL were compared withMycobacterium leprae andM. avium as well as with related organisms (Nocardia asteroides andCorynebacterium psuedotuberculosis). Cytochemical studies were performed at the ultrastructural level after the lead citrate, silver proteinate, acidic phosphotungstic, and ruthenium red colorations. This study showed that, while the organisms belonging to theCorynebacterium-Mycobacterium-Nocardia (CMN) group had only the cytoplasmic membrane but not the cell wall reacting with the silver proteinate coloration, the LDC organisms had both the cell wall and the cytoplasmic membrane reacting with this coloration method. Moreover, the three strains of the LDC organisms differed from one another at the level of their exopolymer content.Mycobacterium leprae, on the other hand, gave a cytochemical response common to other mycobacteria and the members of the CMN group studied. Consequently, the envelopes of the LDC organisms were not identical toM. leprae, neither morphologically nor cytochemically.     

Nomenclatural adjustments in some European monocotyledons

New nomenclatural combinations are validated for fifteen taxa belonging to the generaDanthonia, Stipa, Lolium, Phippsia, Elymus, Schoenoplectus andAllium.     

A comparative study of the 'rhodochrous' complex and related taxa by delayed-type skin reactions on guinea pigs and by polyacrylamide gel electrophoresis.

Cell extracts prepared by ultrasonic disruption of 17 strains of the 'rhodochrous' complex and related taxa were compared by polyacrylamide gel electrophoresis and for immunologic relatedness, by skin test reactions. Two organisms, Jensenia canicruria and Nocardia calcarea, gave similar gel patterns and skin test reactions, and are considered to be identical. Extracts of nocardia rubra showed a strong antigenic relationship with those of three Nocardia pellegrino organisms (N325, N324 and N420) previously assigned to the 'rhodochrous' complex. Two Gordona organisms appeared to be less antigenically related to the 'rhodochrous' complex. Extracts of three of four organisms designated Lspi (Rhodococcus coprophilus Rowbotham & Cross 1976) elicited skin test reactions similar to those of the 'rhodochrous' strains. One Lspi strain, N650, showed striking similarities to the 'rhodochrous' complex strain N420 (Nocardia pellegrino).     

Neue Gattungen der FamilieLecideaceae s. lat. (Lichenes)

Six new genera are designated for the predominantly foliicolous specíes with hyaline, septate ascospores originally included in the artificial generaBacidia, Catillaria andLopadium. These areFellhanera gen. n. which, on the basis of ascus structure, belongs to the familyPilocarpaceae and includes 19 species, as well asBadimia gen. n. (6 species),Barubria gen. n. (1 species),Loflammia gen. n. (3 species),Calopadia gen. n. (6 species) andLogilvia gen. n. (1 species) which with the previously described generaLasioloma R. Sant. andTapellaria Müll. Arg. em.R. Sant. are classified in the familyEctolechiaceae as they are related toSporopodium Mont. The campylidia, special reproductive organs of the lichens concerned, are present in all members of the family. They are considered to be phylogenetically derived from apothecia. The conidia they produce vary in shape and structure and can be divided into different types, each of which is characteristic of a particular genus. The necessary new combinations are introduced in an appendix.     

Phylogenetic analysis ofIridaceae with parsimony and distance methods using the plastid generps4

A molecular phylogeny of the familyIridaceae based on the plastid generps4 was obtained using both parsimony and distance methods. Thirty-four species were examined together with eight outgroup species. Results show that theIridaceae are monophyletic, and thatIsophysis is likely to be the earliest emerging genus. SubfamilyIxioideae plus the generaAristea andNivenia form a strongly supported clade. Within subfam.Iridoideae, the tribeIrideae includes the genusBobartia (of disputed position), and the tribeMariceae includesCypella. The division ofIridoideae into tribes is consistent with their geographical distribution.     

Phylogenetic analysis of the generaCladonia andCladina (Cladoniaceae, lichenizedAscomycota)

A cladistic analysis of 44 species of the generaCladina andCladonia is presented.Pycnothelia papillaria, Cladia aggregata andC. retipora were used as outgroup taxa. The consensus of all equally parsimonious trees suggests a common ancestral origin for species inCladonia andCladina while the generaPycnothelia andCladia cluster outside this group. The results do not support distinction ofCladina at genus level although it is distinguished as a monophyletic group but within the genusCladonia. The current sectional division ofCladonia is not supported. SectionsCocciferae andHelopodium are best supported but even these groups as currently delimited seem to in include elements that are more closely related to species of the other sections, e.g.C. carneola of sect.Cocciferae andC. pityrophylla of sect.Helopodium. Sections such asUnciales andPerviae seem to be artificial assemblages. In general the evolutionary scheme of the genus seems to be more complicated than revealed by the current sectional division.     

Lipid patterns of various hydrogen oxidizing bacterial species

Strains of hydrogen-oxidizing bacteria, Pseudomonas facilis, Nocardia opaca 1 b, Paracoccus denitrificans and Corynebacterium autotrophicum 7 C, were grown both under chemolithoautotrophic (referred to as autotrophic) and under chemoorganoheterotrophic (referred to as heterotrophic) conditions and harvested during the phase of stationary growth. The lipid patterns of all strains were studied by quantitative chemical analyses, UV spectra, TLC and GLC of fatty acid methyl esters. In general, there were no essential qualitative differences between lipid patterns of autotrophically and those of heterotrophically grown bacteria of the same strain. The conditions of growth apparently influence only the quantitative composition of lipids. In particular, Nocardia opaca is comparatively rich in triglycerides. Ubiquinones were found in Pseudomonas facilis and in Corynebacterium autotrophicum. The latter finding is quite unusual in a Corynebacterium. Carotenoid glycosides are probably present in Corynebacterium autotrophicum, thus explaining the orange color of this organism. The bacteria studied contain a C₁₉ cyclopropane acid, Pseudomonas facilis and Corneynebacterium autotrophicum also     

Physicochemical Cell Surface and Adhesive Properties of Coryneform Bacteria Related to the Presence and Chain Length of Mycolic Acids

The presence and chain length of mycolic acids of bacteria of the genera Corynebacterium, Rhodococcus, Gordona, Mycobacterium, and Arthrobacter and of coryneform bacteria containing a type B peptidoglycan were related to the cell surface hydrophobicity of the bacteria, which in turn was related to adhesion of the cells to defined surfaces such as Teflon and glass. The origin of the overall negative charge of these bacteria is discussed.     

Systematische und phylogenetische studie über die GattungenThienemanniola Kieffer undCorynocera Zetterstedt (Diptera,Chironomidae)

Summary In the preceding paper, a revision of the species of the genusThienemanniola Kieffer is presented. The speciesTh. longipennis Kieffer andTh. brevitarsis Kieffer are declared to be synonymous toTh. ploenensis Kieffer.All three stages of the metamorphosis ofTh. ploenensis are described and figured; ecological notes are also given.The speciesCorynocera ambigua Zetterstedt andCorynocera oliveri Lindeberg are briefly characterized and figured.Finally, the systematical classification of the generaCorynocera andThienemanniola into the familyChironomidae and the degree of relationship between the generaCorynocera andThienemanniola are discussed.     

Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA

5S ribosomal RNA sequences were determined for thirteen actinomycetes mainly representatives with the rare group B type peptidoglycan. The primary and secondary structure of the resultant sequences were of the type characteristic of Gram-positive bacteria with DNA rich in guanine plus cytosine. The sequencing and associated chemotaxonomic data provide compelling grounds for classifying actinomycetes with a group B type peptidoglycan in a single family. The familyMicrobacteriaceae fam. nov. is proposed to accommodate actinomycetes classified in the generaAgromyces, Aureobacterium, Clavibacter, Curtobacterium andMicrobacterium.     

Identification and relationships of cultivated accessions fromLolium-Festuca complex based on RAPD fingerprinting

Randomly Amplified Polymorphic DNA (RAPD) technique with 15 arbitrary primers was used to identify and reveal relationships of the accessions comprising 4 species ofLolium-Festuca complex. Altogether 252 RAPD markers were considered in statistical treatment, 60 of which could be identified as potentially taxon-specific. All analyzed taxa were fully distinguishable using RAPD markers.Lolium-Festuca relationships based on RAPD data were evaluated using cluster analysis (UPGMA) and principle coordinate analysis (PCO). The results of UPGMA as well as PCO performed on data pooled from all RAPD profiles support separation of the two generaLolium andFestuca.