Mycolic acids from Rhodococcus, Gordonia, and Dietzia

The mycolic acids from 11 species of Rhodococcus, seven species of Gordonia, and one species of Dietzia were analyzed using capillary gas chromatography and mass spectrometry (GLC/MS). All strains tested in this study were divided into three groups according to the degree of double bonds and the average carbon number (Av.Nc.) of their mycolic acids. The genus Gordonia belongs to the first group possessing an Av.Nc. in the upper 50s and 60s with 0 to 5 double bonds. Some Rhodococcus species possessed Av.Nc. in the 40s with a variety of distributions of polyunsaturated fatty acids from 0 to 4. The rest of the Rhodococcus species and the genus Dietzia possessed Av.Nc. in the 30s with saturated fatty acids. We previously reported on Nocardia strains whose Av.Nc. were in the 50s. Considering the identification of mycolic acid-containing Actinomycetales at the generic level, the Av.Nc. proved to be useful as a means of differentiating the genera Rhodococcus, Gordonia and Nocardia. The genus Dietzia was found to have its own characteristic constitution of mycolic acid molecular species. The mycolic acids from D. maris 58001T were characterized by an almost equal amount of constituents of even- and odd-numbered carbon chains, whereas the major components of mycolic acids in all other strains had even-numbered carbon chains. Another characteristic of Dietzia was some even-numbered mycolic acids which contained odd-numbered straight chains with odd-numbered alpha-branches. These characteristics indicated that Dietzia might possess a novel fatty acid biosynthesis system.     

Novel rhodococci and other mycolate actinomycetes from the deep sea

A large number of mycolate actinomycetes have been recovered from deep-sea sediments in the NW Pacific Ocean using selective isolation methods. The isolates were putatively assigned to the genus Rhodococcus on the basis of colony characteristics and mycolic acid profiles. The diversity among these isolates and their relationship to type strains of Rhodococcus and other mycolate taxa were assessed by Curie point pyrolysis mass spectrometry (PyMS). Three major (A, C, D) and two minor (B, E) groups were defined by PyMS. Cluster A was a large group of isolates recovered from sediment in the Izu Bonin Trench (2679 m); Cluster C comprised isolates from both the Izu Bonin Trench (6390 and 6499 m) and from the Japan Trench (4418, 6048 and 6455 m). These Cluster C isolates showed close similarity to Dietzia maris and this was subsequently confirmed using molecular methods. Cluster D contained isolates recovered from a sediment taken from a depth of 1168m in Sagami Bay and were identified as members of the terrestrial species Rhodococcus luteus. Clusters B and E had close affinities with members of the genera Gordonia and Mycobacterium. The presence of Thermoactinomyces in certain of the deep-sea sediments studied was indicative of the movement of terrestrial material into the ocean depths.16S ribosomal RNA gene sequence analyses produced excellent definition of most genera of the mycolata, and indicated that the among the deep sea isolates (1) were novel species of Corynebacterium, Gordonia and Mycobacterium, and (2) a Sea of Japan isolate the phylogenetic depth of which suggests the possibility of a new genus. Polyphasic taxonomic analysis revealed considerable diversity among the deep sea rhodococci and evidence for recently diverged species or DNA groups.     

Clusterization of halophilic and halotolerant eubacteria using whole-cell protein electrophoresis data

Total cell proteins of the nineteen halophilic and halotolerant eubacteria isolated from marine sediments and highly mineralized formation waters of oil fields were investigated by SDS gel electrophoresis. The microorganisms studied, phenotypically identified as belonging to the genera Dietzia, Rhodococcus, Staphylococcus, Cytophaga, Brevibacterium, and Archangium, were found to form clearly distinguishable clusters (20-30% similarity at the generic level) on the dendrogram derived from electrophoretic protein patterns. Protein similarity data confirmed the heterogeneity of Rhodococcus maris and its relatedness to the genus Dietza.     

Construction of random transposition mutagenesis system in Rhodococcuserythropolis using IS1415

Recent studies on the metabolic activities of genus Rhodococcus have shown rhodococci to be of important use in industrial, pharmaceutical and environmental biotechnology. The increasing economic significance of Rhodococcus encourages renewed efforts to characterize their genetic systems, as Rhodococcus genetics are still poorly understood. The goal of this study is to adapt a transposon system for use in creating random mutagenesis in Rhodococcus erythropolis. A plasmid carrying IS1415, a member of IS21 family identified from Rerythropolis, has been constructed and designated as pTNR. pTNR is a non-replicating transposon tool introduced into target cells by electroporation. During its transposition, the transposable-marker gene is separated from the open reading frames (istAB) of IS1415, which should avoid secondary transposition. Transposition of pTNR into wild-type R. erythropolis created mutagenesis with a high efficiency of 1.23x10(6)mutants per microgram plasmid DNA. However, it could also be transposed into other Rhodococcus spp. at lower frequencies in comparison with that of R. erythropolis. It has been indicated by Southern hybridization that the generated kanamycin-resistant mutants were resulted from single transposition event of pTNR. The results also revealed that the transposable-marker gene of pTNR was randomly inserted into the chromosomal DNA of R. erythropolis. The affected DNA regions carrying the transposed DNA element could be conveniently recovered for further characterization using a plasmid rescue procedure. Sequence data of the insertion sites of 40 random mutants analyzed indicated that transposition of pTNR generated 6-bp direct target duplications in 36 cases, while in the remaining four mutants; it generated 5- or 7-bp target duplications (two cases each). This study concluded that pTNR could be served as an efficient genetic tool for construction of random mutagenesis system in Rhodococcus species.     

Bacterial composition of the biofilm on the surface of course sediment of the Danube: with special reference to the clinically important bacteria

On monthly intervals and over a period of 14 months (November, 1993-December, 1994) biofilm samples from sediments taken at the Szentendre Island on the Danube were culturel and the isolated organisms were examined macromorphologically and micromorphogically and tested for oxidase and catalase production and their ability to oxidise and ferment glucose. The majority (85%) of the strains isolated were catalase positive. 43% were oxidase positive, 38% were glucose oxidisers and only 19% fermented glucose. In the sediment upmost biofilm layers Gram-negatives dominate (10 samples out of 14). A representative set strains has been subjected to complete identification using the Biolog automated identification system. The coryneform bacteria (e.g. Arthrobacter spp.) and members of the genus Rhodococcus dominated the Gram-positive bacteria while the dominant Gram-negative bacteria were facultative H2 autotrophs, methylotrophs (e.g. Xanthobacter flavus, Hydrogenophaga spp.) and different Aeromonas, Enterobacter and Pseudomonas species. Because the water supply of Budapest (the capital of Hungary) comes from bankwall filtred Danube water resources, the presence of clinically important microorganisms (i.e. Aeromonas, Enterobacter, Pseudomonas and Rhodococcus spp) in the Danube-sediments may pose a public health problem to the users (in particular the immunocompromised) of such water supplies.     

Rhodococcus aetherivorans sp. nov., a new species that contains methyl t-butyl ether-degrading actinomycetes

The taxonomic positions of two actinomycetes, strains Bc663 and 10bc312T, provisionally assigned to the genus Rhodococcus were determined using a combination of genotypic and phenotypic properties. The organisms have phenotypic properties typical of members of the genus Rhodococcus and were assigned to the 16S rRNA subgroup which contains Rhodococcus rhodochrous and closely related species. The two strains, which have many phenotypic features in common, belong to the same genomic species albeit one readily separated from Rhodococcus ruber with which they form a distinct phyletic line. The organisms were also distinguished from all of the species classified in the R. rhodochrous subgroup, including R. ruber, using a combination of phenotypic properties. The genotypic and phenotypic data show that strains Bc663 and 10bc312T merit recognition as a new species of Rhodococcus. The name proposed for the new species is Rhodococcus aetherivorans (10bc312T = DSM 44752T = NCIMB 13964T).     

Production of oil-processing compounds by microorganisms from the Daqing oil field,China

Twenty pure cultures isolated from formation waters of the Daqing oil field were studied with respect to their capacity to produce surface-active compounds in media with individual hydrocarbons, lower alcohols, and fatty acids. Aerobic saprotrophic bacteria belonging to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, Clavibacter, Pseudomonas, and Acinetobacter decreased the surface tension of cultivation media from 55-63 to 28-44 mN/m. Strains of Bacillus cereus, Rhodococcus ruber, and Bacillus licheniformis produced biosurfactants most actively. Bacteria of the genera Rhodococcus, Dietzia, Kocuria, and Gordonia produced exopolysaccharides in media with hydrocarbons. Culture liquids of the strains of R. ruber and B. licheniformis exhibited oil-releasing effect. Thus, the Daqing oil field is inhabited by aerobic bacteria capable of producing effective oil-releasing agents.     

Production of Oil-Releasing Compounds by Microorganisms from the Daqing Oil Field,China

Twenty pure cultures isolated from formation waters of the Daqing oil field were studied with respect to their capacity to produce surface-active compounds in media with individual hydrocarbons, lower alcohols, and fatty acids. Aerobic saprotrophic bacteria belonging to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, Clavibacter, Pseudomonas, and Acinetobacter decreased the surface tension of cultivation media from 55–63 to 28–44 mN/m. Strains of Bacillus cereus, Rhodococcus ruber, andBacillus licheniformis produced biosurfactants most actively. Bacteria of the genera Rhodococcus, Dietzia, Kocuria, and Gordonia produced exopolysaccharides in media with hydrocarbons. Culture liquids of the strains of R. ruberand B. licheniformis exhibited an oil-releasing effect. Thus, the Daqing oil field is inhabited by aerobic bacteria capable of producing effective oil-releasing agents.     

Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf

An endophytic actinobacterium, designated YIM 65003(T), was isolated from a surface sterilized leaf sample of Cercidiphyllum japonicum collected from Yunnan province, south-west China. The morphological and chemotaxonomic properties of the isolate were typical of members of the genus Rhodococcus. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Rhodococcus fascians DSM 20669(T) (99.6%) and Rhodococcus yunnanensis YIM 70056(T) (99.0%). DNA-DNA hybridization with the above microorganisms (46.3% and 48.8%, respectively), in combination with differences in the biochemical and physiological properties, suggested that strain YIM 65003(T) should be classified within a novel species of the genus Rhodococcus, for which the name Rhodococcus cercidiphylli sp. nov. is proposed, with YIM 65003(T) (=CCTCC AB 207160(T)=DSM 45141(T)) as the type strain. The 16S rRNA gene sequence of strain YIM 65003(T) has been deposited in GenBank under the accession number EU325542.     

Dietzia natronolimnaios sp. nov., a new member of the genus Dietzia isolated from an East African soda lake

Two novel alkaliphilic aerobic organotrophic bacteria have been isolated from a moderately saline and alkaline East African soda lake. The new isolates grow at pH values between 6 and 10, with a pH optimum for growth of 9.0, and at a salt concentration between 0% and 10% (w/v). Phylogenetic analysis based on 16S rDNA sequence shows that these isolates are very closely related (99.6% similarity) and are members of the monospecific genus Dietzia (98.8% and 98.7% similarity). DNA/DNA hybridization revealed a relatedness of 83% between the two isolates, but only 8% between them and the type strain Dietzia maris. The G + C content as measured by thermal denaturation is 66.1 mol%. Phenotypic comparisons between D. maris and one isolate showed that they share very similar morphological and chemotaxonomic properties, but differ significantly in carbon source utilization profiles and halotolerance in alkaline medium. We propose a second species of this genus which we name Dietzia natronolimnaios (type strain 15LN1 = CBS 107.95). Received: October 14, 1997 / Accepted: February 26, 1998     

The properties of hydrocarbon-oxidizing bacteria isolated from the oilfields of Tatarstan, Western Siberia, and Vietnam

Eleven strains of hydrocarbon-oxidizing bacteria, isolated from oilfields, representing the genera Rhodococcus, Gordonia, Dietzia, and Pseudomonas, were characterized as mesophiles and neutrophiles. Rhodococci were halotolerant microorganisms growing in a media containing up to 15% NaCl. All the strains oxidized n-alkanes of crude oil. An influence of the cultivation temperatures (28 or 45 degrees C) and organic supplements on the degradation of C12-C30 n-alkanes in oxidized oil by two bacterial strains of the genus Pseudomonas was shown. The introduction of acetate, propionate, butyrate, ethanol, and sucrose led mainly to the decreased oxidation of petroleum paraffins. At certain cultivation temperatures, the addition of volatile fatty acid salts increased the content of individual n-alkanes in oxidized vs. crude oil.     

Diversity and occurrence of Burkholderia spp. in the natural environment

Both in natural and in managed ecosystems, bacteria are common inhabitants of the phytosphere and the internal tissues of plants. Probably the most diverse and environmentally adaptable plant-associated bacteria belong to the genus Burkholderia. This genus is well-known for its human, animal and plant pathogenic members, including the Burkholderia cepacia complex. However, it also contains species and strains that are beneficial to plants and can be potentially exploited in biotechnological processes. Here we present an overview of plant-associated Burkholderia spp. with special emphasis on beneficial plant-Burkholderia interactions. A discussion of the potential for utilization of stable plant-Burkholderia spp. associations in the development of low-input cropping systems is also provided.     

Molecular definition and the ubiquity of species in the genus Naegleria

To investigate the variability within species of the genus Naegleria, the ITS1,5.8S and ITS2 rDNA were sequenced of several strains of N. lovaniensis and its Western Australian variants, N. australiensis, N. fowleri, N. andersoni, N. jamiesoni, N. tihangensis, N. pringsheimi, N. pagei, N. gruberi sensu lato and a Naegleria lineage that lost a group I intron from the SSUrDNA twintron. As a result, it is possible to define a molecular species within the Naegleria genus. In addition, one strain of each different allozyme cluster was sequenced to investigate whether they belong to described species or should be treated as distinct new species. This leads to the proposal of eleven new species. The sequencing results from those Naegleria spp. of which several strains are available indicate that these species are ubiquitous. The only exception might be the species represented by the WA variants. However, there are still many Naegleria spp. for which only one strain has been isolated, hence, it is important that the search for more isolates should be continued worldwide.     

Skyttea richardsonii sp. nov. from Maine, with a key to the species known from North America

Skyttea richardsonii sp. nov. is described from a sterile corticolous lichen in Maine. It is closest to S. tavaresae, the only other member of the genus to be reported as having annelations on the excipular hairs, but that species occurs on Loxospora spp. and differs in the K+ reaction of the exciple and ascospore size. Minute Phoma-like conidiomata found in some apothecia may represent an independent fungicolous fungus growing on the new species. This is the 10th species of the genus to have been discovered in North America; a key to these species is provided.     

Genetic manipulation tools for Dietzia spp.

Aim: To develop an applicable vector system and a transformation method for the manipulation of Dietzia spp. Methods and Results: The pNV18 Nocardia‐E. coli shuttle vector was tested and found to be a replicating plasmid in Dietzia sp. E1. With the use of pNV18, an electroporation method was optimized for the transformation of Dietzia sp. E1, and a transformation efficiency suitable for genetic manipulations was achieved (2·18 × 10⁴ transformants μg^?1 DNA). The method was also applied for the transformation of Dietzia cinnamea, D. maris, D. natronolimnaea and D. psychralcaliphila. Conclusions: The first applicable vectors and a simple electroporation protocol enabling the manipulation of several Dietzia spp. are presented. Significance and Impact of the Study: Dietzia spp. have clinical, industrial and great environmental importance; however, the analysis of the Dietzia genus is currently hampered by the lack of manipulation techniques. The presented basic tools allow the genetic analysis of several Dietzia species, including the human disease‐associated Dietzia maris.     

Ability of the Dietzia,Gordonia and Rhodococcus Actinobacteria to Accumulate Nickel Ions

Microbiology - Accumulation of nickel ions by actinobacterial strains of Dietzia, Gordonia, and Rhodococcus from the Regional Specialized Collection of Alkanotrophic Microorganisms (IEGM;...     

Cladistic analysis of Enkianthus with notes on the early diversification of the Ericaceae

The genus Enkianthus (Ericaceae) has been subject to a cladistic analysis of morphological, anatomical, embryological, and cytological data, using two species of Clethra as outgroup. In order to evaluate the monophyly of Enkianthus , the genera Epigaea and Phyllodoce from the subfamily Rhododendroideae, and the genus Andromeda from the subfamily Vaccinioideae were also included in an initial analysis which yielded 20 equally parsimonious cladograms. The results indicated that Enkianthus is monophyletic, and a subsequent analysis with only the outgroup taxa and 14 species of Enkianthus yielded two equally parsimonious cladograms with a more resolved topology. In order to obtain strictly monophyletic taxa, the current subgeneric classification of Enkianthus is revised, recognizing four sections: Enkianthus (9 spp.), Andromedina (2 spp.), Meisteria (2 spp.), and Enkiantella (4 spp.). The paper provides a key, illustrations of representative taxa, a cladogram, and strict consensus trees.     

Characterization of a novel long-chain n-alkane-degrading strain, Dietzia sp. E1

The newly isolated strain E1, identified as a Dietzia sp., proved to have an excellent ability to degrade n-C12 to n-C38 alkane components of crude oil. The preferred substrate was the very long-chain alkane n-eicosane at an optimal temperature of 37 degrees C and an optimal pH of 8 under aerobic conditions. The growth and substrate uptake kinetics were monitored during the n-alkane fermentation process, and Dietzia sp. E1 cells were found to possess three distinct levels of cell-surface hydrophobicity. Gas chromatographic/mass spectrometric analysis revealed that intracellular substrate mineralization occurred through the conversion of n-alkane to the corresponding n-alkanal. The monoterminal oxidation pathway was presumably initiated by AlkB and CYP153 terminal alkane hydroxylases, both of their partial coding sequences were successfully detected in the genome of strain E1, a novel member of the Dietzia genus.