Evaluation of the acetaldehyde production and degradation potential of 26 enological <Emphasis Type="Italic">Saccharomyces</Emphasis> and non-<Emphasis Type="Italic">Saccharomyces</Emphasis> yeast strains in a resting cell model system

Acetaldehyde is relevant for wine aroma, wine color, and microbiological stability. Yeast are known to play a crucial role in production and utilization of acetaldehyde during fermentations but comparative quantitative data are scarce. This research evaluated the acetaldehyde metabolism of 26 yeast strains, including commercial Saccharomyces and non-Saccharomyces, in a reproducible resting cell model system. Acetaldehyde kinetics and peak values were highly genus, species, and strain dependent. Peak acetaldehyde values varied from 2.2 to 189.4 mg l⁻¹ and correlated well (r ² = 0.92) with the acetaldehyde production yield coefficients that ranged from 0.4 to 42 mg acetaldehyde per g of glucose in absence of SO₂. S. pombe showed the highest acetaldehyde production yield coefficients and peak values. All other non-Saccharomyces species produced significantly less acetaldehyde than the S. cerevisiae strains and were less affected by SO₂ additions. All yeast strains could degrade acetaldehyde as sole substrate, but the acetaldehyde degradation rates did not correlate with acetaldehyde peak values or acetaldehyde production yield coefficients in incubations with glucose as sole substrate.     

Profile of the extracellular lignocellulolytic enzymes activities as a tool to select the promising strains of Volvariella volvacea (Bull. ex Fr.) sing

Out of 26 strains of Volvariella volvacea used, 18 were of ‘typical’ type and possessed all the characteristics of a normal V. volvacea mycelium, while the rest 4 ‘atypical’ type strains showed completely distinct mycelial growth characteristics. The remaining 4 strains grew very slowly and exhibited growth characteristics of single spore isolates of V. volvacea. Strains varied in their extracellular lignocellulolytic activities and strains; OE-274, OE-272 and OE-210 with high ligninase enzymes (laccase and polyphenol oxidase) activities, gave highest mushroom yield on pasteurized paddy straw substrate. On the composted paddy straw substrate, additional two strains, OE-213 and OE-215 with lower activities of ligninases also gave higher mushroom yield. Mushrooms were harvested 3 to 4 d early from the composted substrate than on the pasteurized substrate. Activities of endoglucanase, laccase and polyphenol oxidase were found to be more crucial for mushroom yield on pasteurized substrate, while xylanase and β-glucosidase were more important for composted substrate. Strains also varied in their fruiting bodies quality and the substrate used for mushroom cultivation also affected the fruiting body quality. The superior yielding strains varied in shape, size, weight, colour and contents of sodium and potassium in their fruiting bodies; while contents of carbon, calcium and protein did not vary much with the strains.     

Modeling of growth kinetics for Pseudomonas spp. during benzene degradation

A modeling study was conducted on growth kinetics of three different strains of Pseudomonas spp. (Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida) during benzene degradation to determine optimum substrate concentrations for most efficient biodegradation. Batch tests were performed for eight different initial substrate concentrations to observe cell growth and associated substrate degradation using benzene-adapted cells. Kinetic parameters of both inhibitory (Haldane–Andrews, Aiba–Edwards) and noninhibitory (Monod) models were fitted to the relationship between specific growth rate and substrate concentration obtained from the growth curves. Results showed that half-saturation constant of P. fluorescens was the highest among the three strains, indicating that this strain could grow well at high concentration, while P. putida could grow best at low concentration. The inhibition constant of P. aeruginosa was the highest, implying that it could tolerate high benzene concentration and therefore could grow at a wider concentration range. Estimated specific growth rate of P. putida was lower, but half-saturation constant was higher than those from literature study due to high substrate concentration range used in this study. These two kinetic parameters resulted in substantial difference between Monod- and Haldane-type models, indicating that distinction should be made in applying those models.     

Cometabolic degradation of polychlorinated biphenyls (PCBs) by axenic cultures of Ralstonia sp. strain SA-5 and Pseudomonas sp. strain SA-6 obtained from Nigerian contaminated soils

Substantial metabolism of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-tetraCB) and 2,3′,4′,5-tetraCB by axenic cultures of Ralstonia sp. SA-5 and Pseudomonas sp. SA-6 was observed in the presence of biphenyl supplementation, although, the strains were unable to utilize tetrachlorobiphenyls as growth substrate. The former was more amenable to aerobic degradation (∼70% degradation) than the latter (22–45% degradation). Recovery of 2,5-chlorobenzoic acid and chloride from 2,3′,4′,5-tetraCB assay is an indication of initial dioxygenase attack on the 3,4-dichlorophenyl ring. The PCB-degradative ability of both strains was also investigated by GC analysis of individual congeners in Aroclor 1242 (100 ppm) following 12-day incubation with washed benzoate-grown cells. Results revealed two different catabolic properties. Whereas strain SA-6 required biphenyl as inducer of the degradation activity, such induction was not required by strain SA-5. Nearly all the detectable congeners in the mixture were extensively degraded (% reduction in ECD area counts for individual congeners ranged from 50.0 to 100% and 14.2 to 100%, respectively, for SA-5 and SA-6). The two strains exhibited no noticeable specificity for congeners with varying numbers of chlorine substitution and positions. The degradative competence of these isolates most especially SA-5 makes them among the most versatile PCB-metabolizing organisms yet reported.     

Physiological diversity within the <Emphasis Type="Italic">kluyveromyces marxianus</Emphasis> species

The Kluyveromyces marxianus strains CBS 6556, CBS 397 and CBS 712^T were cultivated on a defined medium with either glucose, lactose or sucrose as the sole carbon source, at 30 and 37°C. The aim of this work was to evaluate the diversity within this species, in terms of the macroscopic physiology. The main properties evaluated were: intensity of the Crabtree effect, specific growth rate, biomass yield on substrate, metabolite excretion and protein secretion capacity, inferred by measuring extracellular inulinase activity. The strain Kluyveromyces lactis CBS 2359 was evaluated in parallel, since it is the best described Kluyveromyces yeast and thus can be used as a control for the experimental setup. K. marxianus CBS 6556 presented the highest specific growth rate (0.70 h⁻¹) and the highest specific inulinase activity (1.65 U mg⁻¹ dry cell weight) among all strains investigated, when grown at 37°C with sucrose as the sole carbon source. The lowest metabolite formation and highest biomass yield on substrate (0.59 g dry cell weight g sucrose⁻¹) was achieved by K. marxianus CBS 712^T at 37°C. Taken together, the results show a systematic comparison of carbon and energy metabolism among three of the best known K. marxianus strains, in parallel to K. lactis CBS 2359.     

<Emphasis Type="Italic">Polyporus tenuiculus</Emphasis>: a new naturally occurring mushroom that can be industrially cultivated on agricultural waste

Polyporus tenuiculus is a naturally occurring species from Central and South America that is consumed by different ethnic groups in the region. To determine the optimal conditions for fruiting body production, two strains were assayed on wheat straw and sawdust with or without supplements. Sixty days of incubation at 25°C were needed to produce a solid block. The highest yield was obtained with strain ICFC 383/00 grown on supplemented willow sawdust. In a second experiment the strain ICFC 383/00 and different supplements were used to improve the biological efficiency (BE) and to determine the quality traits and its biodegradation capacity. The highest yields were obtained on sawdust with 25% of supplements reaching 82.7% of BE. Supplements raised the number of flushes, generally from four to five, contributing to increased yields. The type of substrate had a significant effect on fruiting body diameters of P. tenuiculus, and the largest mushrooms were harvested on supplemented substrate with the highest BE coinciding with the highest dry matter loss in substrates. P. tenuiculus showed a capacity to degrade sawdust, causing a decrease of 67.2–74.5% in cellulose, 80.4–85.7% in hemicellulose, and 60.6–66.2% in lignin content at the end of the cultivation cycle. The decrease in hemicellulose was relatively greater than that of cellulose and lignin on supplemented substrates. This is the first report of the cultivation of P. tenuiculus on lignocellulosic waste, and it is a promising species both for commercial production and for its potential use in the degradation of other biowastes.     

Formation of polyhydroxylated isoflavones from the soybean seed isoflavones daidzein and glycitein by bacteria isolated from tempe

Five tempe-derived bacterial strains identified as Micrococcus or Arthrobacter species were shown to transform the soybean isoflavones daidzein and glycitein to polyhydroxylated isoflavones by different hydroxylation reactions. All strains converted glycitein and daidzein to 6,7,4′-trihydroxyisoflavone (factor 2) and the latter substrate also to 7,8,4′-trihydroxyisoflavone. Three strains transformed daidzein to 7,8,3′,4′-tetrahydroxyisoflavone and 6,7,3′,4′-tetrahydroxyisoflavone. In addition, two strains formed 6,7,8,4′-tetrahydroxyisoflavone from daidzein. Conversion of glycitein by these two strains led to the formation of factor 2 and 6,7,3′,4′-tetrahydroxyisoflavone. The structures of these transformation products were elucidated by spectroscopic techniques and chemical degradation. Revision received: 9 September 1995 / Accepted: 21 September 1995     

<Emphasis Type="Italic">Singulispaera mucilagenosa</Emphasis> sp. nov., a novel acid-tolerant representative of the order <Emphasis Type="Italic">Planctomycetales</Emphasis>

Two novel strains of budding bacteria, Z-0071^T and Z-0072, were isolated from dystrophic humified waters formed by xylotrophic fungi in the course of spruce wood degradation. The cells of both strains are coccoid (0.95–1.80 μm), nonmotile, single or arranged in pairs. The cells have a complex system of intracellular membranes and are covered with fimbriae and surrounded by a mucous capsule up to 0.3 μm thick. Both strains are aerobic organoheterotrophic, mesophilic, and acid-tolerant microorganisms that are able to grow under microaerobic conditions. They utilize N-acetyl-glucosamine, carbohydrates, and lactate as growth substrates. The strains grow in a pH range of 4.0–7.5 with an optimum at 6.0–6.5. The temperature range for growth is 4–30°C, with an optimum at 25–28°C. Strains Z-0071^T and Z-0072, inhabitants of dystrophic low-mineral waters, are NaCl-sensitive: the NaCl content in the media above 0.5 g/l inhibited growth. The main fatty acids of strains Z-0071^T and Z-0072 are C_16:0, C_18:1ω9c, and C_{18:2ω9c, 12c}. The DNA G + C base content is 51.2–51.7 mol %. The sequences of the 16S rRNA gene fragments (1310 bp) of strains Z-0071^T and Z-0072 were found to be identical. The obtained sequences showed a 94.3% similarity with the sequences of the type strain of the most closely related species Singulisphaera acidiphila MOB10≅T. The phenotypic and phylogenetic properties of strains Z-0071^T and Z-0072 support classification of these strains within the genus Singulisphaera as a new species Singulisphaera mucilagenosa sp. nov., with the type strain Z-0071^T (VKM B-2626).     

Biodegradation of benzene by pure and mixed cultures of <Emphasis Type="Italic">Bacillus</Emphasis> spp.

Benzene has a wide range of industrial applications, but it is also a major source of environmental pollution. The most eco-friendly/cost-effective method of remediation is biodegradation. In the present study, we used a variety of microbial strains in different combinations on a selection of substrate concentrations to determine the most effective degradation processes. Bacterial strains of pure culture (L₄, N₃, and N₆) were isolated from oil sludge in both Luria–Bertani buffer (LB) and nutrient broth media, and identified by 16S-rRNA analysis (≥98% similarity). The degradation experiments were performed using different combinations of bacterial strains (L₄, N₃, N₆, L₄ + N₃, L₄ + N₆, N₃ + N₆, and L₄ + N₃ + N₆) in modified carbon-free media with different concentrations of benzene as a carbon source (60, 100, and 160 mg l⁻¹) at 30 °C. The isolates of L₄ (Acc no: FJ686821), N₃ (FJ686825) and N₆ (FJ868628) were identified as Bacillus spp. using 16S-rRNA gene sequence analysis. All combinations of isolates have the capacity to degrade benzene. However, the L₄ + N₃ combination was more efficient than the other mixed or single cultures. In the presence of N₆ isolate, the degradation rate of benzene decreased, possibly due to inter- and/or intra species interaction amongst the bacteria. The kinetic parameters ‘K _m’ of the Lineweaver–Burk regressions conducted as part of this experiment showed that the lower the level of K _m was, the better the biodegradation achieved. The results of this study showed that the use of Bacillus strains in benzene decomposition is feasible. In addition, different strain combinations exhibited different degradation patterns, which are attributed to the most efficient mixed cultures of Bacillus spp.     

Isolation and characterization of RDX-degrading <Emphasis Type="Italic">Rhodococcus</Emphasis> species from a contaminated aquifer

Groundwater contamination by the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a global problem. Israel’s coastal aquifer was contaminated with RDX. This aquifer is mostly aerobic and we therefore sought aerobic bacteria that might be involved in natural attenuation of the compound in the aquifer. RDX-degrading bacteria were captured by passively sampling the indigenous bacteria onto sterile sediments placed within sampling boreholes. Aerobic RDX biodegradation potential was detected in the sediments sampled from different locations along the plume. RDX degradation with the native sampled consortium was accompanied by 4-nitro-2,4-diazabutanal formation. Two bacterial strains of the genus Rhodococcus were isolated from the sediments and identified as aerobic RDX degraders. The xplA gene encoding the cytochrome P450 enzyme was partially (~500 bp) sequenced from both isolates. The obtained DNA sequences had 99% identity with corresponding gene fragments of previously isolated RDX-degrading Rhodococcus strains. RDX degradation by both strains was prevented by 200 μM of the cytochrome P450 inhibitor metyrapone, suggesting that cytochrome P450 indeed mediates the initial step in RDX degradation. RDX biodegradation activity by the T7 isolate was inhibited in the presence of nitrate or ammonium concentrations above 1.6 and 5.5 mM, respectively (100 mg l⁻¹) while the T9N isolate’s activity was retarded only by ammonium concentrations above 5.5 mM. This study shows that bacteria from the genus Rhodococcus, potentially degrade RDX in the saturated zone as well, following the same aerobic degradation pathway defined for other Rhodococcus species. RDX-degrading activity by the Rhodococcus species isolate T9N may have important implications for the bioremediation of nitrate-rich RDX-contaminated aquifers.     

The production of eicosapentaenoic acid by representatives of the genus <Emphasis Type="Italic">Mortierella</Emphasis> grown on brewers’ spent grain

Brewers’ spent grain (BSG) was evaluated as substrate for the production of eicosapentaenoic acid (EPA) by solid-state fermentation with 29 fungal strains representing different Mortierella species. The effect of a 10% (w/w) linseed oil (LSO) supplement on EPA production was also determined. All the strains produced EPA on the substrate, while addition of the LSO improved the EPA yield of most strains. The strains producing the most EPA in the absence of additional LSO generally also produced the most EPA when LSO was added to the BSG. The strains, which produced the highest levels of EPA on BSG supplemented with LSO were Mortierella antarctica Mo 67 and Mortierella epicladia Mo 101, which respectively produced 2.8 mg and 2.5 mg EPA per g of BSG.     

Optimization and modeling of phenanthrene degradation by <Emphasis Type="Italic">Mycobacterium</Emphasis> sp. 6PY1 in a biphasic medium using response-surface methodology

In the present paper, the degradation of phenanthrene, a model polycyclic aromatic hydrocarbon compound, by the Mycobacterium strain 6PY1 was optimized in a biphasic culture medium. The optimization and modeling were performed using the design of experiments methodology. The temperature, the silicone oil/mineral salts medium volume ratio, and the initial cell concentration, were used as the central composite design parameters. In all experiments, the phenanthrene was degraded to undetectable levels. Response surface methodology was successfully employed to derive an empirical model describing the rate and time of degradation and to deduce the optimal degradation conditions. As a result of the optimization processes, the optimal responses for the degradation rate, the volumetric degradation rate, and the 90% degradation time were estimated to be 0.172 mg h⁻¹, 22 mg l⁻¹ h⁻¹, and 18 h, respectively.     

Bioconversion of soy isoflavones daidzin and daidzein by <Emphasis Type="Italic">Bifidobacterium</Emphasis> strains

Twenty-two strains of Bifidobacterium, representative of eight major species of human origin, were screened for their ability to transform the isoflavones daidzin and daidzein. Most of the strains released the aglycone from daidzin and 12 gave yields higher than 90%. The kinetics of growth, daidzin consumption, and daidzein production indicated that the hydrolytic activity occurred during the growth. The supernatant of the majority of the strains did not release the aglycone from daidzin, suggesting that cell-associated β-glucosidases (β-Glu) are mainly responsible for the metabolism of soybean glyco-conjugates. Cell-associated β-Glu was mainly intracellular and significantly varied among the species and the strains. The lack of β-Glu was correlated with the inability to hydrolyze daidzin. Although S-equol production by anaerobic intestinal bacteria has been established, information on S-equol-producing bifidobacteria is contradictory. In this study, 22 bifidobacteria failed to transform daidzein into reduced metabolites under all the experimental conditions, excluding any role in the reductive pathway of daidzein toward the production of S-equol. These results suggest that selected probiotic strains of Bifidobacterium can be used to speed up the release of daidzein, improving its bioavailability for absorption by colonic mucosa and/or biotransformation to S-equol by other intestinal microorganisms.     

Analysis of insect toxin complex gene variability of <Emphasis Type="Italic">Yersinia pestis</Emphasis> and <Emphasis Type="Italic">Yersinia pseudotuberculosis</Emphasis> strains

The nucleotide sequences of the Tc’s insect toxin complex genes have been analyzed in 18 natural strains of the main and non-main subspecies of Yersinia pestis isolated in different natural foci in the Russian Federation, as well as neighboring and more remote countries, as compared to the data on Y. pestis and Y. pseudotuberculosis strains stored in the NCBI GenBank database. The nucleotide sequences of these genes in plague agent strains have been found to be highly conserved, in contrast to those of the pseudotuberculosis agent. The sequences of two genes, tcaC and tccC2, have been found to be almost identical in Y. pestis strains, whereas other three genes (tcaA, tcaB, and tccC1) contain a few mutations, which, however, are not common for all strains of the plague agent. Exceptions are only strains of the Y. pestis biovar orientalis, whose tcaB gene is in a nonfunctional state due to a nucleotide deletion. The results suggest that the formation of the species Y. pestis as an agent of a natural focal infection with a transmissive mechanism has not resulted in degradation of the Tc’s complex genes. Instead, these genes are likely to have been altered as the plague agent have been adapting to the new environment.     

Ecophysiological Variabilities in Ectohydrolytic Enzyme Activities of Some <Emphasis Type="Italic">Pseudoalteromonas</Emphasis> Species, <Emphasis Type="Italic">P. citrea,P. issachenkonii</Emphasis>, and <Emphasis Type="Italic">P. nigrifaciens</Emphasis>

The ecophysiological variabilities in the ectohydrolytic enzyme profiles of the three species of Pseudoalteromonas, P. citrea, P. issachenkonii, and P. nigrifaciens, have been investigated. Forty-one bacteria isolated from several invertebrates, macroalgae, sea grass, and the surrounding water exhibited different patterns of hydrolytic enzyme activities measured as the hydrolysis of either native biopolymers or fluorogenic substrates. The activities of the following enzymes were assayed: proteinase, tyrosinase, lipase, amylase, chitinase, agarase, fucoidan hydrolase, laminaranase, alginase, pustulanase, cellulase, β-glucosidase, α- and β-galactosidases, β-N-acetylglucosaminidase, β-glucosaminidase, β-xylosidase, and α-mannosidase. The occurrence and cell-specific activities of all enzymes varied over a broad range (from 0 to 44 μmol EU per hour) and depended not only on taxonomic affiliation of the strain, but also on the source/place of its isolation. This suggests ‘specialization’ of different species for different types of polymeric substrates as, for example, all strains of P. citrea and P. issachenkonii hydrolyzed alginate and laminaran, while strains of P. nigrifaciens were lacking the ability to hydrolyze most of the algal polysaccharides. The incidence of certain enzymes such as fucoidan hydrolases, alginate lyases, agarases, and α-galactosidases might be strain specific and reflect its particular ecological habitat. Received: 15 February 2002 / Accepted: 27 March 2002     

Growth and Mating of <Emphasis Type="Italic">Cryptococcus neoformans</Emphasis> var. <Emphasis Type="Italic">grubii</Emphasis> on Woody Debris

A total of 36 Cryptococcus neoformans strains originating from South Africa were screened for wood degrading enzymes. All strains tested positive for cellulase activity while none where capable of xylan degradation. Three C. neoformans var. grubii strains, originating from clinical and environmental samples, representing the same genotype (VNI/AFLP1—C. neoformans var. grubii) and MATα, were evaluated for growth on debris of two common tree species in South Africa: Acacia mearnsii and Eucalyptus camaldulensis. The mating capability of all the C. neoformans strains was evaluated on similar debris. Strains grown on A. mearnsii yielded substantially greater yeast populations. A total of 26%, 6%, 46%, and 80% of the 36 C. neoformans strains tested were either able to mate or develop filaments when crossed on A. mearnsii and E. camaldulensis debris, V8 juice, and yeast carbon base (YCB) agar, respectively. Filamentation and monokaryotic fruiting was observed in 3% of strains when C. neoformans was cultured on either A. mearnsii, E. camaldulensis debris, or YCB. The results indicate that this fungus is capable of completing its life cycle and can produce basidiospores on woody debris. In the future, these findings should be considered when studying the epidemiology, microbial ecology, and proposed infection process of this global pathogen.     

<Emphasis Type="Italic">Helicobacter</Emphasis> urease: Niche construction at the single molecule level

The urease of the human pathogen, Helicobacter pylori, is essential for pathogenesis. The ammonia produced by the enzyme neutralizes stomach acid; thereby modifying its environment. The dodecameric enzyme complex has high affinity for its substrate, urea. We compared urease sequences and derivative 3D homology model structures from all published Helicobacter genomes and an equal number of genomes belonging to strains of another enteric bacterium, Escherichia coli. We found that the enzyme’s architecture adapts to fit its niche. This finding, coupled to a survey of other physiological features responsible for the bacterium’s acid resistance, suggests how it copes with pH changes caused by disease onset and progression.     

Biochemical characterisation of an allantoate-degrading enzyme from French bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis>): the requirement of phenylhydrazine

In tropical legumes like French bean (Phaseolus vulgaris) or soybean (Glycine max), most of the atmospheric nitrogen fixed in nodules is used for synthesis of the ureides allantoin and allantoic acid, the major long distance transport forms of organic nitrogen in these species. The purpose of this investigation was to characterise the allantoate degradation step in Phaseolus vulgaris. The degradation of allantoin, allantoate and ureidoglycolate was determined “in vivo” using small pieces of chopped seedlings. With allantoate and ureidoglycolate as substrates, the determination of the reaction products required the addition of phenylhydrazine to the assay mixture. The protein associated with the allantoate degradation has been partially purified 22-fold by ultracentrifugation and batch separation with DEAE-Sephacel. This enzyme was specific for allantoate and could not use ureidoglycolate as substrate. The activity was completely dependent on phenylhydrazine, which acts as an activator at low concentrations and decreases the affinity of the enzyme for the substrate at higher concentrations. The optimal pH for the activity of the purified protein was 7.0 and the optimal temperature was 37°C. The activity was completely inhibited by EDTA and only manganese partially restored the activity. The level of activity was lower in extracts obtained from leaves and fruits of French bean grown with nitrate than in plants actively fixing nitrogen and, therefore, relying on ureides as nitrogen supply. This is the first time that an allantoate-degrading activity has been partially purified and characterised from a plant extract. The allosteric regulation of the enzyme suggests a critical role in the regulation of ureide degradation.     

Phenotypic and genotypic diversity among strains of <Emphasis Type="Italic">Aureobasidium pullulans</Emphasis> in comparison with related species

Intra-specific diversity of 200 Aureobasidium pullulans strains isolated from different sources and their relatives Kabatiella lini CBS 125.21 T and Hormonema prunorum CBS 933.72 T were studied by assessment of macromorphological, and physiological tests, sodium dodecyl sulfate-polyacrylamide gel electrophoresis technique (SDS–PAGE) of whole-cell proteins as well as enterobacterial repetitive intergenic consensus (ERIC)-, repetitive extragenic palindromic (REP)- and BOX-PCR techniques (collectively known as rep-PCR). Rep-PCR is an efficient procedure for discrimination of A. pullulans in terms of simplicity and rapidity. RFLP-PCR technique was applied for the identification of A. pullulans isolates and distinction from related species. This technique was insufficient for investigation of intra-specific diversity. The tested strains of A. pullulans could be divided into two groups based on their macromorphological, protein patterns obtained after SDS-PAGE as well as rep-PCR patterns. The first group of strains shared similar characteristics and was very different from the second one, designated as “complex group”, consisting of strains with very little similarities within the group. Phenetic analysis of ERIC banding patterns failed to group the isolates on the basis of their substrate or geographical origin. Using 18S rDNA gene sequence analysis of selected isolates, three strains: HoHe3 km, A. pullulans DSM 62074 and H. prunorum CBS 933.72 T were distinguished from all other analysed members of genera Aureobasidium and Kabatiella. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, <Emphasis Type="Italic">Rhizoctonia solani</Emphasis>

The rRNA cistron (18S–ITS1–5.8S–ITS2–28S) is used widely for phylogenetic analyses. Recent studies show that compensatory base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3–21 nuclei per cell), 1–3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described as R. solani are a species distinct from other AGs. The ITS1–5.8S–ITS2 sequences were analyzed by direct sequencing of PCR products from 497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly, the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.