Jarkko Hantula

Genetic variation in Phlebiopsis gigantea as detected with random amplified microsatellite (RAMS) markers

Random Amplified Microsatellite (RAMS) markers were used to detect variation among Phlebiopsis gigantea isolates from seven European countries. The scoring of 26 bands revealed five markers common to all isolates and 21 variable markers, of which six occurred in only one strain. A considerable amount of variation was observed among the progeny isolates of single strains. The analysis of variable markers resulted in 75 different banding patterns among the 86 isolates studied. The high degree of polymorphism and heterozygosity observed in RAMS markers suggests that the amount of genetic variation within this fungus is considerable. The equal distribution of markers in strains from different locations and the lack of country-specific markers suggests that genetic differentiation among the populations is low. The lack of distinct groups of similar banding patterns supports the idea of P. gigantea being a true biological species consisting of a single intersterility group.

Description of Four Pentachlorophenol-Degrading Bacterial Strains as Sphingomonas chlorophenolica sp. nov.

Summary The chemotaxonomy, physiology and ultrastructure were studied of four pentachlorophenol (PCP) degrading strains known as Arthrobacter sp. ATCC 33790, Flavobacterium sp. ATCC 39723, Pseudomonas sp. RA2 and Pseudomonas sp. SR3. All of them were Gram-negative rods, and electron microscopy revealed an outer membrane in each of the four strains. The whole cell fatty acid compositions of the strains were similar: from 56 to 62% of octadecenoic and from 7 to 15% each of 2-hydroxymyristic, cis-9-hexadecenoic and hexadecanoic acids. All strains contained sphingolipids and no Iipopolysaccharide. The main respiratory quinone was ubiquinone 10, and the G+C contents of the DNA ranged from 63 to 67 mol%. On the basis of chemotaxonomic data, biochemical and physiological properties, and whole cell protein profiles, the four pentachlorophenol-degrading strains Arthrobacter sp. ATCC 33790, Flavobacterium sp. ATCC 39723, Pseudomonas sp. RA2 and Pseudomonas sp. SR3 were reclassified in the genus Sphingomonas as a new species S. chlorophenolica sp. nov.

Description of Chlorophenol-Degrading Pseudomonas sp. Strains KF1T, KF3, and NKF1 as a New Species of the Genus Sphingomonas, Sphingomonas subarctica sp. nov.

Gram-negative polychlorophenol-degrading bacterial strains KF1T (T = type strain), KF3, and NKF1, which were described previously as Pseudomonas saccharophila strains, were studied by chemotaxonomic, genetic, and physiological methods and by electron microscopy and compared with selected xenobiotic compound-degrading bacteria. These strains contained sphingolipids with d-18:0, d-20:1, and d-21:1 as the main dihydrosphingosines, ubiquinone 10 as the main respiratory quinone, and spermidine as the major polyamine, and the DNA G + C content was 66 mol%. The cellular fatty acids included about 60% octadecenoic acid, 9% 2-hydroxymyristic acid, 14% cis-9-hexadecenoic acid, and 10% hexadecanoic acid. These strains exhibited less than 97% 16S ribosomal DNA sequence similarity to all of the other taxa studied. In the DNA-DNA reassociation studies the highest levels of reassociation between these strains and previously described species were less than 40%. Thin sections of cells of strains KF1T, KF3, and NKF1 were examined by electron microscopy, and the results showed that the cells had peculiar concentrically arranged layered membranous blebs that extruded from the outer membrane, especially at the cell division points. On the basis of the results of this study, polychlorophenol-degrading strains KF1T, KF3, and NKF1 are considered members of a new species of the genus Sphingomonas, Sphingomonas subarctica. The polycyclic aromatic hydrocarbon-degrading organism Sphingomonas paucimobilis EPA 505 was closely related to Sphingomonas chlorophenolica as determined by chemotaxonomic, phylogenetic, and physiological criteria. The xenobiotic compound degraders Alcaligenes sp. strain A175 and Pseudomonas sp. strain BN6 were identified as members of species of the genus Sphingomonas.

Variation within Gremmeniella abietina in Finland and other countries as determined by Random Amplified Microsatellites (RAMS)

Genetic variation within Gremmeniella abietina var. abietina was studied using the Random Amplified Microsatellite-technique (RAMS). Ninety-three isolates were investigated, originating mostly from Finland, but also from Canada, U.S.A., Japan, Norway, Italy, Iceland and Sweden. Four banding pattern types were observed corresponding to the present division of this species in Asian, North American and two types of European races. Furthermore, an additional banding pattern was also observed. Intraracial variation was observed within all races, the North American one being the most polymorphic. Isolates of the large tree type (LTT) Gremmeniella from North America, Italy and Iceland contained RAMS alleles not observed in Finland, Sweden or Norway. Therefore, the isolates of LTT Gremmeniella should not be transported even within the area of its natural occurrence.

Characterization of Cyanobacteria by SDS-PAGE of whole-cell proteins and PCR/RFLP of the 16S rRNA gene

Abstract Planktonic, filamentous cyanobacterial strains from different genera, both toxic and nontoxic strains, were characterized by SDS-PAGE of whole-cell proteins and PCR/RFLP of the 16S rRNA gene. Total protein pattern analysis revealed the mutual relationships at the genus level. Restriction fragment length polymorphism (RFLP) of the 16S rRNA gene with reference strains proved to be a good method for the cyanobacterial taxonomy. The nonheterocystous strains outgrouped from the nitrogen-fixing ones. With both methods, Aphanizomenon clustered with Anabaena, and Nodularia with Nostoc. In the RFLP study of Anabaena, the neurotoxic strains were identical, but the hepatotoxic ones formed a heterogeneous group. Genetic distances found in the RFLP study were short, confirming that close genotypic relationships underlie considerable diversity among cyanobacterial genera.

Molecular evidence suggests that Ceratobasidium bicorne has an anamorph known as a conifer pathogen

In Finland and Norway, a uninucleate Rhizoctonia sp. is causing a root dieback disease on nursery-grown Norway spruce and Scots pine seedlings. This Rhizoctonia can be fruited under laboratory conditions and the basidial characters fit well in the species concept of Ceratobasidium bicorne, a species originally described as a moss parasite under forest conditions. Further comparison using traditional methods (cultural morphology, nuclear condition, anastomosis) has not been possible as the forest population of C. bicorne has apparently never been cultured. In the present study, we isolated DNA from a herbarium sample of C. bicorne grown on the moss Polytrichastrum formosum. Sequence analysis of the PCR-amplified rDNA region containing the internal transcribed spacer (ITS) regions and the 5.8S rDNA gene was used to examine the conspecificity of the herbarium sample and the uninucleate Rhizoctonia sp. The nucleotide sequence of the 5.8S rDNA gene was identical between the herbarium sample and five sequenced uninucleate Rhizoctonia strains. Within the uninucleate Rhizoctonia sp., the sequence identity ranged from 96.1 to 100% in ITS1 and from 99.6 to 100% in ITS2. The sequence from the herbarium sample fits well within these limits, strongly suggesting that the uninucleate Rhizoctonia sp. and C. bicorne are conspecific. Interestingly, two of the uninucleate Rhizoctonia strains produced two ITS alleles: the genetic implications are also discussed.

Comparison of partial 16S rRNA gene sequences obtained from activated sludge bacteria

Abstract The cultivated and uncultivated bacterial communities of an activated sludge plant were studied. Two samples were taken and a total of 516 bacterial isolates were classified into groups using their whole-cell protein patterns. The distribution of bacteria into protein-pattern groups differed significantly between the two samples, suggesting variation in culturable bacterial flora. Partial 16S rRNA gene sequences were determined for representatives of the commonest protein-pattern groups. Most of the sequences obtained were previously unknown, but relatively closely related to known sequences of organisms belonging to the α, β or γ subclasses of the proteobacteria, the first two subclasses being predominant. This classification of bacteria isolated on a diluted nutrient-rich medium differed from recent culture-dependent studies using nutrient-rich media. The uncultivated bacterial community was studied by analyzing ten partial 16S rRNA gene sequences cloned directly from activated sludge. None of the cloned sequences was identical to those determined for culturable organisms; or to those in the GenBank database. They were, however, related to the α or β subclasses of the proteobacteria, or to the gram-positive bacteria with a high G+C DNA content.

Sienivirusten potentiaali juurikäävän torjunnassa

Suomessa esiintyvät juurikäävät kuuluvat boreaalisten metsien haitallisimpiin puiden sienitautien aiheuttajiin. Niitä torjutaan aktiivisesti erilaisilla keinoilla, mutta metsätaloudessa olisi edelleen tarvetta uusille torjuntamenetelmille, joita voitaisiin hyödyntää sellaisilla kasvupaikoilla, joille juurikääpä on jo valmiiksi levinnyt. Tässä yhteenvetoartikkelissa tarkastellaan juurikäävän virustorjunnan mahdollisuuksia keräämällä yhteen nykyinen tutkittu tieto juurikäävän virusten vaikutuksista isäntäänsä, niiden biologisesta monimuotoisuudesta ja leviämisbiologiasta sekä juurikäävän puolustautumisesta virusinfektiota vastaan. Juurikäävän virustorjunnan mahdollisuudet näyttävät lupaavilta, mutta sienen ja sen virusten välinen suhde pitäisi tuntea nykyistä paremmin ennen kuin uusi torjuntamenetelmä voidaan ottaa käyttöön.

Determination of taxonomic resolution capacity of conventional one-dimensional SDS-polyacrylamide gel electrophoresis of whole-cell proteins using

The capacity of one-dimensional SDS-PAGE of whole bacterial cells to both separate and cluster taxonomic units is studied using members of Enterobacteriaceae as test material. The results show that intraspecies variation can be detected and on the other hand the degree of taxonomic divergence which still can be grouped together is determined. In addition the system has high tolerance to changes in cell culture conditions making the usage of SDS-PAGE suitable for applications where rapid and reliable bacterial identification is needed.