Olaf Schmidt

The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Comparative genomic analysis of “dry rot” fungus shows both convergent evolution and divergence among fungal decomposers. Brown rot decay removes cellulose and hemicellulose from wood—residual lignin contributing up to 30% of forest soil carbon—and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the “dry rot” fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.

Indoor wood-decay basidiomycetes: damage, causal fungi, physiology, identification and characterization, prevention and control

Indoor wood-decay fungi cause considerable economical damage. Most of the structural damage to the indoors of buildings in Europe and North America is caused by brown-rot fungi that degrade conifer wood; white-rot fungi, which preferentially attack hardwoods, are less common. This review covers the approximately 80 basidiomycetes that commonly occur in buildings. Emphasis was placed on Serpula lacrymans, which is the most common indoor basidiomycete in central Europe. Meruliporia incrassata, the North American pendant to S. lacrymans, has also received considerable attention. In terms of indoor wood decay, moisture and temperature are the most important influences. Wood samples with a low moisture content can be degraded. High temperatures as an alternative control measure do not kill mycelia, with some species surviving in wood samples in the form of heat-resistant arthrospores at temperatures as high 95°C. For refurbishment and scientific purposes, the identity of the causal species should be known. More recently, several molecular techniques have been used to identify fungi; these results are often conflicting with those obtained by other, earlier applied methods. Sequencing of the internal transcribed spacers (ITS) of the rDNA is currently the best molecular tool. Among the other methods available, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) has also been shown to be able to distinguish closely related sister taxa. For further characterization of indoor basidiomycetes, the complete sequences of the 18S, 28S rDNA and the intergenic spacers with the included 5S rDNA have been acquired for some species. If current projects involving whole funal genome sequencing are not taken into account, Antrodia vaillantii is the first basidiomycete for which the complete rDNA sequence has been deposited. The review closes with fundamentals on the prevention and control of indoor wood decay.

Asian origin and rapid global spread of the destructive dry rot fungus Serpula lacrymans

The dry rot fungus Serpula lacrymans (Basidiomycota) is the most damaging destroyer of wood construction materials in temperate regions. While being a widespread aggressive indoor biodeterioration agent, it is only found in a few natural environments. The geographical source of spread and colonization by this fungus in human environments is thus somewhat of an enigma. Employing genetic markers (amplified fragment length polymorphisms, DNA sequences and microsatellites) on a worldwide sample of specimens, we show that the dry rot fungus is divided into two main lineages; one nonaggressive residing naturally in North America and Asia (var. shastensis), and another aggressive lineage including specimens from all continents, both from natural environments and buildings (var. lacrymans). Our genetic analyses indicate that the two lineages represent well‐differentiated cryptic species. Genetic analyses pinpoint mainland Asia as the origin of the aggressive form var. lacrymans. A few aggressive genotypes have migrated worldwide from Asia to Europe, North and South America and Oceania followed by local population expansions. The very low genetic variation in the founder populations indicate that they have established through recent founder events, for example by infected wood materials transported over land or sea. A separate colonization has happened from mainland Asia to Japan. Our data also indicate that independent immigration events have happened to Oceania from different continents followed by admixture.

Identification of indoor rot fungi by taxon-specific priming polymerase chain reaction.

Summary The internal transcribed spacer (ITS) of the nuclear ribosomal DNA (rDNA) of the main fungal species causing wood rot damages in European buildings was amplified by the polymerase chain reaction (PCR). After sequencing the ITS, fungus-specific oligonucleotide primers were designed for taxon-specific priming PCR. These DNA marker molecules were suitable for the differential diagnosis of the Dry rot fungus, Serpula lacrymans, the Wild merulius, S. himantioides, the Oak polypore, Donkioporia expansa, the Brown cellar fungus, Coniophora puteana, the Broad-spored white polypore, Antrodia vaillantii, the Sap polypore, Tyromyces placenta, and the Yellow-red gill polypore, Gloeophyllum sepiarium. Each specific marker identified isolates of its respective target species. Cross reaction with ‘foreign’ fungi was the exception. Species detection from rot samples in buildings was possible, since DNA from contaminating organisms does not response to the marker molecules. The diagnosis was rapid, since preceding fungal pure cultures, special DNA extraction/purification and restriction by endonucleases are not required.

Species-specific PCR primers in the rDNA-ITS region as a diagnostic tool for Serpula lacrymans

The ITS of the nuclear ribosomal DNA of Serpula lacrymans and S. himantioides was amplified by PCR to evaluate this DNA region as a diagnostic tool. Sequencing of the amplified ITS region revealed a size of the complete ITS of 654 bp for S. lacrymans and 650 bp for S. himantioides. The base sequence difference between the two fungi was used to design species-specific oligonucleotide PCR primers for both species. With laboratory and field samples, each primer selectively detected its target organism. No cross reaction occurred with other fungi causing rot of indoor wood.

Differentiation of indoor wood decay fungi with MALDI-TOF mass spectrometry

Abstract MALDI-TOF MS differentiated mycelia within pairs each of the closely related indoor wood decay fungi Serpula lacrymans, S. himantioides, Coniophoraputena, C. marmorata, and Antrodia vaillantii, A. sinuosa. The method is thus suitable to identify unknown samples by spectrum comparison.

Molecular Identity of Species and Isolates of Internal Pore Fungi Antrodia spp. and Oligoporus placenta

Summary Antrodia vaillantii (DC.: Fr.) Ryv., A. serialis (Fr.) Donk, A. sinuosa (Fr.) P. Karsten, A. xantha (Fr.: Fr.) Ryv. and Oligoporus placenta (Fr.) Gilb.& Ryv. form a group of internal brown-rot fungi (‘Porenschwämme’), which are associated with decay of coniferous woodwork in buildings and timber in ground contact. The fungi have similar occurrence, biology, fruit bodies and mycelia. Their nomenclature has a confusing history and is still not uniform. For a better understanding of the domestic pore fungi and for a reliable species differentiation and identification of isolates, the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) was amplified by polymerase chain reaction and sequenced. Isolates from decayed wood and from culture collections were used. The ITS sequences characteristic of A. vaillantii, A. serialis,A. sinuosa, A. xantha and O. placenta were obtained and deposited in the international databases. The ITS size ranges from 636 to 668 bp. Intraspecific variation was low. A dendrogram was performed for the phylogenetic relationship. Some isolates obtained mislabelled were named correctly according to the ITS sequence. The sequences contribute to our collection of ITS data from internal wood decay fungi made to characterize fungi in culture.

Identification of the dry rot fungus, Serpula lacrymans, and the wild merulius, S. himantioides, by amplified ribosomal DNA restriction analysis (ARDRA)

Summary Isolates of the dry rot fungus, Serpula lacrymans, and of the morphologically similar wild merulius, S. himantioides, were investigated by amplified ribosomal DNA restriction analysis (ARDRA) of the internal transcribed spacer (ITS) region to prove this method as diagnosis tool for the economically important indoor rot fungi. The technique uses the polymerase chain reaction (PCR) to amplify the relatively variable sequences of the ITS region arranged between the highly conserved portions of the 18S and 28S RNA genes of the nuclear ribosomal DNA (rDNA) repeat unit. Subsequent digestion of the amplicon with restriction endonucleases may exhibit differences at species and subspecies level. Using the universal ITS 1/ITS 4 primer combination, the ITS region of all isolates of S. lacrymans and S. himantioides was amplified. The size of the amplified products was about 630bp in both species, as estimated from agarose gel electrophoresis. Digestion of the amplicon with the endonuclease pairs AluI/HhaI and AvaII/MboII, respectively, revealed identical rDNA-ITS fragments for the isolates of both species, indicating their genetic relationship. On the other hand, digestion with BglI/Hinf I and HaeIII/TaqI, respectively, separated the fungi by means of different fragment patterns. Thus, ARDRA-ITS proved to be suited for the identification of both fungi.

Occurrence and significance of bacteria in wood

The review covers investigations on wood-inhabiting bacteria and their significance in wood quality carried out in the Hamburg Institute, with some additional literature. It addresses bacteria isolated from various woody tissues, their action on pits and woody cell walls, examples for wood discolouration by bacteria, the degradation of wood in soil and water environments and of timber treated with preservatives, methods for decay measurement, the efficacy of preservatives, trends to detoxify treated timber waste and aspects of bacteria äs bioprotectants.

Characterization and Identification of the Dry Rot Fungus Serpula lacrymans by Polyacrylamide Gel Electrophoresis

Twenty-one cultures of the important wood rot fungus Serpula lacrymans from various origin were subjected to polyacrylamide gel electrophorcsis. The electrophorctic patterns of the differcnt strains of S. lacrymans were quite similar. The protein bands differed considcrably from t hose of othcr wood destroying fungi. Two cultures, previously assumed to be 5. lacrymans, were proved to be other species of the same genus. Rf values of the protein bands did not depend on the age of fungal cultures nor on the culture medium. In general, electrophoresis of the intracellular proteins may be used to identify 5. lacrymans.