Current exploration of the ecology of soil fungal and bacterial communities and microbe-catalyzed processes in soils largely rely on community composition analysis using next-generation-sequencing of PCR amplicons (1). Typically, the relative abundance of individual members of microbial communities are derived from the analyses of 16S rRNA region of prokaryotic microorganisms and 18S rRNA or internal transcribed spacer (ITS) region of the rDNA for fungi and other microeukaryots. The analysis of fungal ITS sequences is helpful tool for molecular systematics at the species level, and even within species, but the quantitative information on the relative abundance of individual taxa is skewed due to the presence of multiple rDNA gene copies per genome, ranging from 10 to 200 (2). On the other hand, it was demonstrated that there is a group of genes like the elongation factor-1 alpha (tef1) or RNA polymerase II second largest subunit (rpb2) that are consistently present in one copy per fungal genome and exhibit sufficient variation to be used for phylogenetic analysis and taxonomic assignment (3). The use of such genes offers the possibility to directly count fungal genomes and improve the knowledge on the relative importance of individual taxa of fungi in the environmental processes. Here we demonstrate that the amount of ITS copies per nanogram DNA shows high variation among soil basidiomycetes and even closely related species largely differ in this respect. We also demonstrate that the use of the rpb2 gene is applicable for analysis of soil fungal communities and that the data derived using this molecular marker are largely different from those based on the amplicon sequencing of the ITS. Although the phylogeneti discriminative power of the rpb2 gene is limited, it still offers a suitable tool to infer fungal taxonomy at least on the level of families.

Cellulose is the main polymeric component of the plant cell wall, the most abundant polysaccharide on Earth, and an important renewable resource. Basidiomycetous fungi belong to its most potent degraders because many species grow on dead wood or litter, in environment rich in cellulose. Fungal cellulolytic systems differ from the complex cellulolytic systems of bacteria. For the degradation of cellulose, basidiomycetes utilize a set of hydrolytic enzymes typically composed of endoglucanase, cellobiohydrolase and beta-glucosidase. In some species, the absence of cellobiohydrolase is substituted by the production of processive endoglucanases combining the properties of both of these enzymes. In addition, systems producing hydroxyl radicals based on cellobiose dehydrogenase, quinone redox cycling or glycopeptide-based Fenton reaction are involved in the degradation of several plant cell wall components, including cellulose. The complete cellulolytic complex used by a single fungal species is typically composed of more than one of the above mechanisms that contribute to the utilization of cellulose as a source of carbon or energy or degrade it to ensure fast substrate colonization. The efficiency and regulation of cellulose degradation differs among wood-rotting, litter-decomposing, mycorrhizal or plant pathogenic fungi and yeasts due to the different roles of cellulose degradation in the physiology and ecology of the individual groups.

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The links among the changes in litter chemistry, the activity of extracellular enzymes and the microbial community composition were observed in Quercus petraea litter. Three phases of decomposition could be distinguished. In the early 4-month stage, with high activities of β-glucosidase, β-xylosidase and cellobiohydrolase, 16.4% of litter was decomposed. Hemicelluloses were rapidly removed while cellulose and lignin degradation was slow. In months 4-12, with high endocellulase and endoxylanase activities, decomposition of cellulose prevailed and 31.8% of litter mass was lost. After the third phase of decomposition until month 24 with high activity of ligninolytic enzymes, the litter mass loss reached 67.9%. After 2 years of decay, cellulose decomposition was almost complete and most of the remaining polysaccharides were in the form of hemicelluloses. Fungi largely dominated over bacteria as leaf endophytes and also in the litter immediately before contact with soil, and this fungal dominance lasted until month 4. Bacterial biomass (measured as phospholipid fatty acid content) in litter increased with time but also changed qualitatively, showing an increasing number of Actinobacteria. This paper shows that the dynamics of decomposition of individual litter components changes with time in accordance with the changes in the microbial community composition and its production of extracellular enzymes.