Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil

The small-scale distribution of activities of extracellular laccase, Mn-peroxidase, endoglucanase, cellobiohydrolase, β-glucosidase, endoxylanase, β-xylosidase, chitinase, and acid phosphatase were studied in the litter (L) and organic (H) horizons of Quercus petraea forest soil and related to the distribution of microbial biomass. Geostatistical analysis showed that the spatial autocorrelation of the enzyme activities and soil microbial biomass measured as phospholipid fatty acids (PLFA) and ergosterol content occurred at similar scales, typically in the range of tens of centimeters. The size of the spatial structures differed between the L and H horizons; for most of the studied enzymatic processes, litter exhibited a higher spatial variability (smaller autocorrelation distances). The distribution of several enzymes, including laccase, Mn-peroxidase, and some hydrolases, reflected the distribution of fungal biomass. Polysaccharide hydrolases exhibited similar spatial distribution patterns in the L horizon, and their activity coincided with a high fungal/bacterial biomass ratio.     

Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED

Fungi are important in soils as both decomposers and plant symbionts, and an understanding of the composition of their complex communities is thus indispensable to answer a variety of ecological questions. 454 Pyrosequencing is currently the method of choice for the in-depth analysis of fungal communities. However, the interpretation of its results is complicated by differences in data analysis approaches that make inter-study comparisons difficult. The pyrosequencing studies published so far have also used variable molecular targets in fungal rDNA. Although the ITS region and, in particular, ITS1 appear to be the most frequent sequencing targets, the use of various primers with different coverages of fungal groups remains a serious problem. Sequence length limits also vary widely across studies, and in many studies, length differences may negatively affect sequence similarity clustering or identification. Unfortunately, many studies neglect the need to correct for method-dependent errors, such as pyrosequencing noise or chimeric sequences. Even when performed, error rates in sequences may be high, and consensus sequences created by sequence clustering therefore better represent operational taxonomic units. We recommend a data analysis workflow that includes sequence denoising, chimera removal, sequence trimming before clustering and random resampling before calculating diversity parameters. The newly developed free pipeline (SEED) introduced here can be used to perform all the required analytical steps. The improvement and unification of data analysis procedures should make future studies both more reliable and comparable and allow meta-studies to be performed to provide more general views on fungal diversity, biogeography or ecology.     

Evaluating the role of biotic and chemical components of plant-soil feedback of primary successional plants

Biology and Fertility of Soils - During primary succession, vegetation and soil form important feedbacks that enhance plant species turnover. However, the mechanisms underlying such plant-soil...     

Enzyme activities and microbial biomass in topsoil layer during spontaneous succession in spoil heaps after brown coal mining

Changes in the activity of extracellular enzymes (cellobiohydrolase, β-glucosidase, β-xylosidase, chitinase, arylsulfatase and phosphatases) and the changes in microbial community and abiotic properties in the topsoil layer, as well as soil abiotic properties during primary succession were investigated in a brown coal mine deposit area near Sokolov, Czech Republic. The study considered the chronosequence of 4 post-mining plots, 4-, 12-, 21- and 45-year old. The 4-year old site had no vegetation cover. Herbs and grasses (mainly Calamagrostis epigeios) were present on the 12-year old plot, shrubs (Salix caprea) occurred on the 21-year old plot and tree cover (Betula spp. and Populus tremuloides) developed on the 45-year old plot. Soil pH gradually decreased with site age, while the content of P, K, C and N peaked in the 21-year old site, being significantly lower in the 45-year old site and much lower in the 4- and 12-year old sites. Phosphatase activities were strongly affected by seasonality while the activities of all the other enzymes measured were more influenced by the effects of succession age and soil layer than by seasonality. Succession age was also the most important factor affecting the total and bacterial PLFA contents, followed by the effects of soil layer and season while for the fungal biomass content-related properties (ergosterol, fungal PLFA and the fungal/bacterial PLFA ratio), season was the most important. Activities of individual enzymes in the topsoil (0–5 cm depth) were significantly affected by both site age and season. Cellobiohydrolase and β-xylosidase were more affected by site age while chitinase and phosphatases were more affected by season. Enzyme activity increased with succession age. Comparison of the effect of site and season on enzyme activity showed that season played a principal role in the enzyme activity of the entire 0–5 cm component of topsoil, as well the soil layers when evaluated separately.     

Litter decomposition along a primary post-mining chronosequence

Biology and Fertility of Soils - The aim of this study was to describe the decomposition of litter along a successive series of sites developed at a post-mining overburden deposit over 12, 21 and...     

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood forest soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β-N-acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea forest soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β-N-acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β-N-acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.     

Production of lignocellulose-degrading enzymes and degradation of leaf litter by saprotrophic basidiomycetes isolated from a Quercus petraea forest

Due to the production of lignocellulose-degrading enzymes, saprotrophic basidiomycetes can significantly contribute to the turnover of soil organic matter. The production of lignin- and polysaccharide-degrading enzymes and changes of the chemical composition of litter were studied with three isolates from a Quercus petraea forest. These isolates were capable of fresh litter degradation and were identified as Gymnopus sp., Hypholoma fasciculare and Rhodocollybia butyracea. Within 12 weeks of incubation, H. fasciculare decomposed 23%, R. butyracea 32% and Gymnopus sp. 38% of the substrate dry mass. All fungi produced laccase and Mn-peroxidase (MnP) and none of them produced lignin peroxidase or other Mn-independent peroxidases. There was a clear distinction in the enzyme production pattern between R. butyracea or H. fasciculare compared to Gymnopus sp. The two former species caused the fastest mass loss during the initial phase of litter degradation, accompanied by the temporary production of laccase (and MnP in H. fasciculare) and also high production of hydrolytic enzymes that later decreased. In contrast, Gymnopus sp. showed a stable rate of litter mass loss over the whole incubation period with a later onset of ligninolytic enzyme production and a longer lasting production of both lignin and cellulose-degrading enzymes. The activity of endo-cleaving polysaccharide hydrolases in this fungus was relatively low but it produced the most cellobiose hydrolase. All fungi decreased the C/N ratio of the litter from 24 to 15-19 and Gymnopus sp. also caused a substantial decrease in the lignin content. Analytical pyrolysis mass spectrometry of litter decomposed by this fungus showed changes in the litter composition similar to those caused by white-rot fungi during wood decay. These changes were less pronounced in the case of H. fasciculare and R. butyracea. All fungi also changed the mean masses of humic acid and fulvic acid fractions isolated from degraded litter. The humic acid fraction after degradation by all three fungi contained more lignin and less carbohydrates. Compared to the decomposition by saprotrophic basidiomycetes, litter degradation in situ on the site of fungal isolation resulted in the relative enrichment of lignin and differences in lignin composition revealed by analytical pyrolysis. It can most probably be explained by the participation of non-basidiomycetous fungi and bacteria during natural litter decomposition.