Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short-term studies, and the guild of mycelium decomposers has been poorly defined. Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21 wk. The community of associated microbes and enzymatic processes in this specific substrate were described. The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer-degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r-strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others. Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community.
- MeSH
- Bacteria classification growth & development MeSH
- Biomass MeSH
- Ecosystem MeSH
- Forests MeSH
- Microbial Consortia * MeSH
- Mycelium metabolism MeSH
- Mycorrhizae classification metabolism MeSH
- Soil chemistry MeSH
- Soil Microbiology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.
- MeSH
- Bacteria classification metabolism MeSH
- Biodiversity MeSH
- Ecosystem MeSH
- Fungi classification metabolism MeSH
- Forests MeSH
- Microbiota * MeSH
- Grassland MeSH
- Soil chemistry MeSH
- Soil Microbiology * MeSH
- RNA, Ribosomal, 16S MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.
- MeSH
- Bacteria classification enzymology genetics MeSH
- Biodiversity MeSH
- Cellulose 1,4-beta-Cellobiosidase genetics MeSH
- Cellulose metabolism MeSH
- Ecosystem MeSH
- Phylogeny MeSH
- Fungi classification enzymology genetics MeSH
- Metagenome MeSH
- Soil Microbiology MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Picea physiology MeSH
- Trees microbiology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Microbial diversity plays a crucial role in litter decomposition. However, the relationships between microbial diversity and substrate successional stage are the drivers of this decomposition. In this study, we experimentally manipulated microbial diversity and succession in post-mining soil. We used leaf litter samples from two forests of a post-mining site near Sokolov, Czech Republic: one alder plantation and one mixed forest with birch aspen and willow. Litter from each site was decomposed in the field for 3 and 12 months. The litter was X-ray sterilized and part of the litter was kept unsterilized to produce inoculum. Leaf litter samples of two different ages (3 and 12 months) from each site were each inoculated with litter of two different ages (3 and 12 months), using less and more diluted inoculum, producing two levels of microbial diversity. In each of these eight treatments, the bacterial community was then characterized by amplicon sequencing of the 16S rRNA gene and microbial respiration was used to assess the rate of decomposition. A significantly higher respiration (p < 0.05) was found for the litter inoculated with the higher level of microbial diversity. Higher respiration was also found for the younger litter compared to the older litter and both litter origins. This shows a reduction in microbial respiration with substrate age and inoculation diversity, suggesting that microbial diversity supports the decomposition of soil organic matter.
- Publication type
- Journal Article MeSH
Saprotrophic wood-inhabiting basidiomycetes are the most important decomposers of lignin and cellulose in dead wood and as such they attracted considerable attention. The aims of this work were to quantify the activity and spatial distribution of extracellular enzymes in coarse wood colonised by the white-rot basidiomycete Fomes fomentarius and in adjacent fruitbodies of the fungus and to analyse the diversity of the fungal and bacterial community in a fungus-colonised wood and its potential effect on enzyme production by F. fomentarius. Fungus-colonised wood and fruitbodies were collected in low management intensity forests in the Czech Republic. There were significant differences in enzyme production by F. fomentarius between Betula pendula and Fagus sylvatica wood, the activity of cellulose and xylan-degrading enzymes was significantly higher in beech wood than in birch wood. Spatial analysis of a sample B. pendula log segment proved that F. fomentarius was the single fungal representative found in the log. There was a high level of spatial variability in the amount of fungal biomass detected, but no effects on enzyme activities were observed. Samples from the fruiting body showed high β-glucosidase and chitinase activities compared to wood samples. Significantly higher levels of xylanase and cellobiohydrolase were found in samples located near the fruitbody (proximal), and higher laccase and Mn-peroxidase activities were found in the distal ones. The microbial community in wood was dominated by the fungus (fungal to bacterial DNA ratio of 62-111). Bacterial abundance composition was lower in proximal than distal parts of wood by a factor of 24. These results show a significant level of spatial heterogeneity in coarse wood. One of the explanations may be the successive colonization of wood by the fungus: due to differential enzyme production, the rates of biodegradation of coarse wood are also spatially inhomogeneous.
- MeSH
- Bacteria enzymology isolation & purification MeSH
- beta-Glucosidase metabolism MeSH
- Biodegradation, Environmental MeSH
- Betula enzymology microbiology MeSH
- Fagus enzymology microbiology MeSH
- Cellulose 1,4-beta-Cellobiosidase metabolism MeSH
- Chitinases metabolism MeSH
- Coriolaceae enzymology isolation & purification MeSH
- DNA, Bacterial analysis MeSH
- DNA, Fungal analysis MeSH
- Wood enzymology microbiology MeSH
- Ecology MeSH
- Laccase metabolism MeSH
- Lignin metabolism MeSH
- Microbial Consortia MeSH
- Peroxidases metabolism MeSH
- Trees enzymology microbiology MeSH
- Xylans metabolism MeSH
- Xylosidases metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m(2)) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.
