Search

Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communities sampled with either traditional, composite samples, or small, 1 cm3 cylinders from a discrete location within decomposing European beech (Fagus sylvatica L.) tree trunks. We found that bacterial richness and evenness is lower in small samples when compared to composite samples. There was no significant difference in fungal alpha diversity between different sampling scales, suggesting that visually defined fungal domains are not restricted to a single species. Additionally, we found that composite sampling may obscure variation in community composition and this affects the understanding of microbial associations that are detected. For future experiments in environmental microbiology, we recommend that scale is explicitly considered as a factor and properly selected to correspond with the questions asked. Studies of microbial functions or associations may require samples to be collected at a finer scale than is currently practised.

Many soil Actinobacteria are potent producers of extracellular enzymes decomposing lignocellulose. Four strains of Actinobacteria with a high potential to hydrolyse cellulose and hemicellulose were identified among environmental isolates. The strains were grown on raw lignocellulosic substrates (olive pomace, oat flakes, sawdust, and wheat straw) under submerged fermentation in a laboratory scale. Modified Melin Norkrans Medium amended with raw lignocellulosic substrates as carbon sources (0.5%) was used to enhance lignocellulosic biomass decomposition. Three strains belonged to the genus Streptomyces and one strain to the genus Mycobacterium. Annotation of genomes showed high proportion of genes encoding for carbohydrate-active enzymes in Streptomyces sp. GESEQ-4 (537, i.e. 6% of 8404 genes), Streptomyces sp. GESEQ-13 (351 (5%) of 6705 genes), Streptomyces sp. GESEQ-35 (608 (6%) of 9788 genes), and Mycolicibacterium fortuitum subsp. fortuitum GESEQ-9 (222 (3%) of 6405 genes). These included plant cell wall-degrading enzymes belonging to the families GH1, GH2, GH3, GH5, GH6, GH9, GH10, GH12, GH16, GH26, GH30, GH39, GH48, GH51, and GH74, of which GH1, GH2, GH3, GH5, GH6, and GH16 were found in all four genomes. Assays for cellulose and hemicellulose degrading extracellular enzymes confirmed the ability of the isolates to decompose cellulose and hemicellulose. The highest endo-cleaving enzyme activities were produced by the strain Steptomyces sp. GESEQ-4 DSM 106287. Our results provide new perspectives into the enzymatic array by which the Actinobacteria break down complex lignocellulosic biomass. It is crucial to assess the genome to determine enzyme function as well as the enzyme families responsible for the degradation process in Actinobacteria. The potential degradation functions for these actinobacterial strains were validated by testing their cellulolytic and hemicellulolytic activities with various lignocellulosic substrates.

The present study discusses the importance of citizen science as a form of scientific research, defined by the participation of the general public. An important factor influencing the success of these projects, although still little studied, is the participants‘ motivation. Based on the results of a questionnaire survey (n = 94), the study tries to outline the issues of motivation and involvement of the general public on the example of citizen science project City Nature Challenge: Prague, which uses the mobile application iNaturalist. The results of the study show that the project participants see its importance in mapping wildlife in collaboration with the public, and at the same time in popularizing urban biodiversity and the need for its protection. It is obvious that a stable community of volunteers interested in nature are emerging around the City Nature Challenge project. We need this community to be properly motivated and further studied in terms of positive motivation, changes in behavior and attitudes.

Fungi play a crucial role in dead wood decay, being the major decomposers of wood and affecting microbiota associated with dead wood. We sampled dead wood from five deciduous tree species over more than forty years of decay in a natural European floodplain forest with high tree species diversity. While the assembly of dead wood fungal communities shows a high level of stochasticity, it also indicates clear successional patterns, with fungal taxa either specific for early or late stages of wood decay. No clear patterns of fungal biomass content over time were observed. Out of 220 major fungal operational taxonomic units, less than 8% were associated with a single tree species, most of them with Quercus robur. Tree species and wood chemistry, particularly pH, were the most important drivers of fungal community composition. This study highlights the importance of dead wood and tree species diversity for preserving the biodiversity of fungi.

Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass., Measurement(s) metagenomic data • metatranscriptomic data • microbiome • RNA-seq of total RNA Technology Type(s) DNA sequencing • RNA-seq of total RNA • amplicon sequencing • RNA sequencing Factor Type(s) time of decomposition Sample Characteristic - Organism Fungi • Bacteria Sample Characteristic - Environment wood Sample Characteristic - Location Narodni prirodni rezervace Zofinsky prales Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14821752

Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers., Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils. IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.

Some microbes are important players in plant fitness, contributing to their nutrient acquisition and protection against diverse biotic and abiotic stresses [...]

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com. The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible., Measurement(s) internal_transcribed_spacer_region Technology Type(s) digital curation Factor Type(s) geographic location • sample type • biome • sampling year Sample Characteristic - Organism Fungi Sample Characteristic - Environment terrestrial biome Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12481946

The evolutionary split between gymnosperms and angiosperms has far‐reaching implications for the current communities colonizing trees. The inherent characteristics of dead wood include its role as a spatially scattered habitat of plant tissue, transient in time. Thus, local assemblages in deadwood forming a food web in a necrobiome should be affected not only by dispersal ability but also by host tree identity, the decay stage and local abiotic conditions. However, experiments simultaneously manipulating these potential community drivers in deadwood are lacking. To disentangle the importance of spatial distance and microclimate, as well as host identity and decay stage as drivers of local assemblages, we conducted two consecutive experiments, a 2‐tree species and 6‐tree species experiment with 80 and 72 tree logs, respectively, located in canopy openings and under closed canopies of a montane and a lowland forest. We sampled saproxylic beetles, spiders, fungi and bacterial assemblages from logs. Variation partitioning for community metrics based on a unified framework of Hill numbers showed consistent results for both studies: host identity was most important for sporocarp‐detected fungal assemblages, decay stage and host tree for DNA‐detected fungal assemblages, microclimate and decay stage for beetles and spiders and decay stage for bacteria. Spatial distance was of minor importance for most taxa but showed the strongest effects for arthropods. The contrasting patterns among the taxa highlight the need for multi‐taxon analyses in identifying the importance of abiotic and biotic drivers of community composition. Moreover, the consistent finding of microclimate as the primary driver for saproxylic beetles compared to host identity shows, for the first time that existing evolutionary host adaptions can be outcompeted by local climate conditions in deadwood.

Deadwood represents a specific habitat of particular importance in natural, unmanaged forests where wood is not harvested. Here, we characterized the basic wood chemistry, enzyme activity, fungal biomass content and community composition of Fagus sylvatica , Abies alba and Picea abies coarse woody debris decomposing for 38 years in a natural temperate forest. The results indicate that coarse deadwood represents a highly diverse substratum in terms of the quality, fungal biomass content and, in particular, the composition of fungal communities whose properties change with time. Because sequences recovered from individual logs were typically dominated by one or few fungal species, which were rarely tree species-specific, the community assembly appeared to show a high level of stochasticity. Among the estimated variables, nitrogen content that increased with decay length was the most important candidate driver of fungal biomass content, community composition and enzyme activity.

The biochemical effects of trees may significantly influence local pedogenesis as well as pedocomplexity, biodiversity and forest dynamics on both stand and landscape scales. One such effect is the decay of tree trunks, which is driven by organisms, and especially by the microbiome. Decomposition modifies soil formation, which due to the existence of many feedbacks affects the composition of the decomposer community. We aimed to uncover general trends in the evolution of Entic Podzols as well as individual trajectories of soil properties below decaying beech trunks in an old-growth mountain forest. In particular, we used mathematical models to distinguish soil convergence, divergence and chaotic behaviour to enhance a general theory of pedogenesis. We further aimed to calculate the depth and time of convergence if this scenario is prevailing in the study plot. Pedogenetic pathways were assessed regarding the changing composition of fungal and bacterial communities in soils to obtain a complex picture of the decaying trunk-soil microbiome system. We sampled the decaying wood layer under 24 lying beech trunks and corresponding organic horizons on adjacent control microsites occupied by decaying beech leaves. At the same time we sampled underlying mineral soil horizons at both microsites (wood vs. leaves), all on Entic Podzols and granite (in total 192 soil samples). Individual trunk fall events were dated using precise dendrochronology, with the resulting chronosequence covering trunks lying for 8–52 years. We analysed decomposition processes (with a wide spectra of organic acids and ions analysed), soil chemistry (28 additional soil properties assessed), and the microbiome composition in both decaying organic matter and soils (relative abundances of the 200 most common bacterial and fungal OTUs analysed). During the first stage of trunk decay, underlying Entic Podzols responded with a significant increase of nutrients, pH, and CEC, and the maximal divergence compared to control sites was reached between 12 and 60 years after the trunk fall. Subsequently, a majority of soil properties slowly converged over a few decades to match the soil properties of control sites. The modelled convergence point occurred at ages between 39 (SO42−) and 229 (Alw) years, with a median convergence time of 53 years. The majority of soil properties converged within 20 cm below the trunk, but mathematical models predicted footprints of some soil properties down to depths of ca 60 cm. In addition, 11 soil properties did not converge at any depth, and for some properties the models even diverged. Differences in bacterial and fungal communities between below-trunk and control positions were relatively minor. Pedochemical drivers of fungal and bacterial communities (nutrients content, Ntot, Cox, Al, Fe, Mn forms) changed significantly in the mineral soil below trunks, and the microbiome partly reflected these depth-related changes. However, we propose that there is a threshold between organic and mineral soil horizons limiting the impacts of trunk decay and pedogenesis in changes to the microbiome.

Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mostly utilize simpler compounds, recent studies have shown that fungi and bacteria overlap in substrate utilization. Here, we studied the microbial contribution to the recycling of dead biomass by analyzing the bacterial and fungal communities in soil microcosms supplemented with 13C-labeled biomass of plant, fungal, and bacterial origin using a combination of DNA-stable isotope probing and metagenomics. Both fungi and bacteria contributed actively to the degradation of complex components of plant and microbial biomass. Specific families of carbohydrate-active enzymes (CAZyme) were involved in the degradation of each biomass type. Moreover, the analysis of five bacterial metagenome-assembled genomes indicated the key role of some bacterial genera in the degradation of plant biomass (Cytophaga and Asticcacaulis) and microbial biomass (Herminiimonas). The enzymatic systems utilized by bacteria are highly complex and complementary but also highly diverse among taxa. The results confirm the importance of bacteria, in addition to fungi, as decomposers of complex organic matter in forest soils.

Litter input is an important source of C and nutrients in forest soils that are liberated and utilized during decomposition. We have investigated the long-term decomposition of Picea abies and Calamagrostis villosa litters in montane spruce forest and the litter-associated fungi. The two litter types differed in initial nutrient content and decomposed at different rates, but in both cases, significant residual mass was left after five years of decomposition – over 30% of the initial mass of Calamagrostis litter and 40% of Picea litter. The litters harbored different fungal communities, though these tended to converge over time. The initial fungal community was dominated by Ascomycota, while the share of Basidiomycota and Mucoromycotina/Mortierellomycotina increased towards the end of the experiment. Individual litter fungi showed variable preference to litter type, succession time and duration of occurrence and we propose these as potential taxon-specific traits requiring further investigation.

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α–proteobacteria, δ–proteobacteria, and γ–proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.

The decomposition of dead plant biomass contributes to the carbon cycle and is one of the key processes in temperate forests. While fungi in litter decomposition drive the chemical changes occurring in litter, the bacterial community appears to be important as well, especially later in the decomposition process when its abundance increases. In this paper, we describe the bacterial community composition in live Quercus petraea leaves and during the subsequent two years of litter decomposition. Members of the classes Alpha-, Beta- and Gammaproteobacteria and the phyla Actinobacteria, Bacteroidetes and Acidobacteria were dominant throughout the experiment. Bacteria present in the oak phyllosphere were rapidly replaced by other taxa after leaf senescence. There were dynamic successive changes in community composition, in which the early-stage (months 2-4), mid-stage (months 6-8) and late-stage (months 10-24) decomposer communities could be distinguished, and the diversity increased with time. Bacteria associated with dead fungal mycelium were important during initial decomposition, with sequence relative abundances of up to 40% of the total bacterial community in months 2 and 4 when the highest fungal biomass was observed. Cellulose-decomposing bacteria were less frequent, with abundance ranging from 4% to 15%. The bacterial community dynamics reflects changes in the availability of possible resources either of the plant or microbial origin.