BACKGROUND: Fine woody debris (FWD; deadwood < 10 cm diameter) is a crucial but often overlooked component of forest ecosystems. It provides habitat for microbial communities and enhances soil fertility through nutrient cycling. This role is especially important in managed forests, which typically have limited deadwood stocks. Climate change is increasing forest disturbances and expanding early successional forests with low canopy cover, yet the effects on microbial communities and related processes remain poorly understood. RESULTS: In a ten-year canopy manipulation experiment, we examined the decomposition of FWD of Fagus sylvatica and Abies alba. Increased canopy openness significantly decreased bacterial diversity in decomposing FWD and altered the community composition in surrounding soil. Decomposition time was the main factor shaping bacterial community structure in FWD, with tree species and canopy cover also contributing. We identified bacterial groups involved in carbohydrate degradation, fungal biomass breakdown, and nitrogen fixation. Importantly, bacterial communities in fully decomposed FWD remained distinct from soil communities. CONCLUSIONS: Deadwood decomposition and nutrient cycling are driven by complex ecological interactions. Microbial community dynamics are influenced by the interplay of FWD decomposition stage, tree species, and microclimatic conditions. Bacterial communities, although less frequently studied in this context, appear more stable over time than previously studied fungi. This stability may help sustain decomposition processes and nutrient turnover under the environmental variability associated with global change.

• Keywords
• Bacterial community, Canopy cover, Deadwood, Decomposition, Ecology, Fine woody debris, Microclimate, Succession, Temperate forest,
• Publication type
• Journal Article MeSH

Mutualistic interactions between plants and soil fungi, mycorrhizas, control carbon and nutrient fluxes in terrestrial ecosystems. Soil of ecosystems featuring a particular type of mycorrhiza exhibit specific properties across multiple dimensions of soil functioning. The knowledge about the impacts of mycorrhizal fungi on soil functioning accumulated so far, indicates that these impacts are of major importance, yet poorly conceptualized. We propose a concept of mycorrhizal fungal environments in soil. Within this concept, we discuss knowledge gaps related to the understanding and quantification of mycorrhizal fungal impacts. We introduce an experimental framework to address these gaps in a quantitative manner, and present the field experiment 'Mycotron', where we established vegetation series featuring three mycorrhizal types; ericoid (ERM), ecto- (ECM), and arbuscular mycorrhiza (AM), to quantitatively assess mycorrhizal fungal impacts on soil functioning. The experimental treatments entail manipulations in dominance levels of vegetation of three mycorrhizal types (AM, ECM, and ERM) in standardized soil conditions. This experiment constitutes a unique testbed to quantitatively evaluate the impacts of distinct mycorrhizal fungal environments on a large variety of ecosystem functions. Our approach aids the quantification of microbiota and plant-microbial interaction impacts on soil biochemical cycles.

• Keywords
• Mycotron experiment, arbuscular mycorrhiza, ectomycorrhiza, ericoid mycorrhiza, soil biochemical cycles, soil properties,
• MeSH
• Ecosystem * MeSH
• Mycorrhizae * physiology   MeSH
• Soil chemistry   MeSH
• Soil Microbiology * MeSH
• Plants microbiology   MeSH
• Symbiosis MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Soil MeSH

Human threats to biodiversity are prevalent within protected areas (PAs), undermining their effectiveness in halting biodiversity loss. Certain threats tend to co-occur, resulting in amplified cumulative impact through synergistic effects. However, it remains unclear which threats are related the most. We analyzed a dataset of 71 human threats in 18 013 terrestrial PAs of the European Union's Natura 2000 network, using a Joint Species Distribution Modelling approach, to assess the threats' co-occurrence patterns and potential drivers. Overall, threats were more frequently correlated positively than negatively. Threats related to agriculture and urbanization were correlated strongly with most other threats. Approximately 70% of the variance in our model was explained by country-specific factors, indicating the importance of local drivers. Minimizing the negative impact of key threats can likely reduce the impact of related threats. However, more research is needed to understand better the relationships among threats and, importantly, their combined impact on biodiversity.

• Keywords
• Anthropogenic impact, Biodiversity conservation, Human pressure, Joint Species Distribution Modeling, Natura 2000, Post-2020 Global Biodiversity Framework,
• MeSH
• Biodiversity * MeSH
• Ecosystem MeSH
• Humans MeSH
• Urbanization MeSH
• Conservation of Natural Resources * methods   MeSH
• Agriculture MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

Dead wood represents an important pool of carbon and nitrogen in forest ecosystems. This source of soil organic matter has diverse ecosystem functions that include, among others, carbon and nitrogen cycling. However, information is limited on how deadwood properties such as chemical composition, decomposer abundance, community composition, and age correlate and affect decomposition rate. Here, we targeted coarse dead wood of beech, spruce, and fir, namely snags and tree trunks (logs) in an old-growth temperate forest in central Europe; measured their decomposition rate as CO2 production in situ; and analyzed their relationships with other measured variables. Respiration rate of dead wood showed strong positive correlation with acid phosphatase activity and negative correlation with lignin content. Fungal biomass (ergosterol content) and moisture content were additional predictors. Our results indicate that dead wood traits, including tree species, age, and position (downed/standing), affected dead wood chemical properties, microbial biomass, moisture condition, and enzyme activity through changes in fungal communities and ultimately influenced the decomposition rate of dead wood.

• Keywords
• chemical properties, extracellular enzymes, fungal biomass, fungal community, respiration, structural equation modeling,
• Publication type
• Journal Article MeSH

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.

• MeSH
• Bacteria classification   MeSH
• Fagus microbiology   MeSH
• Wood microbiology   MeSH
• Ecosystem MeSH
• Fungi classification   MeSH
• Forests MeSH
• Metagenome * MeSH
• DNA, Ribosomal Spacer genetics   MeSH
• Microbiota * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Trees microbiology   MeSH
• DNA Barcoding, Taxonomic MeSH
• Publication type
• Journal Article MeSH
• Dataset MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH
• Names of Substances
• DNA, Ribosomal Spacer MeSH
• RNA, Ribosomal, 16S MeSH

Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction-key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.

• Keywords
• bacterial genomes, cellulose, deadwood, mycophagy, nitrogen fixation,
• Publication type
• Journal Article MeSH

The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.

• Keywords
• Sodalis, deadwood, free-living, insect symbionts, nitrogen fixation, non-symbiotic,
• Publication type
• Journal Article MeSH