Drivers of CO2 Emission Rates from Dead Wood Logs of 13 Tree Species in the Initial Decomposition Phase

Downed woody debris carbon emissions in a European temperate virgin forest as driven by species, decay classes, diameter and microclimate

Downed woody debris (DWD) plays an important role as regulator of nutrient and carbon (C) cycling in forests, accounting for up to the 20 % of the total C stocks in primary forests. DWD persistence is highly influenced by microbial decomposition, which is determined by various environmental factors, including fluctuations in temperature and moisture, as well as in intrinsic DWD properties determined by species, diameter, or decay classes (DCs). The relative importance of these different drivers, as well as their interactions, remains largely unknown. Moreover, the importance of DWD for C cycling in virgin forests remains poorly understood, due to their scarcity and poor accessibility. To address this research gap, we conducted a study on DWD respiration (RDWD), in a temperate virgin forest dominated by European beech and silver fir. Our investigation analysed the correlation between RDWD of these two dominant tree species and the seasonal changes in climate (temperature and moisture), considering other intrinsic DWD traits such as DCs (1, 2 and 4) and diameters (1, 10 and 25 cm). As anticipated, RDWD (normalized per gram of dry DWD) increased with air temperature. Surprisingly, DWD diameter also had a strong positive correlation with RDWD. Nonetheless, the sensitivity to both variables and other intrinsic traits (DC and density) was greatly modulated by the species. On the contrary, water content, which exhibited a considerable spatial variation, had an overall negative effect on RDWD. Virgin forests are generally seen as ineffective C sinks due to their lack of net productivity and high respiration and nutrient turnover. However, the rates of RDWD in this virgin forest were significantly lower than those previously estimated for managed forests. This suggests that DWD in virgin forests may be buffering forest CO2 emissions to the atmosphere more than previously thought.

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities

Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha-1 yr-1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.

Evaluation of Deadwood Characteristics and Carbon Storage under Different Silvicultural Treatments in a Mixed Broadleaves Mountain Forest

The deadwood (DW) of the forest is in the following two forms: standing (snag) and fallen (log). The DW categories and decay stage are important functional and structural components of forest ecosystems. We used a field-based assessment to quantify how the relative contribution of deadwood to total above-ground carbon stock changes across a silvicultural method and stand altitude gradient in mixed broadleaves stands. The characteristics of DW and carbon stock in selection-cutting managed stands (Sc), shelter-wood managed stands (Sh) and protected stands (Pr) were examined in three altitude ranges (low, <600; medium, 600–1200; and high, >1200 m a.s.l.) in a mixed broadleaves high forest. The results showed that with increasing altitude, the volume of DW increased. The volume of DW in Pr stands was about three times higher than Sh stands and twice higher than Sc stands. The volume of the standing DW was greater than that of the fallen DW in all stands. The highest volume ratio of fallen DW to standing DW was found in the medium altitude in the Sc stand. The amount of carbon stock by DW in the Sh, Sc, and Pr stands was 1.53–2.22, 2.29–3.19, and 5.03–6.80 t ha−1, respectively. The DW share of C-stock of above ground biomass was 4%–4.6% in Sh stand, 4.3%–4.8% in Sc stand, and 7.4%–7.9% in the Pr stand. Deadwood assessment and management, in terms of volume, type, species composition, diameter distribution, spatial allocation and decay stage, is one of the new challenges for a proper sustainable forest management.

Microbial Diversity and Ecosystem Functioning in Deadwood of Black Pine of a Temperate Forest

The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.

Decomposition of black pine (Pinus nigra J. F. Arnold) deadwood and its impact on forest soil components

Deadwood decomposition is a complex and dynamic process with large implications for biogeochemical cycling of carbon (C) and nitrogen (N) in forest soil and litter. Moreover, it affects functional and structural diversity of fungal and bacterial communities in these components. Mesocosms with deadwood blocks at progressive decay classes were set in a black pine forest and incubated for 28 months in the field with the aim to assess the impact of deadwood decomposition on i) CO₂, CH₄ and N₂O fluxes; ii) C and N pools and allocation among deadwood, litter and soil; iii) the fungal and bacterial structural diversity and activity. CO₂, CH₄ and N₂O fluxes from deadwood were monitored throughout the field incubation; deadwood biomass loss and decay rate for each decay class were calculated. The stock of C and N, enzyme activities, fungal and bacterial communities in deadwood, litter fractions (fresh, fragmented and humified) and soil at two depths were measured. Emissions of CO₂ and CH₄ increased over the deadwood decomposition advancement and the decay reached the maximum rates in the last decomposition classes. N₂O fluxes were low and showed either production (prevalent in the first year) or consumption. Independent of the decay class, 20% of C stored in deadwood was lost as CO₂ in the atmosphere, whereas 32% was transferred to the fragmented and humified litter fractions in the last decay class. A corresponding increase of cellulose and hemicellulose degrading enzymes was found in deadwood, also favored by substrates accessibility through fragmentation and successional changes in fungal and bacterial communities. Deadwood, litter fractions and soil components were clearly distinguished in terms of chemical and microbiological properties and activities. Fragmented and humified litter fractions were the only components responsive to the advanced stage of deadwood decomposition, being directly affected by the physical redistribution of fragmented organic matter.

Evaluation of the Carbon Dioxide Production by Fungi Under Different Growing Conditions

Production of carbon dioxide, as one of the ultimate products of fungal metabolism, can be used to quantify and measure their metabolic rate under different conditions, thus aiding in finding the optimal substrate and environment for cultivation of wood-destroying fungi. This study is focused on species Pleurotus ostreatus and Ganoderma lucidum,. These species are also cultivated for mycorestoration as well as their medicinal and nutritional value. To quantify their metabolical rate on various substrates (agar medium, wood chips, rye straw), multiple custom-built airtight chambers were equipped with CO₂ probes (GMP 343, Vaisala, Finland) to measure the production of carbon dioxide. The highest values were measured during the primordial production on rye straw substrate, with the average values of 1.09 g CO₂ kg^-1 (substrate) h^-1. These values varied significantly between various substrates, fungal species and development stages.

Bark coverage shifts assembly processes of microbial decomposer communities in dead wood

Bark protects living trees against environmental influences but may promote wood decomposition by fungi and bacteria after tree death. However, the mechanisms by which bark determines the assembly process and biodiversity of decomposers remain unknown. Therefore, we partially or completely removed bark from experimentally felled trees and tested with null modelling whether assembly processes were determined by bark coverage and if biodiversity of molecularly sampled fungi and bacteria generally benefited from increasing bark cover. The community composition of fungi, wood-decaying fungi (subset of all fungi) and bacteria clearly separated between completely debarked, partly debarked and control trees. Bacterial species richness was higher on control trees than on either partly or completely debarked trees, whereas the species richness of all fungi did not differ. However, the species richness of wood-decaying fungi was higher on partially and completely debarked trees than on control trees. Deterministic assembly processes were most important in completely debarked trees, a pattern consistent for fungi and bacteria. Our findings suggest that human disturbances in forests shift the dominant assembly mechanism from stochastic to deterministic processes and thus alter the diversity of wood-inhabiting microorganisms.

Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood

Deadwood represents an important structural component of forest ecosystems, where it provides diverse niches for saproxylic biota. Although wood-inhabiting prokaryotes are involved in its degradation, knowledge about their diversity and the drivers of community structure is scarce. To explore the effect of deadwood substrate on microbial distribution, the present study focuses on the microbial communities of deadwood logs from 13 different tree species investigated using an amplicon based deep-sequencing analysis. Sapwood and heartwood communities were analysed separately and linked to various relevant wood physico-chemical parameters. Overall, Proteobacteria, Acidobacteria and Actinobacteria represented the most dominant phyla. Microbial OTU richness and community structure differed significantly between tree species and between sapwood and heartwood. These differences were more pronounced for heartwood than for sapwood. The pH value and water content were the most important drivers in both wood compartments. Overall, investigating numerous tree species and two compartments provided a remarkably comprehensive view of microbial diversity in deadwood.

Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function

Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood-inhabiting fungi (WIF) and their related ecological functions and processes in a highly N-limited deadwood habitat. Based on high-throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood-inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf-litter, which represent less N-limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial-mediated ecosystem function and processes against N deposition in highly N-limited habitats.

Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests

Wood-inhabiting fungi have essential roles in the regulation of carbon stocks and nutrient cycling in forest ecosystems. However, knowledge pertaining to wood-inhabiting fungi is only fragmentary and controversial. Here we established a large-scale deadwood experiment with 11 tree species to investigate diversity and tree species preferences of wood-inhabiting fungi using next-generation sequencing. Our results contradict existing knowledge based on sporocarp surveys and challenge current views on their distribution and diversity in temperate forests. Analyzing α-, β- and γ-diversity, we show that diverse fungi colonize deadwood at different spatial scales. Specifically, coniferous species have higher α- and γ-diversity than the majority of analyzed broadleaf species, but two broadleaf species showed the highest β-diversity. Surprisingly, we found nonrandom co-occurrence (P<0.001) and strong tree species preferences of wood-inhabiting fungi, especially in broadleaf trees (P<0.01). Our results indicate that the saprotrophic fungal community is more specific to tree species than previously thought.

Fungal community structure of fallen pine and oak wood at different stages of decomposition in the Qinling Mountains, China

Historically, intense forest hazards have resulted in an increase in the quantity of fallen wood in the Qinling Mountains. Fallen wood has a decisive influence on the nutrient cycling, carbon budget and ecosystem biodiversity of forests, and fungi are essential for the decomposition of fallen wood. Moreover, decaying dead wood alters fungal communities. The development of high-throughput sequencing methods has facilitated the ongoing investigation of relevant molecular forest ecosystems with a focus on fungal communities. In this study, fallen wood and its associated fungal communities were compared at different stages of decomposition to evaluate relative species abundance and species diversity. The physical and chemical factors that alter fungal communities were also compared by performing correspondence analysis according to host tree species across all stages of decomposition. Tree species were the major source of differences in fungal community diversity at all decomposition stages, and fungal communities achieved the highest levels of diversity at the intermediate and late decomposition stages. Interactions between various physical and chemical factors and fungal communities shared the same regulatory mechanisms, and there was no tree species-specific influence. Improving our knowledge of wood-inhabiting fungal communities is crucial for forest ecosystem conservation.