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.

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.

We evaluated the carbon budget of coarse woody debris (CWD) in a temperate broad‐leaved secondary forest. On the basis of a field survey conducted in 2003, the mass of CWD was estimated at 9.30 tC ha−1, with snags amounting to 60% of the total mass. Mean annual CWD input mass was estimated to be 0.61 tC ha−1 yr−1 by monitoring tree mortality in the forest from 1999 to 2004. We evaluated the CWD decomposition rate as the CO2 evolution rate from CWD by measuring CO2 emissions from 91 CWD samples (RCWD) with a closed dynamic chamber and infrared gas analysis system. The relationships between RCWD and temperature in the chamber, water content of the CWD, and other CWD characteristics were determined. By scaling the measured RCWD to the ecosystem, we estimated that the annual RCWD in the forest in 2003 was 0.50 tC ha−1 yr−1 or 10%–16% of the total heterotrophic respiration. Therefore, 0.11 tC ha−1 yr−1 or 7% of the forest net ecosystem production was sequestered by CWD. In a young forest, in which CWD input and decomposition are not balanced, the CWD carbon budget needs to be quantified for accurate evaluation of the forest carbon cycle and NEP.

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