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.

Department of Environmental Microbiology Helmholtz Centre for Environmental Research UFZ Permoserstraße 15 04318 Leipzig Germany

Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of Sciences Videnska 1083 14220 Praha 4 Czech Republic

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Luyssaert S, et al. Old-growth forests as global carbon sinks. Nature. 2008;455:213–215. doi: 10.1038/nature07276. PubMed DOI

Pan Y, et al. A large and persistent carbon sink in the world’s forests. Science. 2011;333:988–993. doi: 10.1126/science.1201609. PubMed DOI

Rinne-Garmston KT, et al. Carbon flux from decomposing wood and its dependency on temperature, wood N2 fixation rate, moisture and fungal composition in a Norway spruce forest. Glob. Chang. Biol. 2019;25:1852–1867. doi: 10.1111/gcb.14594. PubMed DOI PMC

Šamonil P, et al. Convergence, divergence or chaos? Consequences of tree trunk decay for pedogenesis and the soil microbiome in a temperate natural forest. Geoderma. 2020;376:114499. doi: 10.1016/j.geoderma.2020.114499. DOI

Tláskal V, et al. Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition. mSystems. 2021;6:e01078–20. doi: 10.1128/mSystems.01078-20. PubMed DOI PMC

Odriozola I, et al. Fungal communities are important determinants of bacterial community composition in deadwood. mSystems. 2021;6:e01017–20. doi: 10.1128/mSystems.01017-20. PubMed DOI PMC

Valášková V, de Boer W, Gunnewiek PJAK, Pospíšek M, Baldrian P. Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood. ISME J. 2009;3:1218–1221. doi: 10.1038/ismej.2009.64. PubMed DOI

Brunner A, Kimmins JP. Nitrogen fixation in coarse woody debris of Thuja plicata and Tsuga heterophylla forests on northern Vancouver Island. Can. J. For. Res. 2003;33:1670–1682. doi: 10.1139/x03-085. DOI

Rinne KT, et al. Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest. Funct. Ecol. 2016;31:530–541. doi: 10.1111/1365-2435.12734. DOI

Põlme S, et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 2020;105:1–16. doi: 10.1007/s13225-020-00466-2. DOI

Tláskal V, Baldrian P. Deadwood-inhabiting bacteria show adaptations to changing carbon and nitrogen availability during decomposition. Front. Microbiol. 2021;12:685303. doi: 10.3389/fmicb.2021.685303. PubMed DOI PMC

Lemos LN, Mendes LW, Baldrian P, Pylro VS. Genome-resolved metagenomics is essential for unlocking the microbial black box of the soil. Trends Microbiol. 2021;29:279–282. doi: 10.1016/j.tim.2021.01.013. PubMed DOI

Větrovský T, et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci. Data. 2020;7:228. doi: 10.1038/s41597-020-0567-7. PubMed DOI PMC

Thompson LR, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–463. doi: 10.1038/nature24621. PubMed DOI PMC

Anderson-Teixeira KJ, Davies SJ, Bennett AC, Muller-landau HC, Wright SJ. CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Glob. Chang. Biol. 2015;21:528–549. doi: 10.1111/gcb.12712. PubMed DOI

Baldrian P, et al. Fungi associated with decomposing deadwood in a natural beech-dominated forest. Fungal Ecol. 2016;23:109–122. doi: 10.1016/j.funeco.2016.07.001. DOI

Smyth CE, et al. Patterns of carbon, nitrogen and phosphorus dynamics in decomposing wood blocks in Canadian forests. Plant Soil. 2016;9:46–62.

Král K, et al. Local variability of stand structural features in beech dominated natural forests of Central Europe: Implications for sampling. For. Ecol. Manage. 2010;260:2196–2203. doi: 10.1016/j.foreco.2010.09.020. DOI

Caporaso JG, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–1624. doi: 10.1038/ismej.2012.8. PubMed DOI PMC

Lanzén A, et al. CREST – Classification resources for environmental sequence tags. PLoS One. 2012;7:e49334. doi: 10.1371/journal.pone.0049334. PubMed DOI PMC

Quast C, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596. doi: 10.1093/nar/gks1219. PubMed DOI PMC

Žifčáková L, Větrovský T, Howe A, Baldrian P. Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ. Microbiol. 2016;18:288–301. doi: 10.1111/1462-2920.13026. PubMed DOI

Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–1676. doi: 10.1093/bioinformatics/btv033. PubMed DOI

Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165. doi: 10.7717/peerj.1165. PubMed DOI PMC

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–1055. doi: 10.1101/gr.186072.114. PubMed DOI PMC

Parks DH, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2017;2:1533–1542. doi: 10.1038/s41564-017-0012-7. PubMed DOI

Parks DH, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 2018;36:996–1004. doi: 10.1038/nbt.4229. PubMed DOI

Lee MD. GToTree: A user-friendly workflow for phylogenomics. Bioinformatics. 2019;35:4162–4164. doi: 10.1093/bioinformatics/btz188. PubMed DOI PMC

Hyatt D, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. doi: 10.1186/1471-2105-11-119. PubMed DOI PMC

Eddy SR. Accelerated profile HMM searches. PLoS Comput. Biol. 2011;7:e1002195. doi: 10.1371/journal.pcbi.1002195. PubMed DOI PMC

Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340. PubMed DOI PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490. doi: 10.1371/journal.pone.0009490. PubMed DOI PMC

Ihrmark K, et al. New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 2012;82:666–677. doi: 10.1111/j.1574-6941.2012.01437.x. PubMed DOI

Větrovský T, Baldrian P, Morais D. SEED 2: A user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics. 2018;34:2292–2294. doi: 10.1093/bioinformatics/bty071. PubMed DOI PMC

Aronesty E. Comparison of sequencing utility programs. Open Bioinforma. J. 2013;7:1–8. doi: 10.2174/1875036201307010001. DOI

Nilsson RH, et al. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecol. 2010;3:284–287. doi: 10.1016/j.funeco.2010.05.002. DOI

Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461. doi: 10.1093/bioinformatics/btq461. PubMed DOI

Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods. 2013;10:996–998. doi: 10.1038/nmeth.2604. PubMed DOI

Nilsson RH, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classification. Nucleic Acids Res. 2018;47:D259–D264. doi: 10.1093/nar/gky1022. PubMed DOI PMC

Wright ES. Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 2016;8:352–359. doi: 10.32614/RJ-2016-025. DOI

Murali A, Bhargava A, Wright ES. IDTAXA: A novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:140. doi: 10.1186/s40168-018-0521-5. PubMed DOI PMC

2020. NCBI BioProject. PRJNA603240

2020. NCBI Sequence Read Archive. PRJNA672674

Sutela S, Poimala A, Vainio EJ. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol. Ecol. 2019;95:fiz119. doi: 10.1093/femsec/fiz119. PubMed DOI

Woodcroft BJ, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54. doi: 10.1038/s41586-018-0338-1. PubMed DOI

Mackelprang R, et al. Microbial community structure and functional potential in cultivated and native tallgrass prairie soils of the Midwestern United States. Front. Microbiol. 2018;9:1775. doi: 10.3389/fmicb.2018.01775. PubMed DOI PMC

Hervé V, et al. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ. 2020;8:e8614. doi: 10.7717/peerj.8614. PubMed DOI PMC

Clissmann F, et al. First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs. FEMS Microbiol. Ecol. 2015;91:fiv050. doi: 10.1093/femsec/fiv050. PubMed DOI

Urich T, et al. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One. 2008;3:e2527. doi: 10.1371/journal.pone.0002527. PubMed DOI PMC

Geisen S, et al. Metatranscriptomic census of active protists in soils. ISME J. 2015;9:2178–2190. doi: 10.1038/ismej.2015.30. PubMed DOI PMC

Tláskal V, Zrůstová P, Vrška T, Baldrian P. Bacteria associated with decomposing dead wood in a natural temperate forest. FEMS Microbiol. Ecol. 2017;93:fix157. doi: 10.1093/femsec/fix157. PubMed DOI

Moll J, et al. Bacteria inhabiting deadwood of 13 tree species reveal great heterogeneous distribution between sapwood and heartwood. Environ. Microbiol. 2018;20:3744–3756. doi: 10.1111/1462-2920.14376. PubMed DOI

Christofides SR, Hiscox J, Savoury M, Boddy L, Weightman AJ. Fungal control of early-stage bacterial community development in decomposing wood. Fungal Ecol. 2019;42:100868. doi: 10.1016/j.funeco.2019.100868. DOI

Nayfach S, et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 2021;39:499–509. doi: 10.1038/s41587-020-0718-6. PubMed DOI PMC

Seibold S, et al. Experimental studies of dead-wood biodiversity — A review identifying global gaps in knowledge. Biol. Conserv. 2015;191:139–149. doi: 10.1016/j.biocon.2015.06.006. DOI

Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes

Bacterial, but not fungal, communities show spatial heterogeneity in European beech (Fagus sylvatica L.) deadwood