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.

Department of Environmental Microbiology UFZ Helmholtz Centre for Environmental Research Leipzig Germany

Department of Forest Science and Resources College of Bioresource Sciences Nihon University Fujisawa Kanagawa Japan

Faculty of Science Charles University Prague Czech Republic

Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic

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Crowther TW, Glick HB, Covey KR, Bettigole C, Maynard DS, Thomas SM, Smith JR, Hintler G, Duguid MC, Amatulli G, Tuanmu MN, Jetz W, Salas C, Stam C, Piotto D, Tavani R, Green S, Bruce G, Williams SJ, Wiser SK, Huber MO, Hengeveld GM, Nabuurs GJ, Tikhonova E, Borchardt P, Li CF, Powrie LW, Fischer M, Hemp A, Homeier J, Cho P, Vibrans AC, Umunay PM, Piao SL, Rowe CW, Ashton MS, Crane PR, Bradford MA. 2015. Mapping tree density at a global scale. Nature 525:201–205. doi:10.1038/nature14967. PubMed DOI

Pan YD, Birdsey RA, Fang JY, Houghton R, Kauppi PE, Kurz WA, Phillips OL, Shvidenko A, Lewis SL, Canadell JG, Ciais P, Jackson RB, Pacala SW, McGuire AD, Piao SL, Rautiainen A, Sitch S, Hayes D. 2011. A large and persistent carbon sink in the world's forests. Science 333:988–993. doi:10.1126/science.1201609. PubMed DOI

Luyssaert S, Schulze ED, Borner A, Knohl A, Hessenmoller D, Law BE, Ciais P, Grace J. 2008. Old-growth forests as global carbon sinks. Nature 455:213–215. doi:10.1038/nature07276. PubMed DOI

Forrester JA, Mladenoff DJ, Gower ST, Stoffel JL. 2012. Interactions of temperature and moisture with respiration from coarse woody debris in experimental forest canopy gaps. Forest Ecol Manag 265:124–132. doi:10.1016/j.foreco.2011.10.038. DOI

Rinne-Garmston KT, Peltoniemi K, Chen J, Peltoniemi M, Fritze H, Makipaa R. 2019. 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 25:1852–1867. doi:10.1111/gcb.14594. PubMed DOI PMC

Bond-Lamberty B, Thomson A. 2010. A global database of soil respiration data. Biogeosciences 7:1915–1926. doi:10.5194/bg-7-1915-2010. DOI

Johnston SR, Boddy L, Weightman AJ. 2016. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 92:fiw179. doi:10.1093/femsec/fiw179. PubMed DOI

Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. 2020. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 7:228. doi:10.1038/s41597-020-0567-7. PubMed DOI PMC

Rayner ADM, Boddy L. 1988. Fungal decomposition of wood: its biology and ecology. Wiley, Chichester, NY.

Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie XF, Kues U, Hibbett DS, Hoffmeister D, Hogberg N, Martin F, Grigoriev IV, Watkinson SC. 2011. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333:762–765. doi:10.1126/science.1205411. PubMed DOI

Kahl T, Arnstadt T, Baber K, Bässler C, Bauhus J, Borken W, Buscot F, Floren A, Heibl C, Hessenmöller D, Hofrichter M, Hoppe B, Kellner H, Krüger D, Linsenmair KE, Matzner E, Otto P, Purahong W, Seilwinder C, Schulze E-D, Wende B, Weisser WW, Gossner MM. 2017. Wood decay rates of 13 temperate tree species in relation to wood properties, enzyme activities and organismic diversities. Forest Ecol Manag 391:86–95. doi:10.1016/j.foreco.2017.02.012. DOI

Weedon JT, Cornwell WK, Cornelissen JH, Zanne AE, Wirth C, Coomes DA. 2009. Global meta-analysis of wood decomposition rates: a role for trait variation among tree species? Ecol Lett 12:45–56. doi:10.1111/j.1461-0248.2008.01259.x. PubMed DOI

Baldrian P, Zrůstová P, Tláskal V, Davidová A, Merhautová V, Vrška T. 2016. Fungi associated with decomposing deadwood in a natural beech-dominated forest. Fungal Ecology 23:109–122. doi:10.1016/j.funeco.2016.07.001. DOI

Smyth CE, Titus B, Trofymow JA, Moore TR, Preston CM, Prescott CE, Grp CW, the CIDET Working Group. 2016. Patterns of carbon, nitrogen and phosphorus dynamics in decomposing wood blocks in Canadian forests. Plant Soil 409:459–477. doi:10.1007/s11104-016-2972-4. DOI

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

Rinne KT, Rajala T, Peltoniemi K, Chen J, Smolander A, Mäkipää R, Treseder K. 2017. Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest. Funct Ecol 31:530–541. doi:10.1111/1365-2435.12734. DOI

Bentzon-Tilia M, Severin I, Hansen LH, Riemann L. 2015. Genomics and ecophysiology of heterotrophic nitrogen-fixing bacteria isolated from estuarine surface water. mBio 6:e00929-15. doi:10.1128/mBio.00929-15. PubMed DOI PMC

Houlton BZ, Wang YP, Vitousek PM, Field CB. 2008. A unifying framework for dinitrogen fixation in the terrestrial biosphere. Nature 454:327–330. doi:10.1038/nature07028. PubMed DOI

Steidinger BS, Crowther TW, Liang J, Van Nuland ME, Werner GDA, Reich PB, Nabuurs GJ, de-Miguel S, Zhou M, Picard N, Herault B, Zhao X, Zhang C, Routh D, Peay KG, Consortium G, GFBI Consortium. 2019. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 569:404–408. doi:10.1038/s41586-019-1128-0. PubMed DOI

Fukami T, Dickie IA, Wilkie JP, Paulus BC, Park D, Roberts A, Buchanan PK, Allen RB. 2010. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecology Lett 13:675–684. doi:10.1111/j.1461-0248.2010.01465.x. PubMed DOI

Probst M, Gomez-Brandon M, Bardelli T, Egli M, Insam H, Ascher-Jenull J. 2018. Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories. Environ Microbiol 20:3657–3670. doi:10.1111/1462-2920.14359. PubMed DOI

Král K, Janík D, Vrška T, Adam D, Hort L, Unar P, Šamonil P. 2010. Local variability of stand structural features in beech dominated natural forests of Central Europe: implications for sampling. Forest Ecology and Management 260:2196–2203. doi:10.1016/j.foreco.2010.09.020. DOI

Cleveland CC, Townsend AR, Schimel DS, Fisher H, Howarth RW, Hedin LO, Perakis SS, Latty EF, Von Fischer JC, Elseroad A, Wasson MF. 1999. Global patterns of terrestrial biological nitrogen (N-2) fixation in natural ecosystems. Global Biogeochem Cycles 13:623–645. doi:10.1029/1999GB900014. DOI

Zheng MH, Chen H, Li DJ, Luo YQ, Mo JM. 2020. Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests. Ecol Lett 23:336–347. doi:10.1111/ele.13437. PubMed DOI

Cleveland CC, Houlton BZ, Smith WK, Marklein AR, Reed SC, Parton W, Del Grosso SJ, Running SW. 2013. Patterns of new versus recycled primary production in the terrestrial biosphere. Proc Natl Acad Sci U S A 110:12733–12737. doi:10.1073/pnas.1302768110. PubMed DOI PMC

Lladó S, Větrovský T, Baldrian P. 2019. Tracking of the activity of individual bacteria in temperate forest soils shows guild-specific responses to seasonality. Soil Biol Biochem 135:275–282. doi:10.1016/j.soilbio.2019.05.010. DOI

Žifčáková L, Větrovský T, Lombard V, Henrissat B, Howe A, Baldrian P. 2017. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 5:122. doi:10.1186/s40168-017-0340-0. PubMed DOI PMC

Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR. 2015. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Front Microbiol 6:337. doi:10.3389/fmicb.2015.00337. PubMed DOI PMC

Lenhart K, Bunge M, Ratering S, Neu TR, Schüttmann I, Greule M, Kammann C, Schnell S, Müller C, Zorn H, Keppler F. 2012. Evidence for methane production by saprotrophic fungi. Nat Commun 3:1046–1046. doi:10.1038/ncomms2049. PubMed DOI

Nelson MB, Martiny AC, Martiny JBH. 2016. Global biogeography of microbial nitrogen-cycling traits in soil. Proc Natl Acad Sci U S A 113:8033–8040. doi:10.1073/pnas.1601070113. PubMed DOI PMC

Mackelprang R, Grube AM, Lamendella R, Jesus EC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK. 2018. Microbial community structure and functional potential in cultivated and native tallgrass prairie soils of the midwestern United States. Front Microbiol 9:1775. doi:10.3389/fmicb.2018.01775. PubMed DOI PMC

Mäkipää R, Leppänen SM, Sanz Munoz S, Smolander A, Tiirola M, Tuomivirta T, Fritze H. 2018. Methanotrophs are core members of the diazotroph community in decaying Norway spruce logs. Soil Biol Biochem 120:230–232. doi:10.1016/j.soilbio.2018.02.012. DOI

Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sánchez-García M, Morin E, Andreopoulos B, Barry KW, Bonito G, Buée M, Carver A, Chen C, Cichocki N, Clum A, Culley D, Crous PW, Fauchery L, Girlanda M, Hayes RD, Kéri Z, LaButti K, Lipzen A, Lombard V, Magnuson J, Maillard F, Murat C, Nolan M, Ohm RA, Pangilinan J, Pereira MdF, Perotto S, Peter M, Pfister S, Riley R, Sitrit Y, Stielow JB, Szöllősi G, Žifčáková L, Štursová M, Spatafora JW, Tedersoo L, Vaario L-M, Yamada A, Yan M, Wang P, Xu J, Bruns T, Baldrian P, Vilgalys R, et al.. 2020. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat Commun 11:5125. doi:10.1038/s41467-020-18795-w. PubMed DOI PMC

Lustenhouwer N, Maynard DS, Bradford MA, Lindner DL, Oberle B, Zanne AE, Crowther TW. 2020. A trait-based understanding of wood decomposition by fungi. Proc Natl Acad Sci U S A 117:11551–11558. doi:10.1073/pnas.1909166117. PubMed DOI PMC

Hiscox J, O'Leary J, Boddy L. 2018. Fungus wars: basidiomycete battles in wood decay. Stud Mycol 89:117–124. doi:10.1016/j.simyco.2018.02.003. PubMed DOI PMC

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

Kohlmeier S, Smits THM, Ford RM, Keel C, Harms H, Wick LY. 2005. Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi. Environ Sci Technol 39:4640–4646. doi:10.1021/es047979z. PubMed DOI

Worrich A, Stryhanyuk H, Musat N, Konig S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Richnow H-H, Miltner A, Kastner M, Wick LY. 2017. Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments. Nat Commun 8:15472–15472. doi:10.1038/ncomms15472. PubMed DOI PMC

Hoppe B, Kahl T, Karasch P, Wubet T, Bauhus J, Buscot F, Krüger D. 2014. Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi. PLoS One 9:e88141. doi:10.1371/journal.pone.0088141. PubMed DOI PMC

Gomez-Brandon M, Probst M, Siles JA, Peintner U, Bardelli T, Egli M, Insam H, Ascher-Jenull J. 2020. Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood. Sci Rep 10:8025. doi:10.1038/s41598-020-64808-5. PubMed DOI PMC

Chen J, Heikkinen J, Hobbie EA, Rinne-Garmston KT, Penttila R, Makipaa R. 2019. Strategies of carbon and nitrogen acquisition by saprotrophic and ectomycorrhizal fungi in Finnish boreal Picea abies-dominated forests. Fungal Biol 123:456–464. doi:10.1016/j.funbio.2019.03.005. PubMed DOI

Lindahl BD, Finlay RD. 2006. Activities of chitinolytic enzymes during primary and secondary colonization of wood by basidiomycetous fungi. New Phytol 169:389–397. doi:10.1111/j.1469-8137.2005.01581.x. PubMed DOI

Šamonil P, Daněk P, Baldrian P, Tláskal V, Tejnecký V, Drábek O. 2020. Convergence, divergence or chaos? Consequences of tree trunk decay for pedogenesis and the soil microbiome in a temperate natural forest. Geoderma 376:114499. doi:10.1016/j.geoderma.2020.114499. DOI

Anderson-Teixeira KJ, Davies SJ, Bennett AC, Gonzalez-Akre EB, Muller-Landau HC, Wright SJ, Abu Salim K, Almeyda Zambrano AM, Alonso A, Baltzer JL, Basset Y, Bourg NA, Broadbent EN, Brockelman WY, Bunyavejchewin S, Burslem DFRP, Butt N, Cao M, Cardenas D, Chuyong GB, Clay K, Cordell S, Dattaraja HS, Deng X, Detto M, Du X, Duque A, Erikson DL, Ewango CEN, Fischer GA, Fletcher C, Foster RB, Giardina CP, Gilbert GS, Gunatilleke N, Gunatilleke S, Hao Z, Hargrove WW, Hart TB, Hau BCH, He F, Hoffman FM, Howe RW, Hubbell SP, Inman-Narahari FM, Jansen PA, Jiang M, Johnson DJ, Kanzaki M, Kassim AR, et al.. 2015. CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Glob Chang Biol 21:528–549. doi:10.1111/gcb.12712. PubMed DOI

Samonil P, Schaetzl RJ, Valtera M, Golias V, Baldrian P, Vasickova I, Adam D, Janik D, Hort L. 2013. Crossdating of disturbances by tree uprooting: can treethrow microtopography persist for 6000 years? Forest Ecol Manag 307:123–135. doi:10.1016/j.foreco.2013.06.045. DOI

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

Leppänen SM, Salemaa M, Smolander A, Mäkipää R, Tiirola M. 2013. Nitrogen fixation and methanotrophy in forest mosses along a N deposition gradient. Environ Exp Bot 90:62–69. doi:10.1016/j.envexpbot.2012.12.006. DOI

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624. doi:10.1038/ismej.2012.8. PubMed DOI PMC

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

Lanzen A, Jorgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Ovreas L, Urich T. 2012. CREST—classification resources for environmental sequence tags. PLoS One 7:e49334. doi:10.1371/journal.pone.0049334. PubMed DOI PMC

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. doi:10.1093/nar/gks1219. PubMed DOI PMC

Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59:143–169. doi:10.1128/MR.59.1.143-169.1995. PubMed DOI PMC

Wilmotte A, Van der Auwera G, De Wachter R. 1993. Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium chlorogloeopsis HTF (mastigocladus laminosus HTF) strain PCC7518, and phylogenetic analysis. FEBS Lett 317:96–100. doi:10.1016/0014-5793(93)81499-P. PubMed DOI

Prévost-Bouré NC, Christen R, Dequiedt S, Mougel C, Lelievre M, Jolivet C, Shahbazkia HR, Guillou L, Arrouays D, Ranjard L. 2011. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS One 6:e24166. doi:10.1371/journal.pone.0024166. PubMed DOI PMC

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

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

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:10.1186/1471-2105-9-386. PubMed DOI PMC

Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao XL, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I. 2014. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42:D699–D704. doi:10.1093/nar/gkt1183. PubMed DOI PMC

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

Prestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe SG, Holman E, Mavromatis K, Jansson JK. 2014. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res 42:e145. doi:10.1093/nar/gku702. PubMed DOI PMC

Huang L, Zhang H, Wu PZ, Entwistle S, Li XQ, Yohe T, Yi HD, Yang ZL, Yin YB. 2018. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res 46:D516–D521. doi:10.1093/nar/gkx894. PubMed DOI PMC

Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. doi:10.1093/nar/gkt1178. PubMed DOI PMC

Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Villarreal Ruiz L, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson K-H, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo L-d, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, et al.. 2014. Global diversity and geography of soil fungi. Science 346:1256688. doi:10.1126/science.1256688. PubMed DOI

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Abreu H, Acinas SG, Allen E, Allen MA, Andersen G, Anesio AM, Attwood G, Avila-Magaña V, Badis Y, Bailey J, Baker B, Baldrian P, Barton HA, Beck DAC, Becraft ED, Beller HR, Beman JM, Bernier-Latmani R, Berry TD, Bertagnolli A, Bertilsson S, Bhatnagar JM, Bird JT, Blumer-Schuette SE. 9 Nov 2020. A genomic catalog of Earth’s microbiomes. Nat Biotechnol doi:10.1038/s41587-020-0718-6. PubMed DOI PMC

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

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

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533–1542. doi:10.1038/s41564-017-0012-7. PubMed DOI

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. doi:10.1038/nbt.4229. PubMed DOI

Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. doi:10.1186/gb-2009-10-3-r25. PubMed DOI PMC

R Core Team. 2016. R: a language and environment for statistical computing. Version 3.3.1. R Foundation for Statistical Computing, Vienna, Austria.

Oksanen J, Blanchet FG, Friendly P, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecz E, Wagner H. 2018. vegan: community ecology package. R package version 2.5–2. https://cran.r-project.org/web/packages/vegan/index.html.

Racine JS. 2012. RStudio: a platform-independent IDE for R and Sweave. J Appl Econ 27:167–172. doi:10.1002/jae.1278. DOI

Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen T, Miller E, Bache S, Müller K, Ooms J, Robinson D, Seidel D, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H. 2019. Welcome to the Tidyverse. Joss 4:1686. doi:10.21105/joss.01686. DOI

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