Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).

ADS 

Google Scholar
 

Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).

ADS 

Google Scholar
 

Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A. & Dufresne, A. The importance of the microbiome of the plant holobiont. New Phytol. 206, 1196–1206 (2015).


Google Scholar
 

Cregger, M. A. et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6, 31 (2018).


Google Scholar
 

Mo, L. et al. Integrated global assessment of the natural forest carbon potential. Nature 624, 92–101 (2023).

ADS 

Google Scholar
 

Falster, D. S. et al. BAAD: a Biomass And Allometry Database for woody plants. Ecology 96, 1445–1445 (2015).


Google Scholar
 

Andrews, J. H. & Harris, R. F. The ecology and biogeography of microorganisms on plant surfaces. Annu. Rev. Phytopathol. 38, 145–180 (2000).


Google Scholar
 

de Habiyaremye, J. D., Goldmann, K., Reitz, T., Herrmann, S. & Buscot, F. Tree root zone microbiome: exploring the magnitude of environmental conditions and host tree impact. Front. Microbiol. 11, 749 (2020).


Google Scholar
 

Sohrabi, R., Paasch, B. C., Liber, J. A. & He, S. Y. Phyllosphere microbiome. Annu. Rev. Plant Biol. 74, 539–568 (2023).


Google Scholar
 

Jeffrey, L. C. et al. Bark-dwelling methanotrophic bacteria decrease methane emissions from trees. Nat. Commun. 12, 2127 (2021).

ADS 

Google Scholar
 

Baldrian, P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol. Rev. 41, 109–130 (2017).


Google Scholar
 

Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).


Google Scholar
 

Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).


Google Scholar
 

Turner, T. R., James, E. K. & Poole, P. S. The plant microbiome. Genome Biol. 14, 209 (2013).


Google Scholar
 

Yip, D. Z., Veach, A. M., Yang, Z. K., Cregger, M. A. & Schadt, C. W. Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides). New Phytol. 222, 115–121 (2019).


Google Scholar
 

Santoyo, G., Moreno-Hagelsieb, G., del Orozco-Mosqueda, M. C. & Glick, B. R. Plant growth-promoting bacterial endophytes. Microbiol. Res. 183, 92–99 (2016).


Google Scholar
 

Yadeta, K. A. & J Thomma, B. P. H. The xylem as battleground for plant hosts and vascular wilt pathogens. Front. Plant Sci. 4, 97 (2013).


Google Scholar
 

Arnold, W. et al. A method for sampling the living wood microbiome. Methods Ecol. Evol. https://doi.org/10.1111/2041-210x.14311 (2024).


Google Scholar
 

Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).


Google Scholar
 

Johnston, S. R., Boddy, L. & Weightman, A. J. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol. Ecol. 92, fiw179 (2016).


Google Scholar
 

Hartmann, H. & Trumbore, S. Understanding the roles of nonstructural carbohydrates in forest trees – from what we can measure to what we want to know. New Phytol. 211, 386–403 (2016).


Google Scholar
 

Morris, H., Brodersen, C., Schwarze, F. W. M. R. & Jansen, S. The parenchyma of secondary xylem and its critical role in tree defense against fungal decay in relation to the CODIT model. Front. Plant Sci. 7, 1665 (2016).


Google Scholar
 

Muhr, J. et al. How fresh is maple syrup? Sugar maple trees mobilize carbon stored several years previously during early springtime sap-ascent. New Phytol. 209, 1410–1416 (2016).


Google Scholar
 

Telichowska, A. et al. Polyphenol content and antioxidant activities of Prunus padus L. and Prunus serotina L. leaves: electrochemical and spectrophotometric approach and their antimicrobial properties. Open Chem. 18, 1125–1135 (2020).


Google Scholar
 

Hofmann, T. et al. Antioxidant and antibacterial properties of Norway Spruce (Picea abies H. Karst.) and Eastern Hemlock (Tsuga canadensis (L.) Carrière) cone extracts. Forests 12, 1189 (2021).


Google Scholar
 

Hardoim Pablo, R. et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).


Google Scholar
 

Song, Z., Kennedy, P. G., Liew, F. J. & Schilling, J. S. Fungal endophytes as priority colonizers initiating wood decomposition. Funct. Ecol. 31, 407–418 (2017).


Google Scholar
 

Lee, J. W. et al. Taxonomic study of the genus Pholiota (Strophariaceae, Basidiomycota) in Korea. Mycobiology 48, 476–483 (2020).


Google Scholar
 

Lodge, D. J. et al. Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales). Fungal Divers. 64, 1–99 (2014).


Google Scholar
 

Dahlman, M., Danell, E. & Spatafora, J. W. Molecular systematics of Craterellus: cladistic analysis of nuclear LSU rDNA sequence data. Mycol. Res. 104, 388–394 (2000).


Google Scholar
 

Saikkonen, K., Faeth, S. H., Helander, M. & Sullivan, T. J. Fungal endophytes: a continuum of interactions with host plants. Annu. Rev. Ecol. Syst. 29, 319–343 (1998).


Google Scholar
 

Rodriguez, R. J., White, J. F. Jr, Arnold, A. E. & Redman, R. S. Fungal endophytes: diversity and functional roles. New Phytol. 182, 314–330 (2009).


Google Scholar
 

Boddy, L. & Griffith, G. Role of endophytes and latent invasion in the development of decay communities in sapwood of angiospermous trees. Sydowia 41, 41–73(2011).

Shortle, W. C., Menge, J. A. & Cowling, E. B. Interaction of bacteria, decay fungi, and live sapwood in discoloration and decay of trees. Eur. J. Forest Pathol. 8, 293–300 (1978).


Google Scholar
 

Shigo, A. L. & Hillis, W. E. Heartwood, discolored wood, and microorganisms in living trees. Annu. Rev. Phytopathol. 11, 197–222 (1973).


Google Scholar
 

Jensen, K. F. Measuring Oxygen and Carbon Dioxide in Red Oak Trees U.S. Forest Service Research Note NE-74 (U.S. Department of Agriculture, 1967).

Hoppe, B. et al. A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies. Sci. Rep. 5, 9456 (2015).


Google Scholar
 

Covey, K. R. et al. Greenhouse trace gases in deadwood. Biogeochemistry 130, 215–226 (2016).


Google Scholar
 

Estrada-De Los Santos, P., Bustillos-Cristales, R. & Caballero-Mellado, J. Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl. Environ. Microbiol. 67, 2790–2798 (2001).

ADS 

Google Scholar
 

Jo, Y. et al. Changes in microbial community structure in response to gummosis in peach tree bark. Plants 11, 2834 (2022).


Google Scholar
 

Phuengjayaem, S. et al. Sporolactobacillus mangiferae sp. nov., a spore-forming lactic acid bacterium isolated from tree bark in Thailand. Int. J. Syst. Evol. Microbiol. 73, e005993 (2023).

Timmusk, S., Grantcharova, N. & Wagner, E. G. H. Paenibacillus polymyxa invades plant roots and forms biofilms. Appl. Environ. Microbiol. 71, 7292–7300 (2005).

ADS 

Google Scholar
 

Tláskal, V., Zrůstová, P., Vrška, T. & Baldrian, P. Bacteria associated with decomposing dead wood in a natural temperate forest. FEMS Microbiol. Ecol. 93, fix157 (2017).

Madhaiyan, M. et al. Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L. Int. J. Syst. Evol. Microbiol. 63, 1241–1248 (2013).


Google Scholar
 

Lorentzen, M. P. G. & Lucas, P. M. Distribution of Oenococcus oeni populations in natural habitats. Appl. Microbiol. Biotechnol. 103, 2937–2945 (2019).


Google Scholar
 

Tang, Q., Puri, A., Padda, K. P. & Chanway, C. P. Biological nitrogen fixation and plant growth promotion of lodgepole pine by an endophytic diazotroph Paenibacillus polymyxa and its GFP-tagged derivative. Botany 95, 611–619 (2017).


Google Scholar
 

Putkinen, A. et al. New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. New Phytol. 231, 524–536 (2021).


Google Scholar
 

Taylor, F. H. Variation in sugar content of maple sap. Vermont Agricultural Experiment Station Bulletin 587, 3–39 (1956).

Argiroff, W. A. et al. Seasonality and longer-term development generate temporal dynamics in the Populus microbiome. mSystems 9, e0088623 (2024).


Google Scholar
 

Frank, A. C., Saldierna Guzmán, J. P. & Shay, J. E. Transmission of bacterial endophytes. Microorganisms 5, 70 (2017).


Google Scholar
 

Abdelfattah, A., Tack, A. J. M., Lobato, C., Wassermann, B. & Berg, G. From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome. Trends Microbiol. 31, 346–355 (2023).


Google Scholar
 

Barka, E. A. et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol. Mol. Biol. Rev. 80, 1–43 (2016).


Google Scholar
 

Zeikus, J. G. & Ward, J. C. Methane formation in living trees: a microbial origin. Science 184, 1181–1183 (1974).

ADS 

Google Scholar
 

Schink, B. & Ward, J. C. Microaerobic and anaerobic bacterial activities involved in formation of wetwood and discoloured wood. IAWA J. 5, 105–109 (1984).


Google Scholar
 

Hoch, G., Richter, A. & Körner, C. Non-structural carbon compounds in temperate forest trees. Plant Cell Environ. 26, 1067–1081 (2003).


Google Scholar
 

Spicer, R. & Holbrook, N. M. Within‐stem oxygen concentration and sap flow in four temperate tree species: does long‐lived xylem parenchyma experience hypoxia? Plant Cell Environ. 28, 192–201 (2005).


Google Scholar
 

Haridas, S. et al. 101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens. Stud. Mycol. 96, 141–153 (2020).


Google Scholar
 

Moll, J. et al. Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood. Environ. Microbiol. 20, 3744–3756 (2018).


Google Scholar
 

Rintala, E. et al. Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. OMICS 15, 461–476 (2011).


Google Scholar
 

Pareek, M., Allaway, W. G. & Ashford, A. E. Armillaria luteobubalina mycelium develops air pores that conduct oxygen to rhizomorph clusters. Mycol. Res. 110, 38–50 (2006).


Google Scholar
 

Carroll, G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69, 2–9 (1988).


Google Scholar
 

Promputtha, I. et al. A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microb. Ecol. 53, 579–590 (2007).

ADS 

Google Scholar
 

Siegenthaler, A. et al. Temperate tree microbiomes: divergent soil and phyllosphere microbial communities share few but dominant taxa. Plant Soil 496, 319–340 (2024).


Google Scholar
 

Pearce, R. B. Antimicrobial defences in the wood of living trees. New Phytol. 132, 203–233 (1996).


Google Scholar
 

Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J. & Dowling, D. N. Bacterial endophytes: recent developments and applications. FEMS Microbiol. Lett. 278, 1–9 (2008).


Google Scholar
 

Zarraonaindia, I. et al. The soil microbiome influences grapevine-associated microbiota. mBio 6, e02527–14 (2015).


Google Scholar
 

Lengrand, S., Pesenti, L., Bragard, C. & Legrève, A. Bacterial endophytome sources, profile and dynamics—a conceptual framework. Front. Sustain. Food Syst. 8, e1378436 (2024).

De La Fuente, L., Merfa, M. V., Cobine, P. A. & Coleman, J. J. Pathogen adaptation to the xylem environment. Annu. Rev. Phytopathol. 60, 163–186 (2022).


Google Scholar
 

Oses, R., Valenzuela, S., Freer, J., Sanfuentes, E. & Rodriguez, J. Fungal endophytes in xylem of healthy Chilean trees and their possible role in early wood decay. Fungal Divers. 33, 77–86 (2008).


Google Scholar
 

Pfautsch, S. Hydraulic anatomy and function of trees—basics and critical developments. Curr. For. Rep. 2, 236–248 (2016).


Google Scholar
 

Carluccio, G. et al. Xylem embolism and pathogens: can the vessel anatomy of woody plants contribute to X. fastidiosa resistance? Pathogens 12, 825 (2023).


Google Scholar
 

Gora, E. M., Lucas, J. M. & Yanoviak, S. P. Microbial composition and wood decomposition rates vary with microclimate from the ground to the canopy in a tropical forest. Ecosystems 22, 1206–1219 (2019).


Google Scholar
 

Harrison, J. G. & Griffin, E. A. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ. Microbiol. 22, 2107–2123 (2020).


Google Scholar
 

Westveld, M. Natural forest vegetation zones of New England. J. For. 54, 332–338 (1956).


Google Scholar
 

Ashton, M. S., Duguid, M. C., Barrett, A. L. & Covey, K. in Forest Plans of North America (eds Siry, J. P. et al.) Ch. 29 (Academic, 2015).

Weber, N. et al. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics 34, 1411–1413 (2018).


Google Scholar
 

Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).


Google Scholar
 

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).


Google Scholar
 

Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).


Google Scholar
 

McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).

ADS 

Google Scholar
 

Liu, C., Cui, Y., Li, X. & Yao, M. microeco: an R package for data mining in microbial community ecology. FEMS Microbiol. Ecol. 97, fiaa255 (2021).


Google Scholar
 

Shenhav, L. et al. FEAST: fast expectation-maximization for microbial source tracking. Nat. Methods 16, 627–632 (2019).


Google Scholar
 

Revell, L. J. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12, e16505 (2024).


Google Scholar
 

Qian, H. & Jin, Y. An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. J. Plant Ecol. 9, 233–239 (2016).


Google Scholar
 

Massicotte, P. & South, A. rnaturalearth: World Map Data from Natural Earth. R package version 4.1.0 https://docs.ropensci.org/rnaturalearth/ (2024).

Beech, E., Rivers, M., Oldfield, S. & Smith, P. P. GlobalTreeSearch: the first complete global database of tree species and country distributions. J. Sustain. For. 36, 454–489 (2017).


Google Scholar
 

McInnes, L., Healy, J., Saul, N. & Großberger, L. UMAP: uniform manifold approximation and projection. J. Open Source Softw. 3, 861 (2018).


Google Scholar
 

Quinn, T. P. et al. A field guide for the compositional analysis of any-omics data. Gigascience 8, giz107 (2019).


Google Scholar
 

Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).

ADS 

Google Scholar
 

Põlme, S. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).


Google Scholar
 

Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).


Google Scholar
 

Anderson, M. J. A new method for non‐parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).


Google Scholar
 

Oksanen, J. et al. vegan: community ecology package. R package version 2.7-1 (2020).

Sender, R., Fuchs, S. & Milo, R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164, 337–340 (2016).


Google Scholar
 

A., T. & Abdul, F. in Cellulose – Fundamental Aspects (ed. Van De Ven, T. G. M.) Ch. 5 (InTech, 2013).

Větrovský, T. & Baldrian, P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE 8, e57923 (2013).

ADS 

Google Scholar
 

Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).

ADS 

Google Scholar
 

Crowther, T. W. et al. Mapping tree density at a global scale. Nature 525, 201–205 (2015).

ADS 

Google Scholar