Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).
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).
Cregger, M. A. et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6, 31 (2018).
Mo, L. et al. Integrated global assessment of the natural forest carbon potential. Nature 624, 92–101 (2023).
Falster, D. S. et al. BAAD: a Biomass And Allometry Database for woody plants. Ecology 96, 1445–1445 (2015).
Andrews, J. H. & Harris, R. F. The ecology and biogeography of microorganisms on plant surfaces. Annu. Rev. Phytopathol. 38, 145–180 (2000).
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).
Sohrabi, R., Paasch, B. C., Liber, J. A. & He, S. Y. Phyllosphere microbiome. Annu. Rev. Plant Biol. 74, 539–568 (2023).
Jeffrey, L. C. et al. Bark-dwelling methanotrophic bacteria decrease methane emissions from trees. Nat. Commun. 12, 2127 (2021).
Baldrian, P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol. Rev. 41, 109–130 (2017).
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).
Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).
Turner, T. R., James, E. K. & Poole, P. S. The plant microbiome. Genome Biol. 14, 209 (2013).
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).
Santoyo, G., Moreno-Hagelsieb, G., del Orozco-Mosqueda, M. C. & Glick, B. R. Plant growth-promoting bacterial endophytes. Microbiol. Res. 183, 92–99 (2016).
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).
Arnold, W. et al. A method for sampling the living wood microbiome. Methods Ecol. Evol. https://doi.org/10.1111/2041-210x.14311 (2024).
Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).
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).
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).
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).
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).
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).
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).
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).
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).
Lee, J. W. et al. Taxonomic study of the genus Pholiota (Strophariaceae, Basidiomycota) in Korea. Mycobiology 48, 476–483 (2020).
Lodge, D. J. et al. Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales). Fungal Divers. 64, 1–99 (2014).
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).
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).
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).
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).
Shigo, A. L. & Hillis, W. E. Heartwood, discolored wood, and microorganisms in living trees. Annu. Rev. Phytopathol. 11, 197–222 (1973).
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).
Covey, K. R. et al. Greenhouse trace gases in deadwood. Biogeochemistry 130, 215–226 (2016).
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).
Jo, Y. et al. Changes in microbial community structure in response to gummosis in peach tree bark. Plants 11, 2834 (2022).
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).
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).
Lorentzen, M. P. G. & Lucas, P. M. Distribution of Oenococcus oeni populations in natural habitats. Appl. Microbiol. Biotechnol. 103, 2937–2945 (2019).
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).
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).
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).
Frank, A. C., Saldierna Guzmán, J. P. & Shay, J. E. Transmission of bacterial endophytes. Microorganisms 5, 70 (2017).
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).
Barka, E. A. et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol. Mol. Biol. Rev. 80, 1–43 (2016).
Zeikus, J. G. & Ward, J. C. Methane formation in living trees: a microbial origin. Science 184, 1181–1183 (1974).
Schink, B. & Ward, J. C. Microaerobic and anaerobic bacterial activities involved in formation of wetwood and discoloured wood. IAWA J. 5, 105–109 (1984).
Hoch, G., Richter, A. & Körner, C. Non-structural carbon compounds in temperate forest trees. Plant Cell Environ. 26, 1067–1081 (2003).
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).
Haridas, S. et al. 101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens. Stud. Mycol. 96, 141–153 (2020).
Moll, J. et al. Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood. Environ. Microbiol. 20, 3744–3756 (2018).
Rintala, E. et al. Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. OMICS 15, 461–476 (2011).
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).
Carroll, G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69, 2–9 (1988).
Promputtha, I. et al. A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microb. Ecol. 53, 579–590 (2007).
Siegenthaler, A. et al. Temperate tree microbiomes: divergent soil and phyllosphere microbial communities share few but dominant taxa. Plant Soil 496, 319–340 (2024).
Pearce, R. B. Antimicrobial defences in the wood of living trees. New Phytol. 132, 203–233 (1996).
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).
Zarraonaindia, I. et al. The soil microbiome influences grapevine-associated microbiota. mBio 6, e02527–14 (2015).
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).
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).
Pfautsch, S. Hydraulic anatomy and function of trees—basics and critical developments. Curr. For. Rep. 2, 236–248 (2016).
Carluccio, G. et al. Xylem embolism and pathogens: can the vessel anatomy of woody plants contribute to X. fastidiosa resistance? Pathogens 12, 825 (2023).
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).
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).
Westveld, M. Natural forest vegetation zones of New England. J. For. 54, 332–338 (1956).
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).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
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).
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).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
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).
Shenhav, L. et al. FEAST: fast expectation-maximization for microbial source tracking. Nat. Methods 16, 627–632 (2019).
Revell, L. J. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12, e16505 (2024).
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).
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).
McInnes, L., Healy, J., Saul, N. & Großberger, L. UMAP: uniform manifold approximation and projection. J. Open Source Softw. 3, 861 (2018).
Quinn, T. P. et al. A field guide for the compositional analysis of any-omics data. Gigascience 8, giz107 (2019).
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).
Põlme, S. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers. 105, 1–16 (2020).
Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
Anderson, M. J. A new method for non‐parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).
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).
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).
Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).
Crowther, T. W. et al. Mapping tree density at a global scale. Nature 525, 201–205 (2015).
