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  • Review Article
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Forest microbiome and global change

Abstract

Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant–microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.

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Fig. 1: Global distribution and features of forest ecosystems.
Fig. 2: Roles of the members of forest microbiomes.
Fig. 3: Global change factors affecting forest ecosystems and their microbiomes.
Fig. 4: Effects of global change in boreal, temperate and tropical forest ecosystems.

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References

  1. Bonan, G. B. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science 320, 1444–1449 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Harris, N. L. et al. Global maps of twenty-first century forest carbon fluxes. Nat. Clim. Chang. 11, 234–240 (2021).

    Article  Google Scholar 

  3. Högberg, P. et al. Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 411, 789–792 (2001).

    Article  PubMed  Google Scholar 

  4. Baldrian, P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol. Rev. 41, 109–130 (2017). This review displays the structure and function of microbiomes across forest habitats and describes the factors affecting the dynamics of microbiomes.

    CAS  PubMed  Google Scholar 

  5. Žifčáková, L. et al. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 5, 122 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Tlaskal, V. et al. Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition. Msystems 6, e01078-20 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Miyauchi, S. et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat. Commun. 11, 5125 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Llado, S., Lopez-Mondejar, R. & Baldrian, P. Forest soil bacteria: diversity, involvement in ecosystem processes, and response to global change. Microbiol. Mol. Biol. Rev. 81, 00063-16 (2017).

    Article  Google Scholar 

  9. Levy-Booth, D. J., Prescott, C. E. & Grayston, S. J. Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil. Biol. Biochem. 75, 11–25 (2014).

    Article  CAS  Google Scholar 

  10. Gao, Z. L., Karlsson, I., Geisen, S., Kowalchuk, G. & Jousset, A. Protists: puppet masters of the rhizosphere microbiome. Trends Plant Sci. 24, 165–176 (2019).

    Article  CAS  PubMed  Google Scholar 

  11. Offre, P., Spang, A. & Schleper, C. Archaea in biogeochemical cycles. Annu. Rev. Microbiol. 67, 437–457 (2013).

    Article  CAS  PubMed  Google Scholar 

  12. Fremin, B. J. et al. Thousands of small, novel genes predicted in global phage genomes. Cell Rep. 39, 110984 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. IPCC in Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (eds Masson-Delmotte, V. et al.) 3–32 (Cambridge Univ. Press, 2021).

  14. Anderegg, W. R. L. et al. Climate-driven risks to the climate mitigation potential of forests. Science 368, aaz7005 (2020).

    Article  Google Scholar 

  15. Mitchard, E. T. A. The tropical forest carbon cycle and climate change. Nature 559, 527–534 (2018).

    Article  CAS  PubMed  Google Scholar 

  16. Gauthier, S., Bernier, P., Kuuluvainen, T., Shvidenko, A. Z. & Schepaschenko, D. G. Boreal forest health and global change. Science 349, 819–822 (2015).

    Article  CAS  PubMed  Google Scholar 

  17. Millar, C. I. & Stephenson, N. L. Temperate forest health in an era of emerging megadisturbance. Science 349, 823–826 (2015).

    Article  CAS  PubMed  Google Scholar 

  18. Hubau, W. et al. Asynchronous carbon sink saturation in African and Amazonian tropical forests. Nature 579, 80–87 (2020).

    Article  CAS  PubMed  Google Scholar 

  19. Norby, R. J. & Zak, D. R. Ecological lessons from free-air CO2 enrichment (FACE) experiments. Annu. Rev. Ecol. Evol. Syst. 42, 181–203 (2011).

    Article  Google Scholar 

  20. Kuzyakov, Y., Horwath, W. R., Dorodnikov, M. & Blagodatskaya, E. Review and synthesis of the effects of elevated atmospheric CO2 on soil processes: no changes in pools, but increased fluxes and accelerated cycles. Soil. Biol. Biochem. 128, 66–78 (2019).

    Article  CAS  Google Scholar 

  21. Patoine, G. et al. Drivers and trends of global soil microbial carbon over two decades. Nat. Commun. 13, 4195 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Brodribb, T. J., Powers, J., Cochard, H. & Choat, B. Hanging by a thread? Forests and drought. Science 368, aat7631 (2020).

    Article  Google Scholar 

  23. Lloret, F. & Batllori, E. in Ecosystem Collapse and Climate Change Vol. 241 (eds Jackson, R. B. & Canadell, J. G.) 155–186 (Springer, 2021).

  24. Wang, C. T., Sun, Y., Chen, H. Y. H., Yang, J. Y. & Ruan, H. H. Meta-analysis shows non-uniform responses of above- and belowground productivity to drought. Sci. Total. Environ. 782, 146901 (2021).

    Article  CAS  PubMed  Google Scholar 

  25. Ackerman, D., Millet, D. B. & Chen, X. Global estimates of inorganic nitrogen deposition across four decades. Glob. Biogeochem. Cycles 33, 100–107 (2019).

    Article  CAS  Google Scholar 

  26. Högberg, M. N. et al. The return of an experimentally N-saturated boreal forest to an N-limited state: observations on the soil microbial community structure, biotic N retention capacity and gross N mineralisation. Plant Soil 381, 45–60 (2014).

    Article  Google Scholar 

  27. Du, E. Z. et al. Global patterns of terrestrial nitrogen and phosphorus limitation. Nat. Geosci. 13, 221–226 (2020).

    Article  CAS  Google Scholar 

  28. Fernandez-Martinez, M. et al. Nutrient availability as the key regulator of global forest carbon balance. Nat. Clim. Change 4, 471–476 (2014).

    Article  CAS  Google Scholar 

  29. Allen, C. D. et al. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. Ecol. Manag. 259, 660–684 (2010).

    Article  Google Scholar 

  30. Brando, P. M. et al. Abrupt increases in Amazonian tree mortality due to drought–fire interactions. Proc. Natl Acad. Sci. USA 111, 6347–6352 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Anderegg, W. R. L., Kane, J. M. & Anderegg, L. D. L. Consequences of widespread tree mortality triggered by drought and temperature stress. Nat. Clim. Change 3, 30–36 (2013).

    Article  Google Scholar 

  32. Jolly, W. M. et al. Climate-induced variations in global wildfire danger from 1979 to 2013. Nat. Commun. 6, 7537 (2015).

    Article  CAS  PubMed  Google Scholar 

  33. Williams, A. P. et al. Temperature as a potent driver of regional forest drought stress and tree mortality. Nat. Clim. Change 3, 292–297 (2013).

    Article  Google Scholar 

  34. Seidl, R. et al. Forest disturbances under climate change. Nat. Clim. Change 7, 395–402 (2017). This paper provides a global synthesis of climate change effects on important abiotic and biotic disturbance agents.

    Article  Google Scholar 

  35. Avolio, M. L. et al. Determinants of community compositional change are equally affected by global change. Ecol. Lett. 24, 1892–1904 (2021).

    Article  PubMed  Google Scholar 

  36. Forzieri, G., Dakos, V., McDowell, N. G., Ramdane, A. & Cescatti, A. Emerging signals of declining forest resilience under climate change. Nature 608, 534–539 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Luyssaert, S. et al. CO2 balance of boreal, temperate, and tropical forests derived from a global database. Glob. Change Biol. 13, 2509–2537 (2007).

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  39. Clemmensen, K. E. et al. Roots and associated fungi drive long-term carbon sequestration in boreal forest. Science 339, 1615–1618 (2013). This paper identifies belowground root and mycorrhizal fungal activities as key processes of carbon sequestration.

    Article  CAS  PubMed  Google Scholar 

  40. Price, D. T. et al. Anticipating the consequences of climate change for Canada’s boreal forest ecosystems. Environ. Rev. 21, 322–365 (2013).

    Article  Google Scholar 

  41. Treseder, K. K., Marusenko, Y., Romero-Olivares, A. L. & Maltz, M. R. Experimental warming alters potential function of the fungal community in boreal forest. Glob. Change Biol. 22, 3395–3404 (2016).

    Article  Google Scholar 

  42. Karhu, K. et al. Temperature sensitivity of soil respiration rates enhanced by microbial community response. Nature 513, 81–84 (2014).

    Article  CAS  PubMed  Google Scholar 

  43. Walker, X. J. et al. Increasing wildfires threaten historic carbon sink of boreal forest soils. Nature 572, 520–523 (2019).

    Article  CAS  PubMed  Google Scholar 

  44. Koster, K. et al. Impacts of wildfire on soil microbiome in boreal environments. Curr. Opin. Environ. Sci. Health 22, 100258 (2021). This paper summarizes the direct and indirect effects of wildfires on the microbiome of boreal forest and changes in resilience and functional recovery of the microbiome due to the increase of return intervals, intensity and severity expected in future.

    Article  Google Scholar 

  45. Bergner, B., Johnstone, J. & Treseder, K. K. Experimental warming and burn severity alter soil CO2 flux and soil functional groups in a recently burned boreal forest. Glob. Change Biol. 10, 1996–2004 (2004).

    Article  Google Scholar 

  46. Holden, S. R., Gutierrez, A. & Treseder, K. K. Changes in soil fungal communities, extracellular enzyme activities, and litter decomposition across a fire chronosequence in Alaskan Boreal Forests. Ecosystems 16, 34–46 (2013).

    Article  CAS  Google Scholar 

  47. Day, N. J. et al. Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada. Glob. Change Biol. 25, 2310–2324 (2019).

    Article  Google Scholar 

  48. Clemmensen, K. E. et al. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. N. Phytol. 205, 1525–1536 (2015).

    Article  CAS  Google Scholar 

  49. Whitman, T. et al. Soil bacterial and fungal response to wildfires in the Canadian boreal forest across a burn severity gradient. Soil. Biol. Biochem. 138, 107571 (2019).

    Article  CAS  Google Scholar 

  50. Nelson, A. R. et al. Wildfire-dependent changes in soil microbiome diversity and function. Nat. Microbiol. 7, 1419–1430 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Hogberg, P., Nasholm, T., Franklin, O. & Hogberg, M. N. Tamm review: on the nature of the nitrogen limitation to plant growth in Fennoscandian boreal forests. Ecol. Manag. 403, 161–185 (2017).

    Article  Google Scholar 

  52. Forsmark, B., Nordin, A., Rosenstock, N. P., Wallander, H. & Gundale, M. J. Anthropogenic nitrogen enrichment increased the efficiency of belowground biomass production in a boreal forest. Soil. Biol. Biochem. 155, 108154 (2021).

    Article  CAS  Google Scholar 

  53. Shao, P., Han, H., Sun, J. & Xie, H. Effects of global change and human disturbance on soil carbon cycling in boreal forest: a review. Pedosphere https://doi.org/10.1016/j.pedsph.2022.06.035 (2022).

    Article  Google Scholar 

  54. Jorgensen, K., Granath, G., Strengbom, J. & Lindahl, B. D. Links between boreal forest management, soil fungal communities and below-ground carbon sequestration. Funct. Ecol. 36, 392–405 (2022).

    Article  CAS  Google Scholar 

  55. Karlsson, P. E., Akselsson, C., Hellsten, S. & Karlsson, G. P. Twenty years of nitrogen deposition to Norway spruce forests in Sweden. Sci. Total Environ. 809, 152192 (2022).

    Article  CAS  PubMed  Google Scholar 

  56. Bebber, D. P. The gap between atmospheric nitrogen deposition experiments and reality. Sci. Total Environ. 801, 149774 (2021).

    Article  CAS  PubMed  Google Scholar 

  57. Schutte, U. M. E. et al. Effect of permafrost thaw on plant and soil fungal community in a boreal forest: does fungal community change mediate plant productivity response? J. Ecol. 107, 1737–1752 (2019).

    Article  Google Scholar 

  58. Zhang, Z. et al. Emerging role of wetland methane emissions in driving 21st century climate change. Proc. Natl Acad. Sci. USA 114, 9647–9652 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hagedorn, F., Gavazov, K. & Alexander, J. M. Above- and belowground linkages shape responses of mountain vegetation to climate change. Science 365, 1119–1123 (2019).

    Article  CAS  PubMed  Google Scholar 

  60. Alvarez-Garrido, L., Vinegla, B., Hortal, S., Powell, J. R. & Carreira, J. A. Distributional shifts in ectomycorrizhal fungal communities lag behind climate-driven tree upward migration in a conifer forest-high elevation shrubland ecotone. Soil. Biol. Biochem. 137, 107545 (2019).

    Article  CAS  Google Scholar 

  61. Norby, R. J., Ledford, J., Reilly, C. D., Miller, N. E. & O’Neill, E. G. Fine-root production dominates response of a deciduous forest to atmospheric CO2 enrichment. Proc. Natl Acad. Sci. USA 101, 9689–9693 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Schlesinger, W. H. & Lichter, J. Limited carbon storage in soil and litter of experimental forest plots under increased atmospheric CO2. Nature 411, 466–469 (2001).

    Article  CAS  PubMed  Google Scholar 

  63. Phillips, R. P. et al. Roots and fungi accelerate carbon and nitrogen cycling in forests exposed to elevated CO2. Ecol. Lett. 15, 1042–1049 (2012).

    Article  PubMed  Google Scholar 

  64. Schleppi, P., Bucher-Wallin, I., Hagedorn, F. & Körner, C. Increased nitrate availability in the soil of a mixed mature temperate forest subjected to elevated CO2 concentration (canopy FACE). Glob. Change Biol. 18, 757–768 (2012).

    Article  Google Scholar 

  65. Dunbar, J. et al. Surface soil fungal and bacterial communities in aspen stands are resilient to eleven years of elevated CO2 and O3. Soil. Biol. Biochem. 76, 227–234 (2014).

    Article  CAS  Google Scholar 

  66. Phillips, R. L., Whalen, S. C. & Schlesinger, W. H. Response of soil methanotrophic activity to carbon dioxide enrichment in a North Carolina coniferous forest. Soil. Biol. Biochem. 33, 793–800 (2001).

    Article  CAS  Google Scholar 

  67. Kirschke, S. et al. Three decades of global methane sources and sinks. Nat. Geosci. 6, 813–823 (2013).

    Article  CAS  Google Scholar 

  68. Melillo, J. M. et al. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 358, 101–104 (2017). This study describes how the response of soil microbial biomass and organic carbon in forest soil to warming changes in time.

    Article  CAS  PubMed  Google Scholar 

  69. DeAngelis, K. M. et al. Long-term forest soil warming alters microbial communities in temperate forest soils. Front. Microbiol. 6, 104 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Pold, G. et al. Long-term warming alters carbohydrate degradation potential in temperate forest soils. Appl. Environ. Microbiol. 82, 6518–6530 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Baldrian, P. et al. Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change. Soil Biol. Biochem. 56, 60–68 (2013).

    Article  CAS  Google Scholar 

  72. Bastida, F. et al. When drought meets forest management: effects on the soil microbial community of a Holm oak forest ecosystem. Sci. Total Environ. 662, 276–286 (2019).

    Article  CAS  PubMed  Google Scholar 

  73. Willing, C. E., Pierroz, G., Coleman-Derr, D. & Dawson, T. E. The generalizability of water-deficit on bacterial community composition; site-specific water-availability predicts the bacterial community associated with coast redwood roots. Mol. Ecol. 29, 4721–4734 (2020).

    Article  CAS  PubMed  Google Scholar 

  74. Gehring, C., Sevanto, S., Patterson, A., Ulrich, D. E. M. & Kuske, C. R. Ectomycorrhizal and dark septate fungal associations of pinyon pine are differentially affected by experimental drought and warming. Front. Plant Sci. 11, 1570 (2020).

    Article  Google Scholar 

  75. Berard, A., Ben Sassi, M., Kaisermann, A. & Renault, P. Soil microbial community responses to heat wave components: drought and high temperature. Clim. Res. 66, 243–264 (2015).

    Article  Google Scholar 

  76. Dannenmann, M. et al. Climate change impairs nitrogen cycling in European beech forests. PLoS ONE 11, e0158823 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Baldrian, P., Merhautová, V., Petránková, M., Cajthaml, T. & Šnajdr, J. Distribution of microbial biomass and activity of extracellular enzymes in a hardwood forest soil reflect soil moisture content. Appl. Soil. Ecol. 46, 177–182 (2010).

    Article  Google Scholar 

  78. Brabcová, V. et al. Fungal community development in decomposing fine deadwood is largely affected by microclimate. Front. Microbiol. 13, 835274 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  79. Hernandez, L., de Dios, R. S., Montes, F., Sainz-Ollero, H. & Canellas, I. Exploring range shifts of contrasting tree species across a bioclimatic transition zone. Eur. J. Res. 136, 481–492 (2017).

    Article  Google Scholar 

  80. Bowd, E. J., Banks, S. C., Bissett, A., May, T. W. & Lindenmayer, D. B. Disturbance alters the forest soil microbiome. Mol. Ecol. 31, 419–435 (2022).

    Article  CAS  PubMed  Google Scholar 

  81. Smith, G. R., Edy, L. C. & Peay, K. G. Contrasting fungal responses to wildfire across different ecosystem types. Mol. Ecol. 30, 844–854 (2021).

    Article  PubMed  Google Scholar 

  82. Dove, N. C., Taş, N. & Hart, S. C. Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential. ISME J. 16, 1853–1863 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Hart, S. C., DeLuca, T. H., Newman, G. S., MacKenzie, M. D. & Boyle, S. I. Post-fire vegetative dynamics as drivers of microbial community structure and function in forest soils. Ecol. Manag. 220, 166–184 (2005).

    Article  Google Scholar 

  84. Pellegrini, A. F. A. et al. Decadal changes in fire frequencies shift tree communities and functional traits. Nat. Ecol. Evol. 5, 504–512 (2021).

    Article  PubMed  Google Scholar 

  85. Kurz, W. A. et al. Mountain pine beetle and forest carbon feedback to climate change. Nature 452, 987–990 (2008).

    Article  CAS  PubMed  Google Scholar 

  86. Quinn Thomas, R., Canham, C. D., Weathers, K. C. & Goodale, C. L. Increased tree carbon storage in response to nitrogen deposition in the US. Nat. Geosci. 3, 13–17 (2010).

    Article  CAS  Google Scholar 

  87. Frey, S. D. et al. Chronic nitrogen additions suppress decomposition and sequester soil carbon in temperate forests. Biogeochemistry 121, 305–316 (2014).

    Article  CAS  Google Scholar 

  88. Frey, B., Carnol, M., Dharmarajah, A., Brunner, I. & Schleppi, P. Only minor changes in the soil microbiome of a sub-alpine forest after 20 years of moderately increased nitrogen loads. Front. Glob. Change 3, 77 (2020).

    Article  Google Scholar 

  89. Hood-Nowotny, R. et al. Functional response of an Austrian forest soil to N addition. Environ. Res. Commun. 3, 025001 (2021).

    Article  Google Scholar 

  90. Wallenstein, M. D., McNulty, S., Fernandez, I. J., Boggs, J. & Schlesinger, W. H. Nitrogen fertilization decreases forest soil fungal and bacterial biomass in three long-term experiments. Ecol. Manag. 222, 459–468 (2006).

    Article  Google Scholar 

  91. Moore, J. A. M. et al. Fungal community structure and function shifts with atmospheric nitrogen deposition. Glob. Change Biol. 27, 1349–1364 (2021).

    Article  CAS  Google Scholar 

  92. Tahovska, K. et al. Positive response of soil microbes to long-term nitrogen input in spruce forest: results from Gardsjon whole-catchment N-addition experiment. Soil Biol. Biochem. 143, 107732 (2020).

    Article  CAS  Google Scholar 

  93. Baldrian, P., Bell-Dereske, L., Lepinay, C., Větrovský, T. & Kohout, P. Fungal communities in soils under global change. Stud. Mycol. 103, 1–24 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. van der Linde, S. et al. Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558, 243–248 (2018). This paper shows that nitrogen deposition affects the communities of symbiotic ectomycorrhizal fungi.

    Article  PubMed  Google Scholar 

  95. Morrison, E. W. et al. Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest. Fungal Ecol. 23, 48–57 (2016).

    Article  Google Scholar 

  96. de Witte, L. C., Rosenstock, N. P., van der Linde, S. & Braun, S. Nitrogen deposition changes ectomycorrhizal communities in Swiss beech forests. Sci. Total Environ. 605, 1083–1096 (2017).

    Article  PubMed  Google Scholar 

  97. Zak, D. R., Holmes, W. E., Burton, A. J., Pregitzer, K. S. & Talhelm, A. F. Simulated atmospheric NO3 deposition increases soil organic matter by slowing decomposition. Ecol. Appl. 18, 2016–2027 (2008).

    Article  PubMed  Google Scholar 

  98. Freedman, Z. B., Upchurch, R. A., Zak, D. R. & Cline, L. C. Anthropogenic N deposition slows decay by favoring bacterial metabolism: insights from metagenomic analyses. Front. Microbiol. 7, 259 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  99. Freedman, Z. et al. Towards a molecular understanding of N cycling in northern hardwood forests under future rates of N deposition. Soil. Biol. Biochem. 66, 130–138 (2013).

    Article  CAS  Google Scholar 

  100. Aber, J. et al. Nitrogen saturation in temperate forests. Bioscience 48, 921–934 (1998).

    Article  Google Scholar 

  101. Venterea, R. T. et al. Nitrogen oxide gas emissions from temperate forest soils receiving long-term nitrogen inputs. Glob. Change Biol. 9, 346–357 (2003).

    Article  Google Scholar 

  102. Boisvert-Marsh, L., Perie, C. & de Blois, S. Shifting with climate? Evidence for recent changes in tree species distribution at high latitudes. Ecosphere 5, 33 (2014).

    Article  Google Scholar 

  103. Reich, P. B. et al. Even modest climate change may lead to major transitions in boreal forests. Nature 608, 540–545 (2022).

    Article  CAS  PubMed  Google Scholar 

  104. Bauer, A., Farrell, R. & Goldblum, D. The geography of forest diversity and community changes under future climate conditions in the eastern United States. Ecoscience 23, 41–53 (2016).

    Article  Google Scholar 

  105. Averill, C., Dietze, M. C. & Bhatnagar, J. M. Continental-scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks. Glob. Change Biol. 24, 4544–4553 (2018).

    Article  Google Scholar 

  106. Jo, I., Fei, S., Oswalt, C. M., Domke, G. M. & Phillips, R. P. Shifts in dominant tree mycorrhizal associations in response to anthropogenic impacts. Sci. Adv. 5, eaav6358 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Averill, C. & Hawkes, C. V. Ectomycorrhizal fungi slow soil carbon cycling. Ecol. Lett. 19, 937–947 (2016).

    Article  PubMed  Google Scholar 

  108. Mushinski, R. M. et al. Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests. Glob. Change Biol. 27, 1068–1082 (2021). This paper links plant mycorrhizal associations with the composition and function of soil microbiomes involved in nitrogen cycling.

    Article  CAS  Google Scholar 

  109. Baccini, A. et al. Tropical forests are a net carbon source based on aboveground measurements of gain and loss. Science 358, 230–233 (2017).

    Article  CAS  PubMed  Google Scholar 

  110. Guerra, C. A. et al. Blind spots in global soil biodiversity and ecosystem function research. Nat. Commun. 11, 3870 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Nottingham, A. T., Meir, P., Velasquez, E. & Turner, B. L. Soil carbon loss by experimental warming in a tropical forest. Nature 584, 234–237 (2020). This paper explores the effects of warming on microbial activity in the context of the tropical forest that is so far rarely studied.

    Article  CAS  PubMed  Google Scholar 

  112. Cunha, H. F. V. et al. Direct evidence for phosphorus limitation on Amazon forest productivity. Nature 608, 558–562 (2022).

    Article  CAS  PubMed  Google Scholar 

  113. Poorter, L. et al. Biodiversity and climate determine the functioning of Neotropical forests. Glob. Ecol. Biogeogr. 26, 1423–1434 (2017).

    Article  Google Scholar 

  114. Bauman, D. et al. Tropical tree mortality has increased with rising atmospheric water stress. Nature 608, 528–533 (2022).

    Article  CAS  PubMed  Google Scholar 

  115. Phillips, O. L. et al. Drought sensitivity of the Amazon rainforest. Science 323, 1344–1347 (2009).

    Article  CAS  PubMed  Google Scholar 

  116. Bouskill, N. J. et al. Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism. Front. Microbiol. 7, 525 (2016).

    PubMed  PubMed Central  Google Scholar 

  117. Oliveira, U. et al. Determinants of fire impact in the Brazilian biomes. Front. Glob. Change 5, 735017 (2022).

    Article  Google Scholar 

  118. Corrales, A., Turner, B. L., Tedersoo, L., Anslan, S. & Dalling, J. W. Nitrogen addition alters ectomycorrhizal fungal communities and soil enzyme activities in a tropical montane forest. Fungal Ecol. 27, 14–23 (2017).

    Article  Google Scholar 

  119. Carey, J. C. et al. Temperature response of soil respiration largely unaltered with experimental warming. Proc. Natl Acad. Sci. USA 113, 13797–13802 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Holden, S. R. & Treseder, K. K. A meta-analysis of soil microbial biomass responses to forest disturbances. Front. Microbiol. 4, 163 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  121. Stursova, M. et al. When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback. ISME J. 8, 1920–1931 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  122. Davison, J. et al. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. N. Phytol. 231, 763–776 (2021).

    Article  CAS  Google Scholar 

  123. Větrovský, T. et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat. Commun. 10, 5142 (2019). This paper identifies climate as the most important driver of fungal distribution with particular effects on ectomycorrhizal fungi.

    Article  PubMed  PubMed Central  Google Scholar 

  124. Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Lennon, J. T., Aanderud, Z. T., Lehmkuhl, B. K. & Schoolmaster, D. R. Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology 93, 1867–1879 (2012).

    Article  PubMed  Google Scholar 

  127. Urbanová, M., Šnajdr, J. & Baldrian, P. Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees. Soil. Biol. Biochem. 84, 53–64 (2015).

    Article  Google Scholar 

  128. Gange, A. C., Gange, E. G., Mohammad, A. B. & Boddy, L. Host shifts in fungi caused by climate change? Fungal Ecol. 4, 184–190 (2011).

    Article  Google Scholar 

  129. Baldrian, P., Větrovský, T., Lepinay, C. & Kohout, P. High-throughput sequencing view on the magnitude of global fungal diversity. Fungal Divers. 114, 539–547 (2022).

    Article  CAS  Google Scholar 

  130. Jansson, J. K. & Hofmockel, K. S. Soil microbiomes and climate change. Nat. Rev. Microbiol. 18, 35–46 (2019).

    Article  PubMed  Google Scholar 

  131. Zak, D. R. et al. Anthropogenic N deposition, fungal gene expression, and an increasing soil carbon sink in the northern hemisphere. Ecology 100, 8 (2019).

    Article  Google Scholar 

  132. Kauserud, H. et al. Warming-induced shift in European mushroom fruiting phenology. Proc. Natl Acad. Sci. USA 109, 14488–14493 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Steidinger, B. S. et al. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 569, 404–408 (2019).

    Article  CAS  PubMed  Google Scholar 

  134. Kluber, L. A., Smith, J. E. & Myrold, D. D. Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi. Soil. Biol. Biochem. 43, 1042–1050 (2011).

    Article  CAS  Google Scholar 

  135. van der Heijden, M. G. A., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present, and the future. N. Phytol. 205, 1406–1423 (2015).

    Article  Google Scholar 

  136. Steidinger, B. S. et al. Ectomycorrhizal fungal diversity predicted to substantially decline due to climate changes in North American Pinaceae forests. J. Biogeogr. 47, 772–782 (2020). This paper makes a prediction of a future loss of diversity of ectomycorrhizal fungi as a consequence of global change.

    Article  Google Scholar 

  137. Miyamoto, Y., Terashima, Y. & Nara, K. Temperature niche position and breadth of ectomycorrhizal fungi: reduced diversity under warming predicted by a nested community structure. Glob. Change Biol. 24, 5724–5737 (2018).

    Article  Google Scholar 

  138. Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).

    Article  CAS  PubMed  Google Scholar 

  139. Delgado-Baquerizo, M. et al. The proportion of soil-borne pathogens increases with warming at the global scale. Nat. Clim. Change 10, 550–554 (2020). This paper analyses the risk of fungal pathogen rise in response to global change.

    Article  Google Scholar 

  140. Guerra, C. A. et al. Global projections of the soil microbiome in the Anthropocene. Glob. Ecol. Biogeogr. 30, 987–999 (2021).

    Article  PubMed  Google Scholar 

  141. Garcia, M. O. et al. Soil microbes trade-off biogeochemical cycling for stress tolerance traits in response to year-round climate change. Front. Microbiol. 11, 616 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  142. Royo, A. A. et al. The forest of unintended consequences: anthropogenic actions trigger the rise and fall of black cherry. Bioscience 71, 683–696 (2021).

    Article  Google Scholar 

  143. McLane, S. C. & Aitken, S. N. Whitebark pine (Pinus albicaulis) assisted migration potential: testing establishment north of the species range. Ecol. Appl. 22, 142–153 (2012).

    Article  PubMed  Google Scholar 

  144. Pedro, M. S., Rammer, W. & Seidl, R. Tree species diversity mitigates disturbance impacts on the forest carbon cycle. Oecologia 177, 619–630 (2015).

    Article  Google Scholar 

  145. Pretzsch, H. et al. Mixing of Scots pine (Pinus sylvestris L.) and European beech (Fagus sylvatica L.) enhances structural heterogeneity, and the effect increases with water availability. Ecol. Manag. 373, 149–166 (2016).

    Article  Google Scholar 

  146. Větrovský, T. et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci. Data 7, 228 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  147. Zimov, S. A., Schuur, E. A. G. & Chapin, F. S. Permafrost and the global carbon budget. Science 312, 1612–1613 (2006).

    Article  CAS  PubMed  Google Scholar 

  148. Averill, C. et al. Defending Earth’s terrestrial microbiome. Nat. Microbiol. 7, 1717–1725 (2022).

    Article  CAS  PubMed  Google Scholar 

  149. Martinović, T. et al. Temporal turnover of the soil microbiome composition is guild-specific. Ecol. Lett. 24, 2726–2738 (2021).

    Article  PubMed  Google Scholar 

  150. Knusel, B. et al. Applying big data beyond small problems in climate research. Nat. Clim. Change 9, 196–202 (2019).

    Article  Google Scholar 

  151. Bullock, E. L., Woodcock, C. E., Souza, C. & Olofsson, P. Satellite-based estimates reveal widespread forest degradation in the Amazon. Glob. Change Biol. 26, 2956–2969 (2020).

    Article  Google Scholar 

  152. Reiche, J. et al. Combining satellite data for better tropical forest monitoring. Nat. Clim. Change 6, 120–122 (2016).

    Article  Google Scholar 

  153. Zou, W., Jing, W., Chen, G., Lu, Y. & Song, H. A survey of big data analytics for smart forestry. IEEE Access. 7, 46621–46636 (2019).

    Article  Google Scholar 

  154. Seibold, S. et al. The contribution of insects to global forest deadwood decomposition. Nature 597, 77–81 (2021). This paper assesses the combined effects of the microbiome and insects on decomposition of deadwood across the globe, pointing to the importance of the interactions between microorganisms and macroorganisms.

    Article  CAS  PubMed  Google Scholar 

  155. Crowther, T. W. et al. Biotic interactions mediate soil microbial feedbacks to climate change. Proc. Natl Acad. Sci. USA 112, 7033–7038 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Ashton, L. A. et al. Termites mitigate the effects of drought in tropical rainforest. Science 363, 174–177 (2019).

    Article  CAS  PubMed  Google Scholar 

  157. Thakur, M. P. et al. Reduced feeding activity of soil detritivores under warmer and drier conditions. Nat. Clim. Change 8, 75–78 (2018).

    Article  Google Scholar 

  158. Cambon, M. C. et al. Drought tolerance traits in neotropical trees correlate with the composition of phyllosphere fungal communities. Phytobiomes J. https://doi.org/10.1094/PBIOMES-04-22-0023-R (2022).

    Article  Google Scholar 

  159. Laforest-Lapointe, I., Paquette, A., Messier, C. & Kembel, S. W. Leaf bacterial diversity mediates plant diversity and ecosystem function relationships. Nature 546, 145–147 (2017).

    Article  CAS  PubMed  Google Scholar 

  160. Vesterdal, L., Clarke, N., Sigurdsson, B. D. & Gundersen, P. Do tree species influence soil carbon stocks in temperate and boreal forests? Ecol. Manag. 309, 4–18 (2013).

    Article  Google Scholar 

  161. Magnusson, R. I., Tietema, A., Cornelissen, J. H. C., Hefting, M. M. & Kalbitz, K. Tamm review: sequestration of carbon from coarse woody debris in forest soils. Ecol. Manag. 377, 1–15 (2016).

    Article  Google Scholar 

  162. Sterck, F. et al. Optimizing stand density for climate-smart forestry: a way forward towards resilient forests with enhanced carbon storage under extreme climate events. Soil. Biol. Biochem. 162, 108396 (2021).

    Article  CAS  Google Scholar 

  163. Lohila, A. et al. Greenhouse gas flux measurements in a forestry-drained peatland indicate a large carbon sink. Biogeosciences 8, 3203–3218 (2011).

    Article  CAS  Google Scholar 

  164. Leppä, K. et al. Selection cuttings as a tool to control water table level in boreal drained peatland forests. Front. Earth Sci. 8, 576510 (2020).

    Article  Google Scholar 

  165. Stephens, S. L. et al. Temperate and boreal forest mega-fires: characteristics and challenges. Front. Ecol. Environ. 12, 115–122 (2014).

    Article  Google Scholar 

  166. Strassburg, B. B. N. et al. Global priority areas for ecosystem restoration. Nature 586, 724–729 (2020).

    Article  CAS  PubMed  Google Scholar 

  167. Hong, P. B. et al. Biodiversity promotes ecosystem functioning despite environmental change. Ecol. Lett. 25, 555–569 (2022).

    Article  PubMed  Google Scholar 

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Acknowledgements

P.K. (grant no. 21-17749S) and R.L.-M. (grant no. 22-30769S) received support from the Czech Science Foundation.

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Glossary

Arbuscular mycorrhizal fungi

(AM). Fungi that form a mycorrhizal symbiosis with a plant host. This is typical for certain trees and most non-woody plants and is characterized by fungal hyphae that penetrate plant cell walls, where they form highly branched structures known as arbuscules. AM belong to a single monopyhyletic lineage of Glomeromycota. They are not able to decompose biopolymers.

Biopolymers

Polymeric molecules consisting of organic building blocks, typically forming cell walls of plant biomass (for example, cellulose, hemicelluloses, lignin, pectin), bacterial biomass (for example, peptidoglycan) or fungal biomass (for example, chitin).

Copiotrophic microorganisms

Microorganisms found in environments or microhabitats rich in nutrients, particularly carbon.

Ectomycorrhizal fungi

Fungi engaged in a mycorrhizal symbiosis that is characterized anatomically by fungal hyphae that wholly enclose the fine roots of the tree host. Ectomycorrhizal fungi include diverse species from the Basidiomycota and Ascomycota phyla. Some ectomycorrhizal fungi are involved in organic matter decomposition.

Ericoid mycorrhizal fungi

Fungi in a mycorrhizal symbiosis with certain members of the plant family Ericaceae that are characterized by the penetration of hair root cells and the formation of hyphal coils. Ericoid mycorrhizal fungi include diverse species from the Basidiomycota and Ascomycota phyla, and can efficiently decompose biopolymers.

Free-air CO2 enrichment

An experimental approach that raises the concentration of carbon dioxide (CO2) in a specified experimental system, such as a forest stand, and allows the response of the ecosystem to be analysed.

Oligotrophic microorganisms

Microorganisms found in environments or microhabitats poor in nutrients, particularly carbon, or those habitats where carbon is contained in complex macromolecules that are difficult to utilize.

Resilience

The capacity of an ecosystem to recover from perturbations.

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Baldrian, P., López-Mondéjar, R. & Kohout, P. Forest microbiome and global change. Nat Rev Microbiol 21, 487–501 (2023). https://doi.org/10.1038/s41579-023-00876-4

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