Editorial: Forest Microbiome: Dynamics and Interactions in the Anthropocene Era

Amrita Chakraborty^1*Amit Roy¹Shulin He²Antonio Castellano-Hinojosa³Fred O Asiegbu⁴Teresa Ann Coutinho⁵

• ¹Czech University of Life Sciences Prague, Prague, Czechia
• ²Chongqing Normal University, Chongqing, China
• ³Universidad de Granada Departamento de Microbiologia, Granada, Spain
• ⁴University of Helsinki, Helsinki, 00014, Finland, Helsinki, Finland
• ⁵University of Pretoria, Pretoria, South Africa

Forests represent one of the most complex and biodiverse ecosystems on Earth, with intricate networks linking trees, vegetation strata, insects, microbial communities, and soil processes. These networks, sustained by feedback loops and finely tuned ecological balances, form the foundation of global biogeochemical cycles and biodiversity conservation. At the core of these dynamics lies the forest microbiome, including a vast, often invisible consortium of bacteria, fungi, archaea, and viruses that mediates nutrient turnover, supports tree health, and shapes interactions across trophic levels (Baldrian 2017, Asiegbu andKovalchuk 2021).Increasingly, forest microbiome research reveals that microbial communities associated with soils, roots, leaves, and even insects form tightly interlinked networks that mediate ecosystem processes and responses to environmental change. In the Anthropocene era, climate change, deforestation, land-use intensification, pollution, and biological invasions are altering the composition and function of forest biomes at unprecedented scales (Baldrian, López-Mondéjar et al. 2023). Shifts in tree diversity, changes in vegetation cover, and disruptions in soil structure ripple through microbial communities, reconfiguring ecological interactions and challenging our capacity to predict ecosystem trajectories (Lladó, López-Mondéjar et al. 2017). Understanding how these elements interact under multidimensional anthropogenic pressures is therefore crucial. The forest microbiome is a pivotal, yet often overlooked, component of ecosystem dynamics. Unravelling its contributions is essential for a complete understanding of how forests respond to anthropogenic pressures. Microbes can also be used as valuable tools for forest pest management (Gupta, Chakraborty et al. 2023). Hence, the current special issue is devoted to highlighting the microbial dimension of forest ecosystems. This special issue explores how vegetation, host traits, soil conditions, nitrogen inputs, and biotic stressors shape the diversity, structure, and function of microbial communities across forest compartments (rhizosphere, phyllosphere, endosphere, soil, and insect-associated niches (Chakraborty, Zádrapová et al. 2023, Zádrapová, Chakraborty et al. 2024). Collectively, these findings reveal that forest soil microbiomes respond sensitively to both natural gradients and anthropogenic interventions and are pivotal to ecosystem recovery, nutrient cycling, and resilience. Hence, the forest microbiome is key to evidence-based forest management and conservation. Tree microbiomes are strongly compartmentalised. Aboveground habitats such as the phyllosphere, stem, and needles, host microbial assemblages with ecological roles that diverge markedly from those in the belowground rhizosphere, one of the most dynamic zones of plant-microbe interaction.Empirical evidence is robust: Enea et al. (doi:10.3389/fmicb.2024.1504444) showed that the phyllosphere and rhizosphere of sugar maple (Acer saccharum Marshall) harbour distinct communities that shift with environmental conditions, while Luo et al.(doi:10.3389/fmicb.2024.1410901) reported pronounced bacterial and fungal turnover across leaves, roots, rhizosphere, and bulk soil in boreal forests. Collectively, these studies suggest that trees recruit and filter microbes through compartment-specific processes that underpin nutrient acquisition, stress tolerance, and overall fitness traits, which may ultimately constrain or facilitate range expansion. Crucially, the magnitude and direction of these nitrogen effects depend on host identity: Hou et al.(doi: 10.3389/fmicb.2025.1534028) documented tree species-specific microbial responses to nitrogen deposition, highlighting interactive controls between host traits and nutrient enrichment on rhizosphere assembly. Forest insects harbour microbes that are central to forest health, and the evidence is now overwhelming: these symbioses simultaneously drive insect adaptation and shape tree outcomes, for better or worse. Consider the bark beetles, where the insect-microbe partnership is anything but incidental. Khara et al. (doi: 10.3389/fmicb.2024.1400894) reveal finely tuned bacterial associations in two pine bark beetles that shift in response to environmental, host, and life-stage factors, forming an adaptive mosaic that equips beetles to navigate heterogeneous forest conditions.Building on this ecological context, Baños-Quintana et al. (doi:10.3389/fmicb.2024.1367127) show that the Eurasian spruce bark beetle (Ips typographus) actively engineers its nursery: adults not only shape the microbiomes of their offspring but also remodel the gallery environment itself, carving out microbial micro-niches that amplify colonisation success and, ultimately, beetle impact.These findings corroborate some of the observations from other studies on the same beetle (Chakraborty, Purohit et al. 2023).At a broader phylogenetic scale, .3389/fmicb .2024 .1360488) map gut fungal assemblages across 14 Dendroctonus species, uncovering a conserved core mycobiome whose functions, such as digestion, nutrient acquisition, and cues for host specialisation, are foundational to beetle fitness. Analogous studies on multiple Ips bark beetle guts also revealed a conserved core microbiota with similar functional potential (Chakraborty, Ashraf et al. 2020, Chakraborty, Modlinger et al. 2020). A microbiome study from termites further underscores that symbiotic interactions with microbes in wood-feeding insects can reverberate beyond nutrition: Nevertheless, forest insects are ecosystem engineers because their microbiomes are ecosystem tools. These invisible microbial communities facilitate host adaptation, enhance digestion, and, in many systems, contribute to exacerbating tree mortality. The intricate microbial contribution also increases the complexity of the forest networks when pests adapt to numerous anthropogenic pressures. Furthermore, the adaptation of pests also poses a significant threat to the forest health under these pressures. Together, these findings highlight that insect-microbe interactions are not peripheral but central to forest health. Ignoring these dynamics risks undermining pest management and forest conservation strategies. Forest management and restoration must be grounded in the trajectories of microbial recovery and the soil functions that underpin them. Drawing on logged Bornean lowland dipterocarp rainforest, assemblages primarily by modifying root traits and soil physicochemical conditions, while soil metabolites contribute comparatively little. Taken together, these studies demand a tighter integration of soil metabolomics with microbial community analyses to elucidate how plant traits and soil chemistry drive microbial dynamics, and to sharpen predictive models guiding forest restoration under diverse reforestation regimes. Forest microbiome represents an integrative, multi-kingdom infrastructure that links soils, roots, leaves, and insects to regulate nutrient cycling, plant health, and ecosystem resilience under global change. Forest microbiomes cannot be understood in isolation, and they form a continuum across compartments that jointly sustain forest health and resilience. We propose a conceptual framework that illustrates how abiotic, biotic, and anthropogenic factors converge to shape the forest microbiome, which in turn drives nutrient recycling, forest regeneration, pest management, and climate change mitigation (Figure 1).The studies featured in this special issue demonstrate that microbial diversity across soil, vegetation, and insect hosts is deeply embedded within the ecological fabric of forest ecosystems.They highlight how abiotic factors (e.g., temperature, precipitation, and soil pH), biotic interactions (e.g., host identity and pest communities), and anthropogenic pressures (e.g., nitrogen deposition and forest management) jointly shape microbial assembly and, ultimately, ecosystem trajectories.Looking forward, advancing from taxonomic surveys toward functional approaches, such as metatranscriptomics, metabolomics, and targeted functional assays, will be essential to uncover the mechanistic links between microbiomes and ecosystem processes. Integrating multi-compartment studies that connect soil, rhizosphere, phyllosphere, and insect-associated microbiomes will enable a deeper understanding of how climate change, nutrient enrichment, and land-use intensification reshape forest stability. Furthermore, the integration of mutualistic desirable microbiomes is expected to be of great significance for sustainable forest production and translational forest management. Additionally, future research directions may explore the application of novel approaches, such as metagenome-wide association studies (MWAS), to link the relative abundance of specific genes in the metagenome with certain forest tree diseases. This knowledge is not merely academic. It provides a foundation for microbiome-informed strategies in forest conservation, restoration, pest management, and climate change mitigation.