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Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term microbiota has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.

A decade ago, tunnels inside mineral grains were found that were likely formed by hyphae of ectomycorrhizal (EcM) fungi. This observation implied that EcM fungi can dissolve mineral grains. The observation raised several questions on the ecology of these ¿rock-eating¿ fungi. This review addresses the roles of these rock-eating EcM associations in plant nutrition, biogeochemical cycles and pedogenesis. Research approaches ranged from molecular to ecosystem level scales. Nutrient deficiencies change EcM seedling exudation patterns of organic anions and thus their potential to mobilise base cations from minerals. This response was fungal species-specific. Some EcM fungi accelerated mineral weathering. While mineral weathering could also increase the concentrations of phytotoxic aluminium in the soil solution, some EcM fungi increase Al tolerance through an enhanced exudation of oxalate. Through their contribution to Al transport, EcM hyphae could be agents in pedogenesis, especially podzolisation. A modelling study indicated that mineral tunnelling is less important than surface weathering by EcM fungi. With both processes taken together, the contribution of EcM fungi to weathering may be significant. In the field vertical niche differentiation of EcM fungi was shown for EcM root tips and extraradical mycelium. In the field EcM fungi and tunnel densities were correlated. Our results support a role of rock-eating EcM fungi in plant nutrition and biogeochemical cycles. EcM fungal species-specific differences indicate the need for further research with regard to this variation in functional traits.