In recent years, plant–microorganism interactions and their impact on plant growth and health, and in turn on plant-driven ecosystem services (e.g., carbon storage, phytoremediation) have gained a lot of interest in the scientific community. This interest has been stimulated by the development of high-throughput sequencing technologies that greatly improved the capacity of scientists to efficiently characterize microbiomes, which are defined as the pool of genomes of the microorganisms (e.g., bacteria, fungi) present in a particular habitat. Among trees, the poplar microbiome is one of the most extensively studied. The goal of this chapter is to summarize the current literature on the poplar microbiome, first by describing the microbiomes of belowground and aboveground parts of poplars, and second by highlighting links between poplar genetic and the microbiome. This second part includes a review of studies specifically addressing the impact of transgenesis on the poplar microbiome. Overall, this chapter highlights the diversity of the poplar microbiome and the importance of further assessing links between tree genetic and the microbiome.

In eastern Canada, boreal forests are locally experiencing a shift between two alternative stable states, productive closed-canopy feather moss (Pleurozium schreberi (Brid.) Mitt.) forests to low-productivity open lichen (Cladonia spp.) woodlands. While this shift has important consequences for ecosystem structure and productivity, little is known about the changes occurring in the diversity and composition of the soil microbial community which may be driven by this process. We evaluated the effects of 10-year moss transplantation on soil microbial communities in an open-lichen woodland. Treatments included: 1) removal of the lichen cover, 2) removal of the lichen cover followed by transplantation of a feather moss cover, 3) a control with the lichen cover kept in place (lichen control), and 4) a natural forest site with a feather moss cover (moss control). We found that changing the forest ground cover has a significant impact on the diversity, composition and function of soil microbial communities. Fungal alpha diversity was more sensitive to changes in lichen and moss cover, compared to bacterial diversity. Soil microbial community composition showed significant differences among all forest ground covers, but with greater similarities between the moss transplantation and control moss treatments. More importantly, changes of forest ground cover significantly affected the structure of microbial communities and fungal functional groups. Moss transplantation significantly increased the relative abundance of the organic nitrogen-scavenging fungal genus, Piloderma. Furthermore, moss transplantation significantly increased the overall relative abundance of ectomycorrhizal fungi and decreased the proportion of ericoid mycorrhizal fungi. Soil moisture and temperature were the main environmental variables associated to the shift in microbial community composition. Our study points out that moss transplantation in open-canopy lichen woodlands contributes to regulate and modify the composition, structure, and function of the soil microbial communities with potential implications for explaining the changes in ecosystem processes associated with these two forest ecosystems.

Global change is shifting ecosystem type relative abundance in boreal forests, while the green energy transition results in increased mining activities around the globe. The interaction and consequent effects of these two trends on biodiversity have not been examined in depth. Bryophytes species can be used as indicators to measure these effects because they play key ecological roles in boreal forests. We identified and evaluated the interaction between ecosystem type (i.e., coniferous, deciduous, mixed forest and open canopy) and mining on microhabitat scale bryophyte diversity and composition in 1-km landscapes surrounding six mine sites at different stages of the mining lifecycle in the Canadian boreal forest. Irrespective of microhabitat type, the combined effects of ecosystem type and mining stage were interactive on bryophytes. Bryophyte richness and community composition were negatively affected by offsite effects of mines in only deciduous and mixed forests. The interacted effects on bryophyte richness mainly occurred on the ground r microhabitats. We also found that deciduous, mixed forests (coniferous forest as a reference) and mines had a negative impact on the abundance of feather mosses and sphagna. Furthermore, indicator species were identified for areas affected by mines (Pohlia nutans and Dicranum polysetum) and for control areas (Sphagnum angustifolium and Plagiomnium cuspidatum). Our results suggest the predicted ecosystem shifts with global changes, from coniferous to deciduous forests, could potentially increase the effects of mining on forest ecosystem resistance through the changes in bryophyte community structure. Adding microhabitats (i.e., adding coarse woody debris) near mine sites is a potential strategy to maintain species richness. Collectively, these findings advance our understanding of how mining affects biodiversity and highlight the importance of considering mine offsite landscapes in future environmental evaluations of development projects in the context of global changes.