How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities.

Roots take on several key functions for trees such as anchoring, storing of nutrients and foraging for water and inorganic nutrients. This last part is actually mainly assumed by symbiotic ectomycorrhizal (EcM) fungi that associate with the short roots of most trees from boreal and temperate forests. Thanks to their very dense network of hyphae, EcM fungi explore large volumes of soil from which they uptake water and nutrients that they later transfer to the roots of their host tree. In exchange, trees provide EcM fungi with carbohydrates that are transferred to the fungal component of the ectomycorriza, i.e. the symbiotic organ formed by tree roots and fungal mycelium. This particular interface connects tree roots to the surrounding soil and supports intensive nutrient fluxes. Ectomycorrhizae are heavily colonized by complex microbial communities (Timonen et al., 1998; Johansson et al., 2004; Uroz et al., 2013). Up to 20% of the carbon fixed by trees is transferred below ground and is shared with EcM fungi and their associated microbial communities, thus giving them an important role in carbon cycling in forest ecosystems (Högberg et al., 2001). In addition to their participation in tree nutrition, nutrient cycling and soil fertility, EcM fungi and their microbial associates are involved in the protection of their host against pathogens (Barea et al., 2002). Giving the importance of EcM fungi and their microbial associates for the biology of trees and for nutrient cycling in forest soils, it is crucial for the management of forest ecosystems to identify the factors that drive the diversity and structure of tree root microbial communities. The analysis of EcM fungal communities and their microbial associates is a very complex task because they are both influenced by multiple factors and they are both highly dynamic. The root system of a single tree is generally simultaneously colonized by dozens of ectomycorrhizal species that differ by their ability to capture and transfer nutrients to their host tree (Courty et al., 2005; Bahram et al., 2011). The composition of this EcM fungal community that colonize a tree root system depends on the tree species, its age, the physico-chemical properties of soil and seasons (Buée et al., 2011; Tedersoo et al., 2012; Sterkenburg et al., 2015). Similarly, the composition and the structure of bacterial communities associated with the EcM fungi are under the influence of host tree, EcM fungi, the reservoir of microorganisms in the adjacent soil, soil edaphic parameters and seasons (Izumi and Finlay, 2011; Uroz et al., 2012; Bonito et al., 2014). However, the relative contribution and importance of each factor is still poorly understood and contradictory results have been obtained in the past. This is partly because those factors act in combination and they are difficult to separate on the field. Marupakula and colleagues (this issue, Marupakula et al., 2016) used an elegant method to start untangling this complexity. They planted seedlings of Pinus sylvestris in a natural soil already colonized by pre-established microbial communities and grew them in a glasshouse for 24 weeks. They regularly sampled seedlings from week 1 to week 24 and harvested EcM root tips of each morphotype detected. Ectomycorrhizal fungi were identified by Internal Transcribed Spacer (ITS) sequencing and the bacterial communities associated with each EcM morphotype was characterized by 454 pyrosequencing. This trapping method allowed them to follow simultaneously the pattern of colonization of P. sylvestris root system by fungi and the potential temporal changes of the associated bacterial communities. Since four EcM fungi were retrieved across all sampling times, Marupakula and colleagues were able to evaluate the influence of different EcM species associated with a same tree species on the ectomycorrhiza associated bacterial community structure, composition and dynamic. An interesting feature of the *For correspondence. E-mail deveau@nancy.inra. fr; Tel. +33 3 83 39 40 88; Fax +33 3 83 39 40 69. Environmental Microbiology (2016) doi:10.1111/1462-2920.13214