Molecular technologies applied to the ecology of ectomycorrhizal communities

The ecology of fungi, and the sub-field of community ecology of ectomycorrhizal (ECM) fungi, has changed significantly since the introduction of PCR and its application to fungal species identification. This chapter discusses recent progress and pitfalls in molecular technologies, and new highlights and future research domains in the ecology of ECM communities, derived from quantitative PCR, Second-Generation Sequencing (SGS), and 'meta-omics' approaches. The recent application of SGS and associated molecular studies has largely increased our understanding of ECM fungal ecology, including studies of factors that influence diversity, community structure, and the distribution and abundance of ECM fungal species at different spatial scales. The chapter presents analyses that were accomplished using bulk soil, but it is also possible to use molecular ecology to unravel which micro-organisms, mainly bacteria, are directly associated with ECM fungi. It highlights how the use of molecular high-throughput techniques improves our knowledge of truffle ecology and the quality of inoculated seedlings.