Metagenomics applied to arbuscular mycorrhizal fungal communities

Metagenomics studies have recently offered new approaches that shed light on microbial communities in a variety of environments. In this context, DNA pyrosequencing is being used more and more to investigate prokaryotic assemblages in soil environment. Fungi, which are crucial components of soil microbial communities, functioning as decomposers, pathogens and mycorrhizal symbionts, have instead been largely neglected. However, the last year has been characterized by an explosion of metagenomic studies applied to fungal communities, based on the pyrosequencing technology. The aim of this chapter is to focus on Arbuscular Mycorrhizal Fungi (AMF), the most widespread symbionts in many ecosystems, and to demonstrate how metagenomics may help us to understand the composition and dynamics of AMF communities. At the moment, only two studies have investigated AMF biodiversity using the pyrosequencing approach and SSU rDNA as the target gene. Although both studies targeted the same group of fungi, they focused on different habitats. Compared to similar studies, carried out using a cloning-sequencing approach or DNA barcoding, the main outcome that emerged from pyrosequencing analyses applied to AMF and to other fungal communities is the unexpected fungal biodiversity observed in the analyzed environments. Interestingly, the pyrosequencing approach applied to isolated spores of AMF has demonstrated that they are a niche for highly polymorphic endobacterial communities. The data confirm the powerfulness of the pyrosequencing approach, which represents a promising new tool to better understand the natural distribution of an essential group of soil microorganisms, such as fungi. The large number of reads that have been obtained increases the likelihood of capturing sequences from rare organisms, which would instead remain undetected with the cloning- sequencing approach.