Plant-mycorrhizal fungi symbiosis: from metabarcoding data to diversity analysis

Next Generation Sequencing (NGS) approaches are currently used as a tool to study communities of plant-associated mycorrhizal symbionts such as arbuscular mycorrhizal fungi (AMF). They enable fungal identification in roots without the need of assessing morphological features and provide sufficient depth and magnitude to get insights into fungal community ecology. DNA metabarcoding infers the species composition of environmental samples by amplifying, sequencing and analysing target genomic regions.

Relatively little is known about the effect of habitat fragmentation on belowground mycorrhizal communities. Gypsum ecosystems are usually characterized by fragmentation phenomena in such a way that they can be considered as a model system to understand the mycorrhizal interaction-area size relationships.

In our study, we assess AMF community composition in plant roots from a fragmented gypsum landscape located in Spain. We sampled 225 individuals corresponding to 28 plant species, along a 15 sized-fragment gradient. DNA was extracted form root samples. Amplicons libraries were prepared using region specific primer NS31 and AML2 to target 18s r-DNA V4 region of Glomeromycota and sequencing performed on Illumina MiSeq 2*300v3. Bioinformatic analysis included demultiplexing, quality filtering, artefacts removal and Operational Taxonomic Unit (OTUs) clustering. MaarjAM data base of Glomeromycota was used to assign OTUs to taxa.

We observed a marked AMF richness and diversity loss when habitat size decreases. Plant individuals have less Glomeromycota OTUs in their roots and number of OTUS in the whole plant community is reduced in small fragments. Plant-AMF interactions loss is nested, with smaller fragments harbouring those interactions that more recurrently appears across fragments. Concerning robustness, fungal community seems more vulnerable to partner loss in small fragments.

Habitat fragmentation may constitute a risk for a loss of plant-mycorrhizal fungi interactions and ultimately for AMF extinction. The implications on nutrient cycle and ecosystem functioning cannot be underestimated.