Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest

Abstract

International audienceThe use of next-generation DNA sequencing methods, which produce massive volumes of data, has transformed fungal molecular ecology. These technologies offer the opportunity to describe microbial communities in depth and to investigate fungal diversity at a large geographical scale. In particular, due to the emergence of studies conducted at a large scale (countries, continents), the definition of a compromise between the optimal and representative description of local diversity (plot scale) and the management of a greater number of sites for these studies is required. This work was performed to explore the local richness and the structure of the ectomycorrhizal (EcM) fungal and oomycete communities in a temperate beech plot using 454 pyrosequencing technology. The internal transcribed spacer 1 (ITS1) region was amplified and sequenced from fine roots and soil sampled from the two upper horizons. Our analyses suggest that soil could be a good substitute for fine roots in studying EcM fungi. The fungal assemblage exhibited a vertical distribution in the soil profile. Only four Pythiaceae were identified, which was insufficient to study the spatial distribution of this group. The fungal and particularly the ectomycorrhizal (EcM) richness was not correlated with any soil variable (pH, C, N or P), but the spatial structure was explained by the C:N ratio and phosphorus content. Our data reveal the importance of maintaining a minimal representative sampling at the plot scale for comparative geographical studies

Mycorrhization of Fagaceae Forests Within Mediterranean Ecosystems

“…A positive correlation between ECM fungal richness and silvo-pastoral exploitation regime and low mortality of cork was detected in this study (Azul et al 2010). In addition, the use of NGS DNA sequencing methods on Fagus sylvatica forest soils revealed that the most abundant fungal genera were Russula, Boletus, but also C. geophilum (Coince et al 2013). Moreover, C. geophilum was the main ECM fungus reported in root tip assessment in Q. rubra forests, although its abundance has oscillated significantly with tree age (Gebhardt et al 2007).…”

Oomycete-specific ITS primers for identification and metabarcoding

“…For example, Vannini et al (2013) recovered only 23 oomycete OTUs from 10 forest soil samples, where oomycetes contributed to 79% of all reads. More recently, Coince et al (2013) recovered a total of 10 oomycete OTUs from 20 samples of forest soil that contributed to 15% of all reads. Sapkota and Nicolaisen (2015) improved the ITS6/ITS7 based method by optimizing the annealing temperature and as a result recovered 67 oomycete OTUs (95% of all reads) from 26 agricultural soil samples, but may have missed multiple taxa due to overly strict PCR conditions.…”

“…Of oomycete-specific ITS primers, ITS6 and ITS7 (Cooke et al 2000) have been used for community studies, but with notable difficulties, as Coince et al (2013) recovered only a small percentage of oomycete sequences using these primers. Sapkota and Nicolaisen (2015) optimized the ITS6/ITS7 assay by raising the annealing temperature and as a result improved the specificity of the primers.…”

Metatranscriptomic census of active protists in soils

“…Oomycetes in soil have been targeted with little success (Coince et al, 2013). Our metatranscriptome approach revealed that Oomycetes were ubiquitous, abundant and active members among soil protists, suggesting a significant role as structuring elements of natural plant communities.…”