The Contribution of DNA Metabarcoding to Fungal Conservation: Diversity Assessment, Habitat Partitioning and Mapping Red-Listed Fungi in Protected Coastal Salix repens Communities in the Netherlands

Abstract

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.

Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach

“…Detection of five phylogenetically diverse fungal phyla from asymptomatic plant rhizosphere and tissues demonstrates that S. chamaejasme harbors a diverse group of rhizospheric and endophytic mycobiota. The very low proportion of Chytridiomycota and Glomeromycota taxa found in the present study is similar with other studies (Geml et al 2014;Mouhamadou et al 2011). These results are similar with other cultureindependent molecular studies dealing with the rhizospheric fungal communities of different plant (Geml et al 2014), and also in agreement with previous reports on endophytic fungal communities of grassy tissues or leaves, stems and roots of different medicinal plant hosts (Kusari et al 2013;Sánchez Márquez et al 2010), which have found coincidental distribution patterns of ascomycetous fungi.…”

“…It is reasonable that soil borne fungi are more prevalent and diversified than air borne fungi (The fungi that infect aerial plant tissues via air-borne spores) (Ghimire et al 2011). These results are similar with other cultureindependent molecular studies dealing with the rhizospheric fungal communities of different plant (Geml et al 2014), and also in agreement with previous reports on endophytic fungal communities of grassy tissues or leaves, stems and roots of different medicinal plant hosts (Kusari et al 2013;Sánchez Márquez et al 2010), which have found coincidental distribution patterns of ascomycetous fungi. Similar result was found by Ghimire et al (2011), who obtained fungal isolates from root tissues was almost three times higher than that from shoot tissues.…”

“…However, dissimilar result is also found in the other study on fungal endophyte communities of the Indian medicinal plant Tinospora cordifolia. Basidiomycota constitute an (Geml et al 2014). Detection of five phylogenetically diverse fungal phyla from asymptomatic plant rhizosphere and tissues demonstrates that S. chamaejasme harbors a diverse group of rhizospheric and endophytic mycobiota.…”

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska

“…(2011) as reference. We used a 97% sequence similarity clustering threshold as has been routinely done in fungal ecology studies (e.g., O'Brien et al ., 2005; Higgins et al ., 2007; Geml et al ., 2008, 2009; Amend et al ., 2010; Tedersoo et al ., 2010; Geml et al ., 2012; Kauserud et al ., 2012; Brown et al ., 2013; Blaalid et al ., 2013; Geml et al ., 2014a). Global singletons were discarded from further analysis.…”

Recognition of the discipline of conservation mycology

“…Molecular techniques will assist greatly in tackling currently intractable aspects. A genealogical concordance approach to the rigorous recognition of phylogenetic species is increasingly applied to fungi, and barcoding is a practical tool for identification (Geml et al 2014). Metabarcoding provides unprecedented characterization of the fungal community in any substrate (e.g., soil, insect guts, plant roots or leaves).…”