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

• Published in: PloS one Vol. 9; no. 6; p. e99852
• Main Authors: Geml, József, Gravendeel, Barbara, van der Gaag, Kristiaan J, Neilen, Manon, Lammers, Youri, Raes, Niels, Semenova, Tatiana A, de Knijff, Peter, Noordeloos, Machiel E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17-06-2014; Public Library of Science (PLoS)
• Subjects: Acidic soils; Arbuscular mycorrhizas; Ascomycota - classification; Ascomycota - genetics; Base Sequence; Biodiversity; Biology and Life Sciences; Coastal ecology; Coastal protection; Coasts; Communities; Community composition; Conservation; Conservation of Natural Resources; Deoxyribonucleic acid; DNA; DNA Barcoding, Taxonomic; DNA, Fungal - genetics; DNA, Ribosomal Spacer - genetics; Dunes; Ecosystem; Ecosystems; Ectomycorrhizas; Endophytes; Flowers & plants; Forests; Fungi; Genera; Hydrogen ions; Laboratories; Nature conservation; Nature reserves; Netherlands; pH effects; Rare species; Salix - microbiology; Salix repens; Sand dunes; Soil chemistry; Soil Microbiology; Soil moisture; Soil pH; Soils; Vegetation; Willow; Netherlands
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0099852

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.