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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.

Geml J, Gravendeel B, van der Gaag KJ, Neilen M, Lammers Y, Raes N, Semenova TA, de Knijff P, Noordeloos ME - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Naturalis Biodiversity Center, Leiden, The Netherlands; Faculty of Science, Leiden University, Leiden, 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.

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Non-metric multidimensional scaling (NMDS) ordination plot for fungal communities from Salix repens sites.Ordinations were based on the square-root transformed abundance of 97% ITS sequence similarity OTUs. Labels, localities and descriptions of the sampling sites are given in Table 1. Vectors are shown for soil pH, total OTU richness, and for the most diverse taxonomic orders (A) and genera (B) that correlated with the ordination axes at r2>0.200.
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pone-0099852-g003: Non-metric multidimensional scaling (NMDS) ordination plot for fungal communities from Salix repens sites.Ordinations were based on the square-root transformed abundance of 97% ITS sequence similarity OTUs. Labels, localities and descriptions of the sampling sites are given in Table 1. Vectors are shown for soil pH, total OTU richness, and for the most diverse taxonomic orders (A) and genera (B) that correlated with the ordination axes at r2>0.200.

Mentions: Ordinations were performed with square-root transformed abundance in the OTU vs. site matrix. Final stress value for the 2-dimensional NMDS solution was 0.03062. Variables with /r/ ≥0.5 values are shown in bold and are displayed in the NMDS ordinations in Figure 3.


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.

Geml J, Gravendeel B, van der Gaag KJ, Neilen M, Lammers Y, Raes N, Semenova TA, de Knijff P, Noordeloos ME - PLoS ONE (2014)

Non-metric multidimensional scaling (NMDS) ordination plot for fungal communities from Salix repens sites.Ordinations were based on the square-root transformed abundance of 97% ITS sequence similarity OTUs. Labels, localities and descriptions of the sampling sites are given in Table 1. Vectors are shown for soil pH, total OTU richness, and for the most diverse taxonomic orders (A) and genera (B) that correlated with the ordination axes at r2>0.200.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4061046&req=5

pone-0099852-g003: Non-metric multidimensional scaling (NMDS) ordination plot for fungal communities from Salix repens sites.Ordinations were based on the square-root transformed abundance of 97% ITS sequence similarity OTUs. Labels, localities and descriptions of the sampling sites are given in Table 1. Vectors are shown for soil pH, total OTU richness, and for the most diverse taxonomic orders (A) and genera (B) that correlated with the ordination axes at r2>0.200.
Mentions: Ordinations were performed with square-root transformed abundance in the OTU vs. site matrix. Final stress value for the 2-dimensional NMDS solution was 0.03062. Variables with /r/ ≥0.5 values are shown in bold and are displayed in the NMDS ordinations in Figure 3.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Naturalis Biodiversity Center, Leiden, The Netherlands; Faculty of Science, Leiden University, Leiden, 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.

Show MeSH
Related in: MedlinePlus