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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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Sampling sites along the coast of the Netherlands.Sites corresponding to the Renodunal and Wadden geological districts are marked with black and white squares, respectively.
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pone-0099852-g001: Sampling sites along the coast of the Netherlands.Sites corresponding to the Renodunal and Wadden geological districts are marked with black and white squares, respectively.

Mentions: The following environmental agencies granted permission for the fieldwork (with sampled field sites): Amsterdamse Waterleidingduinen (Haarlem-Bentveld), Dunea (Wassenaar-Meijendel), Natuurmonumenten (Goeree, Callantsoog-Zwanenwater), and Staatsbosbeheer (Terschelling). GPS coordinates of the sampling sites are listed in Table 1. The field sampling only included soil and did not involve endangered or protected species. The selected sites represented sand dune S. repens beds (European Environment Agency habitat code: 2170) in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing a south-north transect (Figure 1, Table 1). This coastal dune system is characterized by an oceanic climate with mean annual temperature of 9–10°C (July, 16–17°C; January, 2–3°C) and precipitation of 675–800 mm [21]. Sand-lime content varies between 0.1 and 10% [21], with generally calcareous soils in the southern Renodunal district (represented by the sampling sites Goeree, Meijendel, and Haarlem-Bentveld) and more acidic soils in the northern Wadden district (Zwanenwater, Terschelling). In most areas, the height of the dunes reaches 15–25 m [28]. Current management policies are directed toward multiple purposes, such as drinking water supply, defense against storm floods, recreation, and nature conservation [29]. Soil samples were taken at sites monitored by Natuurmonumenten (Goeree and Zwanenwater), Dunea (Meijendel), Staatsbosbeheer (Terschelling), and the Amsterdamse Waterleidingduinen (Haarlem-Bentveld). In March of 2010, 20 soil cores, 2 cm in diameter and ca. 20 cm deep, were taken at each site in a way that cores were at least 2 m from each other to minimize the probability of sampling the same genet repeatedly. For every plot, the 20 cores were pooled, resulting in a composite soil sample for each plot. Soils were deposited in 50 mL Falcon tubes and stored at –80°C until lyophilization.


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)

Sampling sites along the coast of the Netherlands.Sites corresponding to the Renodunal and Wadden geological districts are marked with black and white squares, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099852-g001: Sampling sites along the coast of the Netherlands.Sites corresponding to the Renodunal and Wadden geological districts are marked with black and white squares, respectively.
Mentions: The following environmental agencies granted permission for the fieldwork (with sampled field sites): Amsterdamse Waterleidingduinen (Haarlem-Bentveld), Dunea (Wassenaar-Meijendel), Natuurmonumenten (Goeree, Callantsoog-Zwanenwater), and Staatsbosbeheer (Terschelling). GPS coordinates of the sampling sites are listed in Table 1. The field sampling only included soil and did not involve endangered or protected species. The selected sites represented sand dune S. repens beds (European Environment Agency habitat code: 2170) in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing a south-north transect (Figure 1, Table 1). This coastal dune system is characterized by an oceanic climate with mean annual temperature of 9–10°C (July, 16–17°C; January, 2–3°C) and precipitation of 675–800 mm [21]. Sand-lime content varies between 0.1 and 10% [21], with generally calcareous soils in the southern Renodunal district (represented by the sampling sites Goeree, Meijendel, and Haarlem-Bentveld) and more acidic soils in the northern Wadden district (Zwanenwater, Terschelling). In most areas, the height of the dunes reaches 15–25 m [28]. Current management policies are directed toward multiple purposes, such as drinking water supply, defense against storm floods, recreation, and nature conservation [29]. Soil samples were taken at sites monitored by Natuurmonumenten (Goeree and Zwanenwater), Dunea (Meijendel), Staatsbosbeheer (Terschelling), and the Amsterdamse Waterleidingduinen (Haarlem-Bentveld). In March of 2010, 20 soil cores, 2 cm in diameter and ca. 20 cm deep, were taken at each site in a way that cores were at least 2 m from each other to minimize the probability of sampling the same genet repeatedly. For every plot, the 20 cores were pooled, resulting in a composite soil sample for each plot. Soils were deposited in 50 mL Falcon tubes and stored at –80°C until lyophilization.

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