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Saproxylic insects and fungi in deciduous forests along a rural–urban gradient

Cite this dataset

Meyer, Sandro (2020). Saproxylic insects and fungi in deciduous forests along a rural–urban gradient [Dataset]. Dryad.


Urbanisation is increasing worldwide and is regarded a major threat to biodiversity in forests. As consequences of intensive human use, the vegetation structure of naturally growing urban forests and their amount of deadwood can be reduced. Deadwood is an essential resource for various saproxylic insects and fungi. We assessed the effects of urbanisation and forest characteristics on saproxylic insects and fungi. We exposed standardized bundles consisting of each three fresh-cut beech and oak branches in 25 forests along a rural–urban gradient in Basel (Switzerland). After an exposure of 8 months, we extracted the saproxylic insects for 10 months using an emergence trap for each bundle. We used drilling chips from each branch to determine fungal operational taxonomic units (OTUs). 193,534 insect individuals emerged from the experimental bundles. Our study showed that the abundance of total saproxylic insects, bark beetles, longhorn beetles, total flies, moths and ichneumonid wasps decreased with increasing degree of urbanisation, but not their species richness. However, the taxonomic composition of all insect groups combined was altered by wood moisture of branches and that of saproxylic beetles was influenced by the degree of urbanisation. Unexpectedly, forest size and local forest characteristics had a minor effect on saproxylic insects. ITS (Internal Transcribed Spacer of rDNA) analysis with fungal specific primers revealed a total of 97 fungal OTUs on the bundles. The number of total fungal OTUs decreased with increasing degree of urbanisation and was affected by the volume of naturally occurring fine woody debris. The composition of fungal OTUs was altered by the degree of urbanisation and pH of the branch wood. As a consequence of the altered compositions of saproxylics, the association between total saproxylic insects and fungi changed along the rural–urban gradient. Our study shows that urbanisation can negatively impact saproxylic insects and fungi.


For fungal OTU (operational taxonomic units) data:

We extracted DNA from 200 mg of each sawdust sample using the Quick-DNA Fecal/Soil Microbe Miniprep Kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions. DNA quantity and quality were measured using Nanodrop. We determined fungal OTUs using the F-ARISA method with the fungal-specific primer ITS1 (Gardes & Bruns, 1993) fluorescently labelled at the 5’-end (FAM) and the unlabeled ITS4 (White et al., 1990).

The size of the fluorescent amplified fragments was quantified using Peak Scanner software (version 1.0, Applied Biosystems, Inc.). Peaks with a size ranging from 390 to 1000 bp were considered in the analyses (Ranjard et al., 2001) and according to Taggart et al. (2011), peak sizes obtained were rounded to the nearest base pair. To avoid possible background noise, only peaks with a signal above 1% of the sum of all peak areas were included in the analyses (Li et al., 2007). Peaks that differed in size by more than 2.0 bp were each considered as separate fungal OTU (Barto et al., 2011).

Within the datasets: “Composition_Fungal_OTUs_Beech_Abundance_sites”, “Composition_Fungal_OTUs_Oak_Abundance_sites”, and “Composition_Total_Fungal_OTUs_Abundance_sites” the column headings ex. “OTU_459” or “OTU_461” represent the peak sizes of fungal OTUs. So, each column represents a different fungal operational taxonomic unit (OTU), a potential proxy for fungal species richness.

For description of landscape, forest site, and branch characteristics, see the second excel sheet in the excel data file of "saproxylic_insect_species_taxonomic_composition".

For more details see Materials and Methods section in the article with the same title.