DOI: 10.5061/dryad.gf1vhhmnn
title: Saproxylic insects and fungi in deciduous forests along a rural–urban gradient

description: 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.
description: 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.