DOI: 10.5061/dryad.z8w9ghx9x
title: Anthropogenic disturbance impacts ectomycorrhizal communities and abiotic soil properties: implications for an endemic forest disease

description: In forest ecosystems, habitat fragmentation negatively impacts stand
 structure and biodiversity; the resulting fragmented patches of forest
 have distinct, disturbed edge habitats that experience different
 environmental conditions than the interiors of the fragments. In southwest
 Western Australia, there is a large-scale decline of the keystone tree
 species Corymbia calophylla following fragmentation and land use change.
 These changes have altered stand structure and increased their
 susceptibility to an endemic fungal pathogen, Quambalaria coyrecup, which
 causes chronic canker disease especially along disturbed forest habitats.
 However, the impacts of fragmentation on belowground processes in this
 system are not well understood. We examined the effects of fragmentation
 on abiotic soil properties and ectomycorrhizal (ECM) and arbuscular
 mycorrhizal fungal (AMF) communities, and whether these belowground
 changes were drivers of disease incidence. We collected soil from 17 sites
 across the distribution range of C. calophylla. Soils were collected
 across a gradient from disturbed, diseased areas to undisturbed,
 disease-free areas. We analysed soil nutrients and grew C. calophylla
 plants as a bioassay host. Seedlings were harvested and roots collected
 after six months of growth. DNA was extracted from the roots, amplified
 using fungal specific primers and sequenced using Illumina MiSeq.
 Concentrations of key soil nutrients such as nitrogen, phosphorus and
 potassium were much higher along the disturbed, diseased edges in
 comparison to undisturbed areas. Disturbance altered the community
 composition of ECM and AMF; however, only ECM communities had lower
 rarefied richness and diversity along the disturbed, diseased areas
 compared to undisturbed areas. Accounting for effects of disturbance, ECM
 diversity and leaf litter depth were highly correlated with increased
 disease incidence in C. calophylla. In the face of global change,
 increased virulence of an endemic pathogen has emerged in this
 Mediterranean-type forest.
description: Fifty-one soil samples were collected across seventeen sites in
 southwest Western Australia. Soils were used in a bioassy experiment
 with <em>Corymbia calophylla </em>as the host. Seedlings were
 harvested after six months of growth and the roots were rinsed and soil
 and stripped of fine roots. DNA was extracted from 50mg of fine roots
 using DNeasy PowerPlant Pro kit as per manufacturer's protocol.
 Amplicon library preparation was preformed using the Illumina Demonstrated
 Protocol with exceptions. eDNA was amplified using fungal specific primers
 fITS7 and ITS4 which amplifies the ITS2 region, the universal genetic
 barcode for fungi. Uniquely indexed libraries (265) were pooled for the
 sequencing run preformed on an Illumina MiSeq using 600-cycle V3
 chemistry. Paired-end reads were merged using USEARCH
 v8.0.1623 with a minimum overlap of 50bp with no gaps allowed in the
 merged alignments. Sequence deconvolution was carried out using the
 bioinformatics platform Sequence Clustering and Analysis of Tagged
 Amplicons (SCATA;  scata.mykopat.slu.se), developed and maintained by the
 Swedish University of Agricultural Sciences in Uppsala. Reads with low
 mean quality (&lt;20) and sequences with missing primers were removed.
 Primer sequences were removed and sequences passing quality control were
 then clustered into operational taxonomic units (OTUs). The threshold
 distance for clustering was set at 0.015 (corresponding approximately to
 species level for ITS) and minimum alignment for clusters (i.e., minimum
 length of pairwise alignment in the clustering process required to
 consider a sequence pair for clustering) was 0.85.
description: Sample IDs, OTU table (produced through SCATA) and sample
 information are included in the attached SCATAResults.xlsx.