DOI: 10.5061/dryad.jwstqjqns
title: Diverse ectomycorrhizal fungi communities found in urban reserve soils and scats of small mammals when compared to native forest

description: Ectomycorrhizal fungi (EMF) play an essential role in forest health. In
 urban reserves, there is a complex interplay between environmental
 factors, including anthropogenic stressors that influence the composition
 and structure of EMF communities, which in turn may affect their plant
 hosts and the presence of small mammals as dispersers. We aimed to assess
 the response of EMF to urbanisation by comparing the diversity and
 composition of their communities in small mammal scats and soil samples
 from urban reserves to those in native forest sites through ITS1
 barcoding. Additionally, we analysed the effect of seasonality and the
 identity of small mammal vectors on EMF diversity present in scat samples.
 The datasets linked to our analyses include csv files with the identified
 EMF species and their abundance in samples of small mammal scats and soil.
 We found that EMF diversity was strongly influenced by the sample type
 (soil vs. scats). In soil samples, EMF communities in urban reserves were
 as diverse as in forest sites, with similar richness and Shannon’s
 diversity index (H’); however, their composition differed. In scat
 samples, we found no differences in EMF richness, H’, or composition
 between site types. Seasonality did not affect EMF diversity in soil
 samples, while in scat samples, EMF diversity was higher in autumn,
 characterised by higher agaricoid EMF richness compared to scats collected
 in spring. Hypogeous gasteroid EMF richness was higher in scat samples
 collected in spring than in autumn. The lack of seasonal patterns we
 observed in our soil samples may reflect abrupt changes in rainfall in our
 study area. We found that scats of Antechinus stuartii had higher EMF
 diversity compared to those of Rattus fuscipes. This finding is surprising
 as A. stuartii is primarily insectivorous. We conclude that urban reserves
 serve as important refuges for EMF and that the small mammal vectors
 within these reserves may disperse a significantly diverse pool of EMF.
description: # Diverse ectomycorrhizal fungi communities found in urban reserve soils
 and scats of small mammals when compared to native forest Dataset DOI:
 [10.5061/dryad.jwstqjqns](10.5061/dryad.jwstqjqns) ## Description of the
 data and file structure The files are in csv format and contain modified
 pre-curated and curated datasets used for the analyses. Soil and small
 mammal scat samples were collected in five forest sites and five urban
 reserves. The natural forest sites were located in Ku-ring-gai Chase
 National Park (KNP), whereas the five urban reserve sites were located
 around the boundary of KNP. For small mammal scat collection we sampled
 each pair of sites (forest and urban reserve) simultaneously for three
 consecutive nights. At each site, we installed 50 Elliot traps (33 cm x 8
 cm x 9 cm) in a sampling grid spaced at 10 m intervals. We sampled the
 sites during both spring (September 2023) and autumn (April 2024) due to
 their contrasting rainfall patterns. Fresh scats were collected in 1.5 ml
 Eppendorf tubes from inside the Elliot traps when captures of small
 mammals occurred. In addition to the scat samples, we also collected three
 soil samples from each site in spring and two soil samples from each site
 in autumn. Soil samples were collected using a sterilised 5 cm diameter
 PVC tube to extract two soil cores from approximately 30 cm of the base of
 the trunk of Eucalyptus *trees, each tree separated by at least 20 m from
 the next one. At each site, we sampled soils around 25* Eucalyptus trees
 per site in total. We combined the cores collected from five Eucalyptus
 trees (i.e., ten soil cores) into one sample, and a final sample was
 collected in a 1.5 ml Eppendorf tube. We collected a total of 50 soil
 samples. We extracted DNA from both the scat and soil samples after each
 sampling season using the DNeasy PowerSoil Pro kit from Qiagen® and
 following the manufacturer’s protocol. The DNA samples were submitted to
 AGRF ([https://www.agrf.org.au/](https://www.agrf.org.au/)) for library
 preparation and amplicon sequencing. The amplicons were generated using
 the fungal-specific primers ITS1F (CTTGGTCATTTAGAGGAAGTAA) and ITS2R
 (GCTGCGTTCTTCATCGATGC). The sequenced samples were processed with the
 DADA2 Pipeline in R. The taxonomic classification of the ASVs was
 performed using the UNITE database for fungi version 10.0 (Abarenkov et
 al., 2024). ### Files and variables #### File: 20241123_sample_depth.csv
 **Description:** Data on sample depth of soil and scat samples collected
 in forest and urban reserves.  ##### Variables * ID: Consecutive
 identifier number * sample: Sample ID * depth: Sequence reading depth *
 site_type: forest vs urban reserves * site: site identifier * sample_type:
 scat or soil #### File: 20241123_allasv_mat.csv **Description:** Matrix of
 all the ASV (Amplicon Sequent Variants) ##### Variables * ASV_ID: ASV
 identifier * K-1-1 to U-5-E2: Sample identifiers #### File:
 20241123_allasv_taxmat.csv **Description:** Taxonomy matrix for all the
 ASV (Amplicon Sequent Variants) ##### Variables * ASV_ID: Consecutive
 identifier number * Kingdom: Taxonomy * Phyllum: Taxonomy *
 Class: Taxonomy * Order: Taxonomy * Family: Taxonomy * Genus: Taxonomy *
 Species: Taxonomy * Taxonomy: Species * boot.Genus: confidence for genus
 clasification * boot.Species: confidence for species clasification ####
 File: 20241123_allasv_40r_biom.csv **Description:** BIOM file of taxonomy
 and samples. ##### Variables * Kingdom: Taxonomy * Phyllum: Taxonomy *
 Class: Taxonomy * Order: Taxonomy * Family: Taxonomy * Genus: Taxonomy *
 Species: Taxonomy * Taxonomy: Species * boot.Genus.80: confidence for
 genus clasification * boot.Species.80: confidence for genus clasification
 * K.1.1 to U.5.E2: Sample identifiers. Row numbers represent the number of
 reads per species. #### File: 20241123_sp_mat_40r.csv
 **Description:** Matrix of ASV/species rarefied to 40,000 sequence depth
 per sample.  ##### Variables * ASV_mock: ASV identifier * K.1.1 to U.5.E2
 the row numbers represent the number of reads per ASV. #### File:
 20241123_sample_depth_40r.csv **Description:** Sample depth of
 ASV rarefied to 40,000 sequence depth per sample. ##### Variables * ID:
 Consecutive row number * sample: Sample ID * depth: Sequencing depth *
 site_type: Forest vs urban reserve * site: Site identifier * sample_type:
 Soil or scat #### File: 20241123_sp_taxmat_40r.csv
 **Description:** Taxonomy matrix for rarefied to 40,000 sequence depth per
 sample ##### Variables * ASV_mock: Consecutive ASV number * Kingdom:
 Taxonomy * Phyllum: Taxonomy * Class: Taxonomy * Order: Taxonomy *
 Family: Taxonomy * Genus: Taxonomy * Species: Taxonomy * Taxonomy: Species
 * boot.Genus.80: Confidence clasification * boot.Species.80: Confidence
 clasification * reads.50: Number of reads per species #### File:
 20250628_sp80_40r_hellinger.csv **Description:** Selection of mycorrhizal
 fungi species with a bootstrap confidence of at least 80%. ##### Variables
 * sp_ID: Species number ID * Kingdom: Taxonomy * Phyllum: Taxonomy *
 Class: Taxonomy * Order: Taxonomy * Family: Taxonomy * Genus: Taxonomy *
 Species: Taxonomy * Taxonomy: Species taxonomy * boot.Genus.80:
 Clasification confidence * boot.Species.80: Clasification confidence *
 reads.50: Number of reads per species * K.1.1 to U.5.E2: Sample
 identifiers. Row values represent the number of reads per ectomycorrhizal
 fungi species. #### File: 20250628_emf_sm_soil_hellinger.csv
 **Description:** Fully curated dataset of ectomycorrhizal fungi found on
 each small mammal scat and soil sample.  ##### Variables * site: Site
 identifier * sample.ID: Sample ID * date: Sample collection date * season:
 Season of collection (autumn vs spring) * season.sample: combination of
 season and sample type * sex: small mammal sex * vector.genus: small
 mammal genus * vector: small mammal species * sample.type: sample type
 (soil vs scat) * site.type: site type (forest vs urban reserve) *
 site.sample: combination between site type and sample type *
 Amanita.fuscosquamosa to Xerocomus.squamulosus: Ectomycorrhizal fungi
 species. Row values represent Hellinger transformed sequence reads per
 sample. #### File: 20241124_emf_urb_scat.csv **Description:** Sequence
 data for scats collected in urban reserves. ##### Variables * ID: Species
 ID * U.3.2 to U.5.4: Sample identifiers. Row numbers represent Hellinger
 transformed sequence reads per sample. #### File:
 20241124_emf_urb_soil.csv **Description:** Sequence data for soil
 collected in urban reserves. ##### Variables * ID: Species ID * U.2.E1 to
 U.3.C: Sample identifiers. Row numbers represent Hellinger transformed
 sequence reads per sample. #### File: 20241124_emf_kur_soil.csv
 **Description:** Sequence read data for soil collected in Ku-ring-gai
 Chase National Park. ##### Variables * ID: Species ID * K.5.C to
 K.3.B: Sample identifiers. Row numbers represent Hellinger transformed
 sequence reads per sample. #### File: 20241124_emf_kur_scat.csv
 **Description:** Sequence read data for scat collected in Ku-ring-gai
 Chase National Park. ##### Variables * ID: Species ID * K.3.18 to
 K.1.22: Sample identifiers. Row numbers represent Hellinger transformed
 sequence reads per species. #### File:
 20241123_emf_sm_soil_hellinger_nozeros.csv **Description:** Variation of
 the main dataset without overall 0 values. ##### Variables * site: Site
 identifier * sample.ID: Sample identifier * date: Sample collection date *
 season: Season of collection * trap.id: ID of the trap of capture * sex:
 Small mammal sex * host.genus: small mammal genus * host.species: small
 mammal species * sample.type: sample type (soil vs scat) * site.type: site
 type (fores vs urban reserve) * site.sample: combination between site type
 and sample type * nmds_id: nmds identifier * Amanita.fuscosquamosa to
 Xerocomus.squamulosus: Ectomycorrhizal fungi species. Row numbers
 represent Hellinger transformed sequence reads per sample. #### File:
 20241125_emf_scat_nozeros.csv **Description:** Variation of the main
 dataset for scats without overall 0 values. ##### Variables * site: Site
 identifier * sample.ID: Sample identifier * date: Sample collection date *
 season: Season of sample collection * trap.id: ID of the trap of capture *
 sex: Small mammal sex * host.genus: Small mammal genus *
 host.species: Small mammal species * sample.type: sample type (soil vs
 scat) * site.type: site type (fores vs urban reserve) *
 site.sample: combination between site type and sample type *
 Austroboletus.asper to Xerocomus.squamulosus: Ectomycorrhizal fungi
 species. Row numbers represent Hellinger transformed sequence reads per
 sample. #### File: 20241129_agaricoids_scat_soil_hellinger.csv
 **Description:** Filtered data for agaricoid ectomycorrhizal fungi
 species. ##### Variables * site: Site identifier * sample.ID: Sample
 identifier * date: Sample collection date * season: Season of sample
 collection * season.sample: combination between season and sample type *
 sex: Small mammal sex * vector.genus: Small mammal genus * vector: Small
 mammal species * sample.type: sample type (soil vs scat) * site.type: site
 type (fores vs urban reserve) * site.sample: combination between site type
 and sample type * Amanita.fuscosquamosa to
 Xerocomus.squamulosus: Ectomycorrhizal fungi species. Row numbers
 represent Hellinger transformed sequence reads per sample. #### File:
 20241129_agaricoids_scat_nozeros.csv **Description:** Filtered data for
 agaricoid ectomycorrhizal fungi species without 0 values overall #####
 Variables * site: Site identifier * sample.ID: Sample identifier *
 date: Sample collection date * season: Season of sample collection *
 season.sample: combination between season and sample type * sex: Small
 mammal sex * vector.genus: Small mammal genus * vector: Small mammal
 species * sample.type: sample type (soil vs scat) * site.type: site type
 (fores vs urban reserve) * site.sample: combination between site type and
 sample type * Austroboletus.asper to
 Xerocomus.squamulosus: Ectomycorrhizal fungi species. Row numbers
 represent Hellinger transformed sequence reads per sample. #### File:
 20241129_hypogeous_scat_soil_hellinger.csv **Description:** Filtered data
 for hypogeous ectomycorrhizal fungi species ##### Variables * site: Site
 identifier * sample.ID: Sample identifier * date: Sample collection date *
 season: Season of sample collection * season.sample: combination between
 season and sample type * sex: Small mammal sex * vector.genus: Small
 mammal genus * vector: Small mammal species * sample.type: sample type
 (soil vs scat) * site.type: site type (fores vs urban reserve) *
 site.sample: combination between site type and sample type *
 Amylascus.herbertianus to Thaxterogaster.nebulobrunneus: Ectomycorrhizal
 fungi species. Row numbers represent Hellinger transformed sequence reads
 per sample. #### File: 20241129_hypogeous_scat_hellinger_nozeros.csv
 **Description:** Filtered data for hypogeous ectomycorrhizal fungi species
 without 0 overall. ##### Variables * site: Site identifier *
 sample.ID: Sample identifier * date: Sample collection date *
 season: Season of sample collection * season.sample: combination between
 season and sample type * sex: Small mammal sex * vector.genus: Small
 mammal genus * vector: Small mammal species * sample.type: sample type
 (soil vs scat) * site.type: site type (fores vs urban reserve) *
 site.sample: combination between site type and sample type *
 Austrogautieria.costata to Thaxterogaster.nebulobrunneus: Ectomycorrhizal
 fungi species. Row numbers represent Hellinger transformed sequence reads
 per sample. #### File: 20241125_emf_astuartii.csv **Description:** Data
 filtered for *Antechinus stuartii* scat samples. ##### Variables * ID:
 Ecotmycorrhizal fungi species * K.3.11 to U.4.1: Sample ID. Row values
 represent number of reads per ectomycorrhizal fungi taxa per sample. ####
 File: 20241125_emf_rfuscipes.csv **Description:** Data filtered for Rattus
 fuscipes scat samples.  ##### Variables * ID: Ecotmycorrhizal fungi
 species * K.3.18 to U.5.1: Sample ID. Row values represent number of reads
 per ectomycorrhizal fungi taxa per sample. #### File:
 20241125_emf_astu-rfus_nozeros.csv **Description:** Data filtered for
 Antechinus stuartii and Rattus fuscipes scat samples without overall 0
 values. ##### Variables * site: Site identifier * sample.ID: Sample
 identifier * date: Sample collection date * season: Season collection date
 * trap.id: Trap of capture identifier * sex: Small mammal sex *
 vector.genus: Small mammal genus * vector: Small mammal species *
 sample.type: sample type (soil vs scat) * site.type: site type (fores vs
 urban reserve) * site.sample: combination between site type and sample
 type * Austroboletus.asper to Xerocomus.squamulosus: Sample ID. Row values
 represent number of reads per ectomycorrhizal fungi taxa per sample. ##
 Code/software The code used in our analyses was developed by Margarita
 Gil-Fernandez, and can be found in the attached files under the name
 of 20250429_fungi_ASV_AUS_V2.R  The code was developed using R version
 4.4.1, in RStudio 2025.05.1+513 "Mariposa Orchid" Release
 (ab7c1bc795c7dcff8f26215b832a3649a19fc16c, 2025-06-01) for windows
 Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like
 Gecko) RStudio/2025.05.1+513 Chrome/132.0.6834.210 Electron/34.5.1
 Safari/537.36, Quarto 1.6.42 ## Access information Other publicly
 accessible locations of the data: * 
 
 Data was derived from the following sources: *