The impact of anthropogenic disturbance on mycorrhizal fungi and their associations with rodents: insights from a temperate forest in Mexico
Data files
May 31, 2025 version files 1.99 MB
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20240223_all_fungi_97h.csv
1.79 MB
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20240223_amf_97h_scats_disturbed.csv
2.66 KB
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20240223_amf_97h_scats_undisturbed.csv
3.20 KB
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20240223_amf_97h_soil_disturbed.csv
1.16 KB
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20240223_amf_97h_soil_undisturbed.csv
1.25 KB
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20240227_emf_97h_scats_disturbed.csv
10.04 KB
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20240227_emf_97h_scats_undisturbed.csv
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20240227_emf_97h_soil_disturbed.csv
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20240227_emf_97h_soil_undisturbed.csv
4.83 KB
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20240307_amf_rodents_hellinger.csv
25.20 KB
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20240313_emf_rodents_hellinger.csv
69.32 KB
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20240502_amf_genus_reads.csv
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20240502_amf_genus_rodents_MX_V1.csv
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20240502_emf_genus_reads.csv
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20240502_emf_genus_rodents_MX_V1.csv
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README.md
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Abstract
Ecosystem functioning is influenced by biological diversity, ecological interactions, abiotic conditions, and anthropogenic disturbance. This study examines how anthropogenic disturbance (i.e., land use change) affects arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) in soil and rodent scat samples. We collected soil samples and rodent scats at five pairs of sites (i.e., anthropogenically disturbed vs. undisturbed temperate forests), in Michoacan, Mexico. Using DNA barcoding of partial internal transcribed region 1 (ITS) sequences, we identified 112 mycorrhizal fungi species. We found that there was a higher richness of EMF in undisturbed soil samples compared to disturbed soil samples and a higher AMF diversity in rodent scats for disturbed sites. Additionally, scat samples showed a high incidence of both AMF (75%) and EMF (100%) in rodent scats. However, we found significant differences in the diversity of both AMF and EMF depending on the rodent species acting as vectors. We also found a higher diversity of EMF in the wet season in the scat samples. Our study highlights the role of rodents as important vectors of mycorrhizal fungi, particularly for EMF, which could be essential to build up mycorrhizal fungi spore banks in disturbed forests.
https://doi.org/10.5061/dryad.stqjq2cct
Description of the data and file structure
The data consists on sequence readings of DNA extracted from soil and scat samples using the segment of the internal transcribed region, ITS1, which was amplified using the primer set ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-3') and ITS1/2 (5'-TCCTCCGCTTATTGATATGC-3'). Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) on an Illumina MiSeq following the manufacturer’s guidelines. The resulting DNA sequences were processed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA). All zOTUs were taxonomically classified using the Basic Local Alignment Search Tool (BLAST) in the National Center for Biotechnology Information (NCBI) Genbank online repository (www.ncbi.nlm.nih.gov). The species or genera identified with >97% homology were classified by functional guild using the FUNGuild database (Nguyen et al. 2016) and the *FUNGuildR R package(Furneaux and Song 2021; R Core Team 2024). *We used a Hellinger transformation of the count of reads for beta diversity analyses using the *microbiome *R package.
Files and variables
File: 20240307_amf_rodents_hellinger.csv
Description: Metadata associated with each soil or scat sample, as well as hellinger-tranformed readings of DNA sequences per arbuscular mycorrhizal species.
Variables
- ID: Consecutive number per sample
- sample_ID: Sample ID
- site: Site identifier, from U1 to U5 for undisturbed sites, and D1 to D5 for disturbed sites.
- pair: Sampling pair consisting of one disturbed site and one undisturbed site (e.g. U1 and D1 are P1), which were sampled simultaneously for rodent scats and soil samples.
- site_type: Categorical variable for site type; disturbed (forest cover <60%) and undisturbed (forest cover = 100%)
- date: Date of sample collection
- event: Consecutive sampling event
- season: Dry (May 2022) or wet (August 2022) season when the sample was collected
- latitude: site latitude
- longitude: site longitude
- dshrub: shrub density on rodent trapping grid
- dtree: tree density on rodent trapping grid
- pcover: percentage of forest cover on rodent trapping grid
- weight: rodent weight in grams
- body_length: body lenght of rodent in mm
- sex: rodent sex
- host_genus: rodent genus
- species: rodent species
- code_sp: code for rodent species
- habitat_domain: preferred habitat for the rodent species
- site_sample: variables for site type and sample type combined
- rai_rodents: relative abundance of rodent calculated based on the trapping success per site
- sample_type: soil or rodent scat sample from which the DNA was extracted
- Ambispora_leptoticha: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Acaulospora_laevis: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Acaulospora_paulinae: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Acaulospora_spinosa: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Diversispora_aurantia: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Diversispora_eburnea: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Diversispora_versiformis: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Redeckera_fulvum: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Entrophospora_infrequens: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Scutellospora_gilmorei: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Scutellospora_nodosa: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Scutellospora_pellucida: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Scutellospora_reticulata: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Funneliformis_mosseae: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Glomus_dimorphicum: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Glomus_indicum: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Glomus_macrocarpum: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Rhizophagus_clarus: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Rhizophagus_intraradices: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Rhizophagus_irregularis: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
- Paraglomus_brasilianum: Arbuscular mycorrhizal fungi species' values of Hellinger tranformed reads.
File: 20240223_amf_97h_scats_disturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of arbuscular mycorrhizal fungi species per rodent scat sample collected in disturbed sites
Variables
- Taxonomy: arbuscular mycorrhizal fungi species.
- Columns D.1.1 to D.3.13 represent each sample and its values for Hellinger-transformed sequence reads per arbuscular mycorrhizal fungi species (rows).
File: 20240223_amf_97h_scats_undisturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of arbuscular mycorrhizal fungi species per rodent scat sample collected in undisturbed sites.
Variables
- Taxonomy: arbuscular mycorrhizal fungi species.
- Columns C.1.1 to C.4.2 represent each sample and its values for Hellinger-transformed sequence reads per arbuscular mycorrhizal fungi species (rows).
File: 20240223_amf_97h_soil_disturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of arbuscular mycorrhizal fungi species per soil sample collected in disturbed sites.
Variables
- Taxonomy: arbuscular mycorrhizal fungi species.
- Columns D.1.SV to D.3.A.asterisk represent each sample and its values for Hellinger-transformed sequence reads per arbuscular mycorrhizal fungi species (rows).
File: 20240223_all_fungi_97h.csv
Description: Sequence read data of all fungi identified with >97% homology
Variables
- otu_name: Operational taxonomic unit identifier
- Taxonomy.complete: complete taxonomic identity per zOTU
- Taxonomy.ID: taxonomy ID
- Kingdom: Taxonomic identification at the level of Kingdom
- Phyllum: Taxonomic identification at the level of Phyllum
- Class: Taxonomic identification at the level of Class
- Order: Taxonomic identification at the level of Order
- Family: Taxonomic identification at the level of Family
- Genus: Taxonomic identification at the level of Genus
- Taxonomy: Taxonomic identification at the level of species
- Percent Homology: Percentage of homology between the sequence and the National Center for Biotechnology Information (NCBI) Genbank online repository (www.ncbi.nlm.nih.gov).
- evalue: The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. The closer to zero, the better.
- bitscore: Quality of the alignment between a query sequence and a subject sequence in the database.
- Columns C.1.1 to D.3.A represent scat or soil samples, where the rows display the raw values of readings per zOTU.
File: 20240223_amf_97h_soil_undisturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of arbuscular mycorrhizal fungi species per soil sample collected in undisturbed sites.
Variables
- Taxonomy: Species of Arbuscular mycorrhizal fungi
- Columns C.2.SV to C.2.P represent each sample and its values for Hellinger-transformed sequence reads per arbuscular mycorrhizal fungi species (rows).
File: 20240313_emf_rodents_hellinger.csv
Description: Metadata associated with each soil or scat sample, as well as hellinger-tranformed readings of DNA sequences per ectomycorrhizal fungi species.
Variables
- ID: Consecutive number per sample
- sample_ID: Sample ID
- sample_type: soil or rodent scat sample from which the DNA was extracted
- site: Site identifier, from U1 to U5 for undisturbed sites, and D1 to D5 for disturbed sites.
- pair: Sampling pair consisting of one disturbed site and one undisturbed site (e.g. U1 and D1 are P1), which were sampled simultaneously for rodent scats and soil samples.
- site_type: Categorical variable for site type; disturbed (forest cover <60%) and undisturbed (forest cover = 100%)
- date: Date of sample collection
- event: Consecutive sampling event
- season: Dry (May 2022) or wet (August 2022) season when the sample was collected
- latitude: site latitude
- longitude: site longitude
- dshrub: shrub density on rodent trapping grid
- dtree: tree density on rodent trapping grid
- pcover: percentage of forest cover on rodent trapping grid
- x: trap X location within grid
- y: trap Y location within grid
- weight: rodent weight in grams
- body_length: body lenght of rodent in mm
- sex: rodent sex
- host_genus: rodent genus
- species: rodent species
- code_sp: code for rodent species
- habitat_domain: preferred habitat for the rodent species
- site_sample: variables for site type and sample type combined
- rai_rodents: relative abundance of rodent calculated based on the trapping success per site
- Columns Elaphomyces_muricatus to Tomentellopsis_zygodesmoides represent ectomycorrhizal fungi species and their values of Hellinger-tranformed sequence reads (in rows).
File: 20240227_emf_97h_scats_disturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of ectomycorrhizal fungi species per rodent scat sample collected in disturbed sites.
Variables
- Taxonomy: Species of ectomycorrhizal fungi
- Columns D.1.1 to D.3.13 represent rodent scat samples collected in disturbed sites and their Hellinger-transformed values per ectomycorrhizal fungi species.
File: 20240227_emf_97h_scats_undisturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of ectomycorrhizal fungi species per rodent scat sample collected in undisturbed sites.
Variables
- Taxonomy: Species of ectomycorrhizal fungi
- Columns C.1.1 to C.4.2 represent rodent scat samples collected in undisturbed sites and their Hellinger-transformed values per ectomycorrhizal fungi species.
File: 20240227_emf_97h_soil_undisturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of ectomycorrhizal fungi species per soil sample collected in undisturbed sites.
Variables
- Taxonomy: Species of ectomycorrhizal fungi
- Columns C.2.SV to C.2.P represent soil samples collected in undisturbed sites and their Hellinger-transformed values per ectomycorrhizal fungi species.
File: 20240227_emf_97h_soil_disturbed.csv
Description: Values of Hellinger-transformed sequence reads of each species of ectomycorrhizal fungi species per soil sample collected in disturbed sites.
Variables
- Taxonomy: Species of ectomycorrhizal fungi
- Columns D.1.SV to D.3.A represent soil samples collected in disturbed sites and their Hellinger-transformed values per ectomycorrhizal fungi species.
File: 20240502_amf_genus_rodents_MX_V1.csv
Description: Sequence reads of each genus of arbuscular mycorrhizal fungi found in soil and rodent scat samples with metadata of samples.
Variables
- ID: Consecutive number per sample
- sample_ID: Sample ID
- site_pair: Sampling pair consisting of one disturbed site and one undisturbed site (e.g. U1 and D1 are P1), which were sampled simultaneously for rodent scats and soil samples.
- site_type: Categorical variable for site type; disturbed (forest cover <60%) and undisturbed (forest cover = 100%) rodent genus
- host_genus: rodent genus
- sample_type: soil or rodent scat sample from which the DNA was extracted
- Columns Acaulospora to Scutellospora represent each genus of arbuscular mycorrhizal fungi and rows are the values of sequence reads per sample for each genus.
File: 20240502_amf_genus_reads.csv
Description: Sequence reads of each genus of arbuscular mycorrhizal fungi found in soil and rodent scat samples.
Variables
- Genus: Arbuscular mycorrhizal fungi genus
- Columns C-1-1 to D-5-SV represent DNA samples, where rows are the values of sequence reads for each genus of arbuscular mycorrhizal fungi.
File: 20240502_emf_genus_reads.csv
Description: Sequence reads of each genus of ectomycorrhizal fungi found in soil and rodent scat samples.
Variables
- Genus: Ectomycorrhizal fungi genus
- Columns C.1.1 to D.5.SV represent DNA samples, where rows are the values of sequence reads for each genus of ectomycorrhizal fungi.
File: 20240502_emf_genus_rodents_MX_V1.csv
Description: Sequence reads of each genus of ectomycorrhizal fungi found in soil and rodent scat samples with metadata of samples.
Variables
- ID: Consecutive number per sample
- sample_ID: Sample ID
- site_pair: Sampling pair consisting of one disturbed site and one undisturbed site (e.g. U1 and D1 are P1), which were sampled simultaneously for rodent scats and soil samples.
- sample_type: soil or rodent scat sample from which the DNA was extracted
- site_type: Categorical variable for site type; disturbed (forest cover <60%) and undisturbed (forest cover = 100%)
- host_genus: rodent genus
- Columns Alpova to Wilcoxina represent DNA samples, where rows are the values of sequence reads for each genus of ectomycorrhizal fungi.
Code/software
Data was analysed using R for Windows version 4.4.2, and RStudio 2024.12.0+467 "Kousa Dogwood" Release (cf37a3e5488c937207f992226d255be71f5e3f41, 2024-12-11) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2024.12.0+467 Chrome/126.0.6478.234 Electron/31.7.6 Safari/537.36, Quarto 1.5.57. Used packages and the workflow are contained explanatory notes along the attached RScript.
Access information
Other publicly accessible locations of the data:
- None
Data was derived from the following sources:
- Original data
This study was conducted in the municipality of Nuevo San Juan Parangaricutiro, Michoacan, Mexico. We selected ten sites in the area to assess the effects of anthropogenic disturbance (i.e., land use change) on mycorrhizal fungal communities and their associations with their putative rodent dispersers. We followed a paired design, where five of the sites were located under continuous forest cover (undisturbed) and the other five were in small patches that had undergone significant anthropogenic change (disturbed).
Soil samples were collected during the wet season (August 2022). Each sample was composed of ten soil cores collected with a sterilised PVC tube of 5 cm in diameter at a depth of 5 cm. For pine and shrub soil samples we selected five individual plants, spaced at least 20 m from each other, within the rodent trapping grid (see below). We then collected two soil cores at 30 cm to the base of each individual plant. For the bare soil samples, we collected a pair of soil cores along the closest access path, every 20 m until completing ten cores. Each collected sample was mixed in an ethanol-sterilised 2 L container for 2 minutes to homogenise the soil. Afterwards, a subsample of the homogenised soil was taken in a 1.5 mL Eppendorf tube.
Sampling for rodent scats was conducted in the dry (May 2022) and wet (August 2022) seasons. Pairs of disturbed and undisturbed sites were simultaneously sampled for two nights. We set up 50 Sherman traps at each sampling site in a 5 × 10 grid arrangement (spaced at 10 m). We completed a total sampling effort of 1,997 trap nights. We extracted DNA from all samples using the DNeasy PowerSoil Pro Kit (Qiagen®), following the manufacturer's protocol. DNA was dehydrated in a void vacuum to avoid degradation during shipping. The segment of the internal transcribed region, ITS1, was amplified using the primer set ITS1F and ITS1/2. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) on an Illumina MiSeq following the manufacturer’s guidelines. The resulting DNA sequences were processed using the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA). All zOTUs were taxonomically classified using the Basic Local Alignment Search Tool (BLAST) in the National Center for Biotechnology Information (NCBI) Genbank online repository (www.ncbi.nlm.nih.gov). Only the species with a matching score >97% were included in further analyses. All the resulting species were classified by functional guild using the FUNGuild database (Nguyen et al. 2016) and the FUNGuildR R package (Furneaux and Song 2021; R Core Team 2024). We only included EMF and AMF taxa with a confidence ranking of “probable” or “highly probable”.