Description
Forests and woodlands in the Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi, which facilitate plant growth by increasing nutrient and water uptake. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in two vegetation types dominated by ECM host tree species. Sequencing of the entire ITS region and much of the LSU region allows us to infer a phylogeny for all detected soil fungal species. This data resource contain amplicon sequence variants (ASVs) generated from the dataset using the procedure established in Kalsoom-Khan et al. (2020) after accessing general read quality and ensuring that the majority of reads fell within the expected length (1-2 kb). In brief, raw sequence reads were filtered and trimmed, and PacBio-type chimeras were detected and removed using the tool cutadapt. Amplicons sequenced in reverse were reverse complemented. Reads were filtered using DADA2, discarding sequences with more than 3 expected errors as well as those with a length outside the range of 1200–1800 bases. Filtered sequences were then denoised using DADA2, with complete pooling and an increased alignment band size of 32. Singleton ASVs are not included in DADA2 denoising output. De novo chimera detection and removal were also performed in DADA2, with a minimum parent overabundance of 3.5 and allowing detection of chimeras with a single base difference from their parent sequence. This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/).
Data Records
The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 6,144 records.
2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.
This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
Rosling A, Furneaux B, Meidl P (2024). Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. Version 1.6. Biology Section, Uppsala University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=ps155_westafrica_asv&v=1.6
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is Biology Section, Uppsala University. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: 26d7ac29-8e7e-4449-985b-2f12b6ec282f. Biology Section, Uppsala University publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Sweden.
Keywords
Occurrence; Observation
Contacts
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https://orcid.org/0000-0002-7003-5941
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Geographic Coverage
A total of seven locations with nine sites were sampled: Kota Waterfall (KOTA-G and KOTA-W) in Benin, Kou Forest Reserve (KOUF-G) and Niangoloko Forest Reserve (NIAN-W) in Burkina Faso, Farako Forest Reserve (FA01-W and FA15-W) in Mali, Bissandougou Forest Reserve (BISS-W) and Moussaya Forest Reserve (MOUS-W) in Guinea and Kouadianikro Forest Reserve (KDNK-W) in Ivory Coast.
| Bounding Coordinates | South West [7.624, -10], North East [11.24, 2.725] |
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Taxonomic Coverage
N/A
| Kingdom | Fungi |
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| Phylum | Mortierellomycota, Entorrhizomycota, Mucoromycota, Glomeromycota, Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota |
| Class | Geminibasidiomycetes, Rhizophydiomycetes, Paraglomeromycetes, Tremellomycetes, Atractiellomycetes, Mortierellomycetes, Microbotryomycetes, Glomeromycetes, Pezizomycotina_cls_Incertae_sedis, Dothideomycetes, Eurotiomycetes, Lecanoromycetes, Umbelopsidomycetes, Sordariomycetes, Saccharomycetes, Lobulomycetes, Geoglossomycetes, Mucoromycotina_cls_Incertae_sedis, Mucoromycetes, Rhizophlyctidomycetes, Archaeorhizomycetes, Agaricomycetes, Cystobasidiomycetes, Rozellomycotina_cls_Incertae_sedis, Pezizomycetes, Leotiomycetes, Orbiliomycetes |
| Order | Gigasporales, GS23, Agaricomycetes_ord_Incertae_sedis, Auriculariales, Mucoromycotina_ord_Incertae_sedis, Leotiomycetes_ord_Incertae_sedis, Sordariales, Rhizophlyctidales, Orbiliales, Onygenales, Microascales, Jahnulales, Cystofilobasidiales, Sebacinales, Geminibasidiales, Corticiales, Geoglossales, Acrospermales, Mortierellales, Helotiales, Mucorales, Agaricales, GS11, Trechisporales, Geastrales, Pleosporales, Umbelopsidales, Pezizales, Glomerales, Polyporales, Sporidiobolales, Mycosphaerellales, Eurotiales, Capnodiales, Eurotiomycetes_ord_Incertae_sedis, Hymenochaetales, Xylariales, Lecanorales, Russulales, Atractiellales, Hypocreales, Botryosphaeriales, Tremellales, Chaetothyriales, Venturiales, Peltigerales, Muyocopronales, GS36, Mytilinidales, Tubeufiales, Magnaporthales, Thelephorales, Rhizophydiales, Lobulomycetales, Saccharomycetales, Boletales, Sakaguchiales, Archaeorhizomycetales, Paraglomerales, Cantharellales, Cystobasidiales, Dothideales, Diaporthales |
Temporal Coverage
| Start Date / End Date | 2018-06-22 / 2018-07-11 |
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Project Data
No Description available
| Title | Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa |
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| Funding | National Geographic Society as part of exploration grant #CP-126R-17 Bioinformatic analysis was possible thanks to the National Bioinformatics Infrastructure Sweden (NBIS) and enabled by resources provided by the Swedish Na- tional Infrastructure for Computing (SNIC), partially funded by the Swedish Research Council through grant agreement no. 2018-05973. |
| Study Area Description | Field collections were carried out during June and July of 2018 in five West African countries: Benin, Burkina Faso, Mali, Guinea and Ivory Coast. A total of seven locations with nine sites were sampled: Kota Waterfall (KOTA-G and KOTA-W) in Benin, Kou Forest Reserve (KOUF-G) and Niangoloko Forest Reserve (NIAN-W) in Burkina Faso, Farako Forest Reserve (FA01-W and FA15-W) in Mali, Bissandougou Forest Reserve (BISS-W) and Mous- saya Forest Reserve (MOUS-W) in Guinea and Kouadianikro Forest Reserve (KDNK- W) in Ivory Coast |
| Design Description | Sites were selected op- portunistically from natural areas where ECM host trees were present, with relatively uniform vegetation and slope. |
Sampling Methods
Two soil samples were collected roughly one meter on either side of each selected tree, using a small sterilized spade to collect the top 5 cm of soil, after which the two samples were pooled and homogenized. A sub-sample of around 250 mg of soil was placed in a separate 2.0 ml tube containing 750 ml of field lysis and preservation buffer (Zymo Research Xpedition) and homogenized in the field using a portable bead beater, and was used for DNA extraction (Zymo Research Soil/Fecal DNA mini-prep). Approximately 1500 bp of the rDNA from soil DNA extracts was amplified using the primer set ITS1 and LR5. Both primers were indexed for multiplexing to allow pooling of the samples during sequencing. The pooled library was sent for sequencing at Uppsala Genome Center (Sweden) using two cells on a Sequel system (Pacific Biosciences, Menlo Park, CA, USA).
| Study Extent | Field collections were carried out during June and July of 2018 in five West African countries: Benin, Burkina Faso, Mali, Guinea and Ivory Coast. Sites were selected opportunistically from natural areas where Ectomycorrhizal (ECM) host trees were present, with relatively uniform vegetation and slope. In each plot, ten trees with Ectomycorrhizal (ECM) symbiosis were chosen in proportion to the relative abundance of ECM tree species in the plot, while ensuring that each species in the plot was represented at least once, and that all sampled trees were at least eight meters apart. |
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Method step description:
- Raw sequence reads were filtered and trimmed, and PacBio-type chimeras were detected and removed using the tool cutadapt. Amplicons sequenced in reverse were reverse complemented. Reads were filtered using DADA2, discarding sequences with more than 3 expected errors as well as those with a length outside the range of 1200–1800 bases. Filtered sequences were then denoised using DADA2, with complete pooling and an increased alignment band size of 32. Singleton ASVs are not included in DADA2 denoising output. De novo chimera detection and removal were also performed in DADA2, with a minimum parent overabundance of 3.5 and allowing detection of chimeras with a single base difference from their parent sequence.; https://doi.org/10.3897/mycokeys.81.66249"
Bibliographic Citations
- https://doi.org/10.3897/mycokeys.81.66249
Additional Metadata
| Alternative Identifiers | 26d7ac29-8e7e-4449-985b-2f12b6ec282f |
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| https://www.gbif.se/ipt/resource?r=ps155_westafrica_asv |