Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa
Citation
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://doi.org/10.15468/vdavsc accessed via GBIF.org on 2024-08-23.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/).Sampling Description
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.Sampling
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).Method steps
- 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"
Taxonomic Coverages
N/A
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Gigasporalesrank: order
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Mortierellomycotarank: phylum
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GS23rank: order
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Agaricomycetes_ord_Incertae_sedisrank: order
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Geminibasidiomycetesrank: class
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Entorrhizomycotarank: phylum
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Rhizophydiomycetesrank: class
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Paraglomeromycetesrank: class
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Auricularialesrank: order
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Mucoromycotina_ord_Incertae_sedisrank: order
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Leotiomycetes_ord_Incertae_sedisrank: order
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Sordarialesrank: order
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Rhizophlyctidalesrank: order
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Tremellomycetesrank: class
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Orbilialesrank: order
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Fungirank: kingdom
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Onygenalesrank: order
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Atractiellomycetesrank: class
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Mucoromycotarank: phylum
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Microascalesrank: order
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Mortierellomycetesrank: class
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Jahnulalesrank: order
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Cystofilobasidialesrank: order
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Sebacinalesrank: order
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Geminibasidialesrank: order
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Microbotryomycetesrank: class
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Corticialesrank: order
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Geoglossalesrank: order
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Acrospermalesrank: order
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Mortierellalesrank: order
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Helotialesrank: order
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Glomeromycetesrank: class
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Mucoralesrank: order
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Agaricalesrank: order
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GS11rank: order
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Pezizomycotina_cls_Incertae_sedisrank: class
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Trechisporalesrank: order
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Dothideomycetesrank: class
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Glomeromycotarank: phylum
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Geastralesrank: order
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Pleosporalesrank: order
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Umbelopsidalesrank: order
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Eurotiomycetesrank: class
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Pezizalesrank: order
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Lecanoromycetesrank: class
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Glomeralesrank: order
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Polyporalesrank: order
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Umbelopsidomycetesrank: class
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Sporidiobolalesrank: order
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Mycosphaerellalesrank: order
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Eurotialesrank: order
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Capnodialesrank: order
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Sordariomycetesrank: class
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Saccharomycetesrank: class
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Lobulomycetesrank: class
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Ascomycotarank: phylum
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Eurotiomycetes_ord_Incertae_sedisrank: order
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Hymenochaetalesrank: order
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Xylarialesrank: order
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Geoglossomycetesrank: class
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Mucoromycotina_cls_Incertae_sedisrank: class
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Lecanoralesrank: order
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Russulalesrank: order
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Mucoromycetesrank: class
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Atractiellalesrank: order
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Hypocrealesrank: order
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Botryosphaerialesrank: order
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Tremellalesrank: order
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Chaetothyrialesrank: order
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Venturialesrank: order
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Rhizophlyctidomycetesrank: class
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Archaeorhizomycetesrank: class
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Peltigeralesrank: order
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Muyocopronalesrank: order
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GS36rank: order
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Agaricomycetesrank: class
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Cystobasidiomycetesrank: class
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Mytilinidalesrank: order
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Tubeufialesrank: order
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Rozellomycotarank: phylum
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Magnaporthalesrank: order
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Thelephoralesrank: order
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Rhizophydialesrank: order
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Basidiomycotarank: phylum
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Rozellomycotina_cls_Incertae_sedisrank: class
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Lobulomycetalesrank: order
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Saccharomycetalesrank: order
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Boletalesrank: order
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Sakaguchialesrank: order
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Archaeorhizomycetalesrank: order
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Pezizomycetesrank: class
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Paraglomeralesrank: order
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Cantharellalesrank: order
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Chytridiomycotarank: phylum
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Cystobasidialesrank: order
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Leotiomycetesrank: class
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Orbiliomycetesrank: class
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Dothidealesrank: order
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Diaporthalesrank: order
Geographic Coverages
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.
Bibliographic Citations
- https://doi.org/10.3897/mycokeys.81.66249 -
Contacts
Anna Roslingoriginator
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: https://orcid.org/0000-0002-7003-5941
Brendan Furneaux
originator
position: PhD student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: brendan.r.furneaux@jyu.fi
userId: https://orcid.org/0000-0003-3522-7363
Peter Meidl
originator
position: Master student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: pmeidl@outlook.com
Brendan Furneaux
metadata author
position: PhD student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: brendan.r.furneaux@jyu.fi
userId: https://orcid.org/0000-0003-3522-7363
Peter Meidl
metadata author
position: Master student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: pmeidl@outlook.com
Anna Rosling
metadata author
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: https://orcid.org/0000-0002-7003-5941
Kassim I. Tchan
author
position: PhD student
Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, LEB, University of Parakou,
Parakou
BJ
email: kassimtchan@gmail.com
Marie-Laure Guissou
author
position: Professor
Université Norbert Zongo, Unité de Formation et de Recherches en Sciences et technologies.
Koudougou
BP 376
BF
email: guissoulaure@gmail.com
Bakary Soro
author
position: Professor
Université Nangui Abrogoua, URF Sciences de la Nature, Laboratoire d’écologie et de Développement Durable,
Abidjan
CI
email: s.y.bakary.1@gmail.com
Aïssata Traoré
author
position: Professor
Institut d’Economie Rurale (IER)
Rue Mohammed V, Bozola
Bamako,
BP 258
email: aissathe@yahoo.fr
Gbamon Konomou
author
position: Professor
Herbier National de Guinée / Université Gamal Abdel Nasser de Conakry
Conakry,
BP: 1147
GN
Nourou S. Yorou
author
position: Professor
Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, LEB, University of Parakou
Parakou
BJ
email: n.s.yorou@gmail.com
Martin Ryberg
author
position: Associate professor
Department of Organismal Biology, Systematic Biology, Uppsala University
Norbyvägen 18D
Uppsala
752 36
SE
email: martin.ryberg@ebc.uu.se
Kerri Kluting
author
position: PhD student
Department of Ecology and Genetics, Evolutionary Biology, Uppsala University,
Norbyvägen 18D
Uppsala
752 36
SE
email: klutingkl@gmail.com
Anna Rosling
administrative point of contact
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: https://orcid.org/0000-0002-7003-5941