Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa

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

1. 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"

N/A

1. Gigasporales
   rank: order
2. Mortierellomycota
   rank: phylum
3. GS23
   rank: order
4. Agaricomycetes_ord_Incertae_sedis
   rank: order
5. Geminibasidiomycetes
   rank: class
6. Entorrhizomycota
   rank: phylum
7. Rhizophydiomycetes
   rank: class
8. Paraglomeromycetes
   rank: class
9. Auriculariales
   rank: order
10. Mucoromycotina_ord_Incertae_sedis
    rank: order
11. Leotiomycetes_ord_Incertae_sedis
    rank: order
12. Sordariales
    rank: order
13. Rhizophlyctidales
    rank: order
14. Tremellomycetes
    rank: class
15. Orbiliales
    rank: order
16. Fungi
    rank: kingdom
17. Onygenales
    rank: order
18. Atractiellomycetes
    rank: class
19. Mucoromycota
    rank: phylum
20. Microascales
    rank: order
21. Mortierellomycetes
    rank: class
22. Jahnulales
    rank: order
23. Cystofilobasidiales
    rank: order
24. Sebacinales
    rank: order
25. Geminibasidiales
    rank: order
26. Microbotryomycetes
    rank: class
27. Corticiales
    rank: order
28. Geoglossales
    rank: order
29. Acrospermales
    rank: order
30. Mortierellales
    rank: order
31. Helotiales
    rank: order
32. Glomeromycetes
    rank: class
33. Mucorales
    rank: order
34. Agaricales
    rank: order
35. GS11
    rank: order
36. Pezizomycotina_cls_Incertae_sedis
    rank: class
37. Trechisporales
    rank: order
38. Dothideomycetes
    rank: class
39. Glomeromycota
    rank: phylum
40. Geastrales
    rank: order
41. Pleosporales
    rank: order
42. Umbelopsidales
    rank: order
43. Eurotiomycetes
    rank: class
44. Pezizales
    rank: order
45. Lecanoromycetes
    rank: class
46. Glomerales
    rank: order
47. Polyporales
    rank: order
48. Umbelopsidomycetes
    rank: class
49. Sporidiobolales
    rank: order
50. Mycosphaerellales
    rank: order
51. Eurotiales
    rank: order
52. Capnodiales
    rank: order
53. Sordariomycetes
    rank: class
54. Saccharomycetes
    rank: class
55. Lobulomycetes
    rank: class
56. Ascomycota
    rank: phylum
57. Eurotiomycetes_ord_Incertae_sedis
    rank: order
58. Hymenochaetales
    rank: order
59. Xylariales
    rank: order
60. Geoglossomycetes
    rank: class
61. Mucoromycotina_cls_Incertae_sedis
    rank: class
62. Lecanorales
    rank: order
63. Russulales
    rank: order
64. Mucoromycetes
    rank: class
65. Atractiellales
    rank: order
66. Hypocreales
    rank: order
67. Botryosphaeriales
    rank: order
68. Tremellales
    rank: order
69. Chaetothyriales
    rank: order
70. Venturiales
    rank: order
71. Rhizophlyctidomycetes
    rank: class
72. Archaeorhizomycetes
    rank: class
73. Peltigerales
    rank: order
74. Muyocopronales
    rank: order
75. GS36
    rank: order
76. Agaricomycetes
    rank: class
77. Cystobasidiomycetes
    rank: class
78. Mytilinidales
    rank: order
79. Tubeufiales
    rank: order
80. Rozellomycota
    rank: phylum
81. Magnaporthales
    rank: order
82. Thelephorales
    rank: order
83. Rhizophydiales
    rank: order
84. Basidiomycota
    rank: phylum
85. Rozellomycotina_cls_Incertae_sedis
    rank: class
86. Lobulomycetales
    rank: order
87. Saccharomycetales
    rank: order
88. Boletales
    rank: order
89. Sakaguchiales
    rank: order
90. Archaeorhizomycetales
    rank: order
91. Pezizomycetes
    rank: class
92. Paraglomerales
    rank: order
93. Cantharellales
    rank: order
94. Chytridiomycota
    rank: phylum
95. Cystobasidiales
    rank: order
96. Leotiomycetes
    rank: class
97. Orbiliomycetes
    rank: class
98. Dothideales
    rank: order
99. Diaporthales
    rank: order

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.