Computational protocol: Edaphic Selection Pressures as Drivers of Contrasting White Spruce Ectomycorrhizal Fungal Community Structure and Diversity in the Canadian Boreal Forest of Abitibi-Témiscamingue Region

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Protocol publication

[…] Phylogenetic analyses were performed using Mega 6.0 software developed by Tamura et al. []. Phylogenetic trees were constructed using maximum parsimony and bootstraping. GenBank taxa that showed the most similar BLASTn results and which had been utilised for ECM fungal identification were included in the first phylogenetic tree. All of our ECM fungal sequences were submitted to the GenBank search engine for public consultation. Genetic distance represented the genetic divergence among species and was calculated for each site. Smaller genetic distances meant that individuals in the same population had more similar genes and were more closely related genetically compared to greater genetic distances.For each of the four sites, ECM fungal species richness was measured by counting the number of species that were found in the community. Shannon and Simpson’s diversity indices were calculated using species relative abundance data following the method used by Wright et al. []. Species relative abundance was established as the number of root tips colonized by each fungal species divided by the total number of root tips that were sampled per site, multiplied by 100. Species relative frequency was calculated for each sampling site by dividing the number of samples in which a species occurred by the total number of samples. Mean percentage of roots that were colonised by ECM fungi (± standard error) was calculated for each site by averaging the percentage of ECM root tips from the 10 tree samples. No data transformation was necessary in order to meet ANOVA assumptions. Significantly different means at P-value ≤ 0.05 were determined based on one-way ANOVA followed by Tukey tests [].All multivariate analyses were executed with PC-ORD 6 (MJM Software Design, Gleneden Beach, OR) []. A PerMANOVA (permutational MANOVA) analysis including pairwise comparisons was performed to determine whether any of the sampling sites differ significantly in terms of their ECM fungal species composition. Additionally, two-way cluster analysis was performed to identify which groups of ECM fungi were abundant in same habitat and which sites had similar species compositions. Species relative abundance data served as the starting point for these analyses. Species with horizontal line above the 75% of information remaining are considered to be significantly in the same ecological group in PC-ORD 6, as recommended by Peck []. In order to recognize similar linear patterns among soil chemical properties (pH, % N, % C, C/N, P, Ca, K, Mg, Fe, Na, Mn, and AlOH) and mycorhization variables across the ecological gradient, principal component analysis (PCA) was subsequently conducted on the four sampling sites in PC-ORD 6, as recommended by Peck []. The significance of differences and linear patterns was set at P ≤ 0.05 for all multivariate analyses. […]

Pipeline specifications

Software tools MEGA, BLASTN
Application Phylogenetics
Organisms Picea glauca
Chemicals Calcium, Magnesium, Potassium, Sodium