Computational protocol: Comparison of soil bacterial communities in a natural hardwood forest and coniferous plantations in perhumid subtropical low mountains

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Protocol publication

[…] We compared our data with that four soil bacterial communities from a hardwood forest in Huoshaoliao (with climate similar to Wulai but with higher disturbance), hardwood and Calocedrus forests in Lienhuachi (with less precipitation (2,200 mm) than in Wulai) and a Chamaecyparis forest in Yuanyang Lake forest (with perhumid (precipitation >4,000 mm) and cooler (mean annual temperature 12°C) conditions, as compared with Wulai) described previously (Table ) (Lin et al. [, , ]). The soils in Huoshaoliao and Lienhuach were classified as Dystrudept (U.S. Soil Taxonomy) (Lin et al. [, ]), same as soils in Wulai; while soils in Yuanyang Lake forest were Dystrochrept (Lin et al. []). The soils in Yuanyang Lake forest were more acidic (pH 3.5) (Lin et al. []), and pH value in Huoshaoliao and Lienhuach is 4.5 and 3.9-4.0, respectively (Lin et al. [, ]). Diversity estimates, including ACE, Chao1 estimator, Shannon diversity index, and rarefaction curve were calculated for operational taxonomic units (OTUs) with evolutionary distance (D) of 0.03 (or about 97% 16S rRNA gene sequence similarity) using the DOTUR software package (Schloss and Handelsman []). To analyze the distribution of abundant taxa within libraries, groups were constructed by use of DOTUR at a distance of ≤0.03. The taxonomic affiliation of the most abundant OTUs was screened by use of BLAST program in the NCBI Genbank database. These groups were then analyzed by use of the Fisher exact test (Agresti []). UniFrac (Lozupone et al. []) was used to compare the clone libraries on the basis of the phylogenetic information. The UniFrac Significance test option with 100 permutations was used to determine significant differences between each pair of samples on the basis of phylogenetic information. Jackknife Environment Clusters was used with the weighted algorithm (which considers relative abundance of OTUs) and the normalization step. Relationships between phylogenetic distances of bacterial communities and soil properties were assessed by Mantel tests as implemented in PRIMER v6 (Clarke and Gorley []). […]

Pipeline specifications

Software tools DOTUR, UniFrac
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Calocedrus formosana, Cryptomeria japonica