Computational protocol: Seasonal Transition of Active Bacterial and Archaeal Communities in Relation to Water Management in Paddy Soils

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Protocol publication

[…] Chimeric sequences from these 16S rRNA clone libraries were detected using the Mallard program with a 99.9% cutoff () and removed from the libraries. The resulting sequences were processed for taxonomic assignment at the family and higher levels using RDP Classifier program ver. 2.2 () with an 80% confidence threshold. Archaeal or bacterial nucleotide sequences from the five clone libraries were aligned using ClustalW2 (), and community similarity among the libraries was examined using the Fast UniFrac web interface (). Rarefaction curves, Chao1 and ACE richness indices, and Shannon and Simpson’s diversity indices were calculated using Mothur program ver. 1.14.0 (). Sequences from each library were also clustered into OTUs with 3% differences using the Mothur program. OTUs specific to each library and shared OTUs between two libraries were identified using the template match method with a similarity index of <0.10 as a cutoff value (, ) using R software ver. 2.10.1. ( Phylogenetic tree was constructed using the neighbor-joining method with bootstrap test (1,000 replicates) using MEGA ver. 4.0.2 (). […]

Pipeline specifications

Software tools RDP Classifier, Clustal W, Fast Unifrac, mothur, MEGA
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Oryza sativa
Chemicals Ammonia, Hydrogen