Computational protocol: Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

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Protocol publication

[…] To compare the mean value of water quality parameters, algal cell concentration and algal biomass, statistical analyses were performed using one-way variance (ANOVA) followed by a Tukey HSD post-hoc test using SPSS (version 17.0, SPSS Inc, Chicago, IL, USA). The significance level was set at α = 0.05.The Illumina MiSeq DNA sequences were determined with the Quantitative Insights Into Microbial Ecology (QIIME, version 1.9.1) software []. Water bacterial and fungal community sequence reads were first filtered by the QIIME pipeline []. The quality-trimmer removed reads are shorter than 50  bp []. After quality filtering and chimera removal, the abundance-based coverage estimator (ACE) index, Chao richness estimator (Chao1), Shannon diversity (H') and Simpson diversity (1/D) indices were calculated by the MOTHUR package (version 1.22.2 http://www.mothur.org) using Operational Taxonomic Units (OTUs) grouped at 0.97 level []. Water bacterial and fungal taxonomic assignments were performed using the Ribosomal Database Project (RDP) classifier (RDP Release 11.5, https://rdp.cme.msu.edu/), UNITE database (http://unite.ut.ee), and NCBI Taxonomy Browser [,,]. Heat map profiles were performed using R software (version 3.2.3) [,]. Redundancy analysis (RDA) was conducted to reveal the water quality variables that correlated to changes in the structures of water microbial communities using the CANOCO software (version 4.5, Wageningen, The Netherlands). All data were log (x+1) transformed, and the water quality parameters best revealing the most influential gradients in the water bacterial and fungal community structure were assessed with Monte Carlo permutation test (p < 0.05) [,]. […]

Pipeline specifications

Software tools QIIME, mothur, RDP Classifier
Application 16S rRNA-seq analysis
Organisms Bacteria, Fungi, Synechococcus sp.
Chemicals Carbon, Nitrogen, Phosphorus