Computational protocol: Cyanobacteria in lakes on Yungui Plateau, China are assembled via niche processes driven by water physicochemical property, lake morphology and watershed land-use

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Protocol publication

[…] Pyrosequencing flowgrams were converted to sequence reads by using MOTHUR 1.15.0. Trimmed sequences were produced by removing low quality sequences (quality scores <25, sequences lengths <200bp) and ambiguous reads (ambiguous base >0) using QIIME v. 1.3.0. Then, sequences were denoised using DeNoiser (v0.851) and screened for chimeras using UCHIME. All Archaea, Eukaryota, chloroplasts, mitochondria and unknown sequences were removed. The filtered sequences were then clustered into operational taxonomic units (OTUs) at a 3% dissimilarity level using the average neighbor method. Finally, taxonomy was assigned against the SILVA database using k-mer searching method by MOTHUR. [...] Chao1 richness estimator, Shannon-Wiener diversity index (H’) and Pielou evenness index (J) were calculated by MOTHUR 1.15.0. The ‘niche breadth’ approach was used to identify specialization level of cyanobacteria, in which B-value was calculated by where Bj indicates niche breadth and Pij is the relative abundance of OTU j present in a given habitat i. Principal coordinate analysis (PCoA) was conducted by using CANOCO for Windows Version 5.0 to demonstrate the dissimilarity of OTU0.03 compositions among different lakes. Pearson correlation analysis was carried out by SPSS version 17. Trophic status index was calculated using five variables - Chl-a (mg/m3), TN (mg/L), TP (mg/L), CODmn (mg/L) and SD (m) according to China National Environmental Monitoring Center (2001) and Jin (1990). Trophic status index = ∑Wj·TLIj, where Wj is the weight of the variable j, TLIj is the value of the variable j; (rij-the Pearson correlation between Chl-a and the variable j, m- the number of variables)(). Effects of selected environmental variables were summarized using (partial) canonical correspondence analysis (CCA) by CANOCO for Windows Version 5.0. The contributions of water physicochemical property (P), lake morpholoy (M) and watershed land-use (L) to cyanobacteria variation was evaluated using variance partitioning analysis (VPA) by CANOCO for Windows Version 4.5 (Plant Research International, Wageningen, The Netherlands). The significance test was carried out by Monte Carlo permutation (999 times). The neutral community model (NCM) proposed by Sloan et al. was employed to quantify the importance of neutral drivers in community assembly of cyanobacteria. Model description was detailed in Liao et al.. […]

Pipeline specifications

Software tools mothur, QIIME, UCHIME, SPSS
Applications Miscellaneous, 16S rRNA-seq analysis
Organisms Hemisus marmoratus
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Oxygen