Computational protocol: Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems

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Protocol publication

[…] Microbial numbers (gene copies/mL water) were log-transformed [log10(x + 1)], with L. pneumophila numbers below detection treated as zero. T tests and correlation analyses were performed in JMP Pro 12 (Cary, NC, USA). 16S rRNA gene sequences were analyzed in mothur (1.36.0). Sequences with an average similarity ≥ 97% were assigned an operational taxonomic unit (OTU). Each sample was rarefied to 12,430 sequences for comparison. Alpha and beta diversities were determined as mean values of 1000 random rarefactions. Bray-Curtis similarity matrix and jclass matrix were applied to analysis of similarity (ANOSIM) in mothur, non-metric multi-dimensional scaling (NMDS) in Primer-E 6.0 (Plymouth, UK), and Adonis in R. Adonis analysis served to quantify the relative influences of temperature, pipe material, and dosed AOC level in shaping the hot water microbiota composition. “Persistent” OTUs were defined as being detected at all temperatures for any AOC level after rarifying to 12,430 sequences/sample. “Enriched” OTUs were those OTUs firstly identified by an indicator in mothur and then selected either having an indicator value > 80 or a relative abundance > 1%. […]

Pipeline specifications

Software tools JMP Pro, mothur
Application Miscellaneous
Organisms Legionella pneumophila, Bacteria
Chemicals Carbon, Copper, Polyethylene