Fig. 3

Impact of primers, sample types, farms, and production cycles on community patterns derived from 16S sequencing. Multidimensional scaling analysis using the Bray–Curtis distance matrix is visualized with MDS plots at the phylum level. A MiSeq primers. Axes 1 and 2 achieve a clear separation of all samples. Replicates cluster together closely to the point of overlapping, whereas sample types, compartments, and farms form separate clusters. B Earth primers. Earth primers achieve an identical overall pattern but in a distinct area of the morphospace. The mock communities cluster in the exact location independently of primer choice, further stressing the equivalence of primers at this level of analysis. C Farms. Farms separate along axis 2. Panel C visualizes this for MiSeq primers, but the pattern holds with Earth primers (Panel B). D Tank and Time. Both primers can distinguish the biofilm samples collected in farm A from two tanks of different operational times but within the same circuit, emphasizing that a short-read approach is sufficient to achieve fine-scale resolution at the community level