Supplementary Figure 1. Workflow for Sequence Handling and Analyses

Supplementary materials

Supplementary figure 1. Workflow for sequence handling and analyses.

Supplementary figure 2. Heatmap of operational taxonomic units represented by at least ten reads after resampling by daisychopper to the smallest sample size and standardization by z-score which shows how many standard deviations an observations is above or below the mean. Taxonomic affiliations of the OTUs are given based on both the Freshwater (Newton et al., 2011) and the rdp taxonomic framework.

Supplementary figure 3. Relative abundance of bacterial phyla for each sampling occasion and in the total dataset. Abundances are based on annotations against Silva 102 and the rdp taxonomic framework.

Supplementary figure 4. Dynamics of chlorophyll-a, total nitrogen (TN) and nitrogen species over an annual cycle in Lake Erken. Amm = ammonium, PN = particulate nitrogen.

Supplementary figure 5. Circular network showing all significant interactions in the LSA (p<0.01, q<0.05). Nodes are sorted by the number of interactions with other nodes. Red rectangles represent freshwater bacterial tribes with abbreviation according to Newton et al. (2011). Blue hexagons represent environmental variables. Black lines indicate positive correlations, red lines indicate negative correlations, dashed lines indicate a time shift in the correlations. Abbreviations for the environmental variables are translated as following: BA bacterial abundance, chla chlorophyll-a, Cond conductivity, LOI loss of ignition, PN particulate nitrogen , PP particulate phosphorus, secchi secchi depth, Si silicate concentration, SM suspended matter, SRP soluble reactive phosphorus, Temp temperature, TN total nitrogen, TP total phosphorus, Turb turbidity and WC water color.

Supplementary table 1. Method references for water chemistry analyses according to SS-ISO standard methods at the certified water chemistry laboratory at the Lake Erken Limnological Field Station.

Supplementary table 2. Molecular barcode specific for each sample and the environmental metadata in MIMARKS format.

Supplementary table 3. Taxonomy table containing the taxonomic outline with the number of sequences in each group and per sample. A freshwater taxonomic framework was used (Newton et al., 2011).

Supplementary table 4. Taxonomy table containing the taxonomic outline with the number of sequences in each group and per sample. The rdp taxonomic framework was used.

Supplementary table 5. Results from local similarity analysis (Ruan et al. 2006). Interactions are described according type; pu = positive without lag; pdl = positive with delay of target; pdr = positive with delay of source; nu = negative without delay; ndl = negative with delay of target; ndr = negative with delay of source.