Additional file 1: Supplementary Table S1. Detailed profiles of the lakes sampled in the present study. Data were collected from Okazaki et al. [38] and Okazaki et al. [73]. † Sampling date and depths in 2010 are shown in parentheses.

Additional file 1: Supplementary Table S1. Detailed profiles of the lakes sampled in the present study. Data were collected from Okazaki et al. [38] and Okazaki et al. [73]. † Sampling date and depths in 2010 are shown in parentheses.

Additional file 4: Supplementary Dataset. Summarized dataset related to amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). The Excel file consists of two worksheets. In the first sheet (named “by_ASV”), each row represents an individual ASV. The columns indicate the corresponding SSU-ASV and OTU IDs, the taxonomy assigned to the OTU, and read abundance in each sample. The nucleotide sequences of the ASVs are shown in the last column. In the second sheet (named “by_OTU”), each row represents an individual OTU. The columns indicate the taxonomy, classification based on freshwater bacterioplankton nomenclature (see Methods for details), the number of SSU-ASVs and ASVs assigned to the OTU, the number of samples in which the OTU was detected, and read abundances in total and in each sample. OTUs are sorted based on the total read number. Representative 16S rRNA gene sequences of the OTUs are shown in the last column. In each sheet, the total number of the reads assigned to each sample is shown in the first row. Abbreviations for sample names follow those in Fig. 5.

Additional file 4: Supplementary Dataset. Summarized dataset related to amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). The Excel file consists of two worksheets. In the first sheet (named “by_ASV”), each row represents an individual ASV. The columns indicate the corresponding SSU-ASV and OTU IDs, the taxonomy assigned to the OTU, and read abundance in each sample. The nucleotide sequences of the ASVs are shown in the last column. In the second sheet (named “by_OTU”), each row represents an individual OTU. The columns indicate the taxonomy, classification based on freshwater bacterioplankton nomenclature (see Methods for details), the number of SSU-ASVs and ASVs assigned to the OTU, the number of samples in which the OTU was detected, and read abundances in total and in each sample. OTUs are sorted based on the total read number. Representative 16S rRNA gene sequences of the OTUs are shown in the last column. In each sheet, the total number of the reads assigned to each sample is shown in the first row. Abbreviations for sample names follow those in Fig. 5.