Sequence data processing
The DADA2 pipeline was implemented to process the sequences (Callahan et al ., 2016). Primers were trimmed, and reads were truncated where the quality score fell below Q30. The quality-filtered forward and reverse reads were merged, and an amplicon sequence variant (ASV) abundance table was generated. Taxonomy was assigned to each exact ASV using the naive Bayesian classifier (Wang et al ., 2007) against the PR2database v4.14.0 (Guillouet al ., 2013). The sequences were rarefied to a uniform sequencing depth of 14,936 reads and two samples that did not meet the rarefaction depth were excluded.
ASV abundance was converted to relative abundance, and ASVs were filtered according to taxonomy to remove those unidentified at the phylum level. Heterotrophic groups that were outside of the scope of the microscopy-based monitoring record were excluded from analysis. Chlorophytes, dinoflagellates, ochrophytes and bacillariophytes were well-represented in both the microscopy and 18S rRNA sedDNA records and were therefore included for in-depth analysis.