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.