Sequencing results and overall taxonomic composition of the
zooplankton community
A total of 242 (122 and 120 for 18S rRNA and COI, respectively)
zooplankton community libraries were successfully amplified. Overall,
sequencing produced more than 28.5 million paired-end reads, and 24.4
million sequences (~86% of the total number of reads)
met quality control tests. After library curation, an inflection point
in ASV abundance was observed at 1.2 and 1.3 log value for 18S rRNA and
COI, respectively (Supplementary Information Fig. S1A and S1B).
Moreover, ASVs below these threshold values were generally detected for
only one station and were considered as in vitro local artifacts that
likely rose during amplification and/or sequencing. Therefore, further
analyses were carried out with ASVs with a minimum number of reads,
namely 12 (log value ~1.1) and 21 (log value
~1.3) for 18S rRNA and COI, respectively. The final
datasets included 13,088,619 reads representing 1,247 ASVs for 18S and
8,573,204 reads representing 14,795 ASVs for COI (Supplementary
Information Table S2 and Table S3). The number of reads and ASVs removed
during the quality control tests for both loci are reported in
Supplementary Information Table S4.
According to the asymptotic shape of the rarefaction curves
(Supplementary Information Fig. S3 and Fig. S4) and the closeness
between the detected ASVs to Chao1 (Supplementary Information Fig. S2),
zooplankton communities were exhaustively sampled for both genetic
markers. The minimum number of reads was 20,076 and 57,585 for the COI
and 18S datasets, respectively. Thus, the samples were rarefied to these
read numbers.
Taxonomic classification varied somewhat depending on the molecular
marker. For example, some taxa were exclusively detected with either 18S
rRNA (e.g., Brachyopoda, Bryozoa, Ctenophora, Hemichordata, and
Nemertea) or COI (e.g., Chordata and Rotifera). Moreover, we observed a
discrepancy in the relative abundance of taxa depending on the locus
(e.g., Calanoida and Euphausiacea; Fig. 2A and 2B). Specifically, the
most common orders and their relative abundance based on COI and 18S
rRNA, respectively, were (abundance percentages in parenthesis):
Calanoida (42.5%, 51.1%),
Euphausiacea (17.5%, 19.5%), Aphragmophora (9.3%, 2.3%), Halocyprida
(8.7%, 1%), Siphonophorae (5.9%, 5.1%), Decapoda (2.6%, 2.1%), and
Phyllodocida (0.06%, 1.2%) Oegopsida (2%, 0.1%). Additionally, the
predominant orders detected only with COI were Myctophiformes (2%),
Stomiiformes (1.6%), and Clupeiformes (1.6%), while those detected
only with 18S rRNA included Salpida (1.3%) and Doliolida (1.3%).