Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

The biogeography of eukaryotes in drinking water systems
is poorly
understood relative to that of prokaryotes or viruses, limiting the
understanding of their role and management. A challenge with studying
complex eukaryotic communities is that metagenomic analysis workflows
are currently not as mature as those that focus on prokaryotes or
viruses. In this study, we benchmarked different strategies to recover
eukaryotic sequences and genomes from metagenomic data and applied
the best-performing workflow to explore the factors affecting the
relative abundance and diversity of eukaryotic communities in drinking
water distribution systems (DWDSs). We developed an ensemble approach
exploiting k-mer- and reference-based strategies
to improve eukaryotic sequence identification and identified MetaBAT2
as the best-performing binning approach for their clustering. Applying
this workflow to the DWDS metagenomes showed that eukaryotic sequences
typically constituted small proportions (i.e., <1%) of the overall
metagenomic data with higher relative abundances in surface water-fed
or chlorinated systems with high residuals. The α and β
diversities of eukaryotes were correlated with those of prokaryotic
and viral communities, highlighting the common role of environmental/management
factors. Finally, a co-occurrence analysis highlighted clusters of
eukaryotes whose members’ presence and abundance in DWDSs were
affected by disinfection strategies, climate conditions, and source
water types.