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INTRODUCTION
Zooplankton play important ecological roles in pelagic marine
ecosystems, transferring energy and elements to higher trophic levels,
such as fishes, cetaceans, and others, through classical and microbial
food webs (Azam et al., 1983; Miller and Wheeler, 2012). Zooplankton
comprise hundreds of species spanning major animal phyla, and they can
be divided into two groups based on their life cycles. Holoplankton are
planktic organisms throughout the entire lifecycle. In contrast,
meroplankton develop through planktic larval stages and subsequently
metamorphose into nektonic or benthic organisms. Due to their small
sizes and the difficulty of unambiguously identifying the larvae with
traditional morphological tools, monitoring the diversity and
distribution dynamics of zooplankton through space and time have
remained a substantial challenge (Lenz, 2012).
The ratio between the regional diversity (gamma diversity) and the local
diversity (alpha diversity) describes the effective number of
communities in a region (beta diversity). These local communities are
assembled by four processes that have a direct impact on all diversity
levels: ecological drift, selection, dispersal, and speciation (Velland,
2016). Zooplankton are drifting organisms and are as such expected to
have a higher dispersal ability, making communities homogeneous. In
contrast, empirical evidence demonstrates that zooplankton are not
merely simple passive drifting particles (e.g., Mackas et al., 1985).
Instead, they may actively translocate over long distances through
active swimming, ultimately resulting in higher movement potential or
even aggregation. These characteristics are linked to a higher number of
effective communities in a region and entail elevated beta diversities.
Generally, a negative relationship between dispersal and beta diversity
is commonly observed in various communities (Grainger and Gilbert, 2016;
Catono et al., 2017). However, the role of size, one of the most
fundamental life-history traits of an organism (Brown, 2004), remains
unexplored in zooplankton communities.
Metabarcoding, the analyses of single or multiple gene sequences of
PCR-amplified community samples, have been popular for studying
zooplankton diversities and compositions (e.g., Machida et al., 2009;
Lindeque et al., 2013). However, two significant concerns have been
raised regarding this approach. Firstly, PCR amplification bias is
expected to underestimate assessment of taxon abundance through
primer/template mismatches (Machida et al., 2009; Krehenwinkel et al.,
2017) or alternatively fail to detect taxa at all (Lopez et al., 2022a).
Secondly, using genomic DNA severely increases the chances of
contaminating downstream analyses with nuclear mitochondrial pseudogenes
(NUMTs) (Machida et al., 2009; 2021; Schultz and Hebert, 2021). These
NUMTs have been reported in many animal phyla (Bensasson et al., 2001;
Hazkani-Covo et al., 2010), and if amplified and sequenced, species
diversity assessments might be spuriously inflated (Song et al. 2008;
Machida et al., 2021; Machida and Lin, 2017; Schultz and Hebert, 2021).
Metatranscriptomics, which relies on shotgun sequencing of mRNA/total
RNA templates from community samples, has recently been introduced to
study zooplankton diversities and compositions (Lenz et al., 2020; Lopez
et al., 2022a; 2022b; Machida et al., 2021). This approach has the
advantage of avoiding issues associated with PCR bias and pseudogene
contamination, as (i) PCR amplification of target genes is not required
for the analyses and (ii) the majority of pseudogenes are not
transcribed and processed to functional mature RNAs (Pink and Carter,
2013).
Coral reefs form some of the Earth’s most diverse ecosystems (Knowlton
et al., 2010). A large portion of the primary production in these
ecosystems are derived from photosynthetic algae symbionts. In contrast,
the pelagic system (water column) is supported by classical and
microbial food webs of drifting organisms, a role largely overlooked in
classical ecology surveys (Nakajima et al., 2008; 2009; 2014).
Zooplankton play a key role in energy and nutrient transfer to higher
trophic levels by creating a link between small producers and large
consumers (Nakajima et al., 2017).
In the present study, we use metatranscriptomics to
investigate the spatial and temporal dynamics of zooplankton diversity
over a tropical coral reef ecosystem. We observed a clear pattern of
change in the degree of species compositional homogeneity through the
different size fractions, with higher/lower homogeneity in
smaller/larger zooplankton compositions. These observations indicate
that sizes may mediate shifts in the role of dispersal in the
zooplankton community assembly process.