1 | 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.