Eukaryote biodiversity in supratidal microbialite pools: A foundational environmental DNA assessment

Coastlines are a mosaic of habitats, including rocky shores, sandy beaches, estuaries, and artificial substrata. Although modern microbialite pool formations were only recently discovered as an additional coastal habitat along the southern African coastline, they are now known to be surprisingly common to this region. These ecosystems function similarly to estuaries, where seawater and freshwater mix, but with groundwater as the freshwater source instead of river flow. Traditional community assessments from morphological identifications have revealed some similarities between the organisms inhabiting microbialite pools to those of nearby estuaries, but no systematic comparison has so far been undertaken. Here, we used molecular methods based on environmental DNA (eDNA) metabarcoding to characterise the eukaryote assemblages within and between three coastal southern African microbialite pools. We hypothesised that the three sites are taxonomically analogous to one another, which would support the existence of similar core ecological communities. Three genetic markers, one for metazoans (COI) and two for algae (rbcL and the V2+V3 regions of 18S rRNA) were targeted for metabarcoding. Our results show that the biodiversity of the pools was dominated by diatoms (particularly of the genera Navicula and Nitzschia ) and, among the metazoans, by malacostracans, rotifers and nematodes. Although the three microbialite pools had similar broadscale community compositions at higher taxonomic levels (class and family), distinct community structure at lower taxonomic levels was observed, which may be a result of numerous opportunistic species being present in addition to the core organisms. The macroinvertebrate fauna of microbialite pools (e.g. peracarid crustaceans, polychaetes and insects) is well documented, although most are still missing from the DNA barcoding reference library. In contrast, the meiofauna (e.g. rotifers, nematodes and ostracods) is understudied. It remains unclear whether the two dominant diatom genera are the primary contributors to microbialite formation, or if other yet-undescribed species also contribute to the process. This study serves as an initial step in uncovering the hidden level of biodiversity within the unique microbialite ecosystems along the southern African coastline. • Biodiversity interpretations can differ when using morphological versus molecular taxonomy. • Eukaryotes are diverse in modern supratidal microbialite ecosystems. • Meiofauna are more important than prior traditional approaches have shown. • Integrated taxonomy and an expansion of local barcoding libraries is needed.