Microbial dynamics in coral reef waters: Diel cycles in contrasting seasons

Coral reefs are dynamic ecological hotspots, yet their influence on surrounding microbial plankton remains poorly studied. High-frequency diel sampling of Red Sea reef waters during mesotrophic winter and oligotrophic summer conditions revealed distinct prokaryotic and microeukaryotic communities compared to nonreef waters, along with previously undescribed diel cycles. Sequencing of 16S and 18S ribosomal RNA gene amplicons showed enrichment in sequences affiliated with copiotrophs, specialized hydrocarbon degraders, parasites, and mutualistic symbionts. Symbiodiniaceae sequence reads consistently peaked at midday. Cell counts by flow cytometry revealed that reef water contained 20 to 60% fewer bacteria and up to 75% fewer microalgae than adjacent open seawaters. In winter, cell drawdown was often more pronounced at dusk, while summer cell density showed no consistent diel pattern. Heterotrophic protist densities increased up to 80% in reef water at night, suggesting predation as a regulatory force on microbial populations. Our findings show that the reef not only reshapes microbial communities but also imposes a pronounced diel structure on planktonic life.