Sequences of zooplankton and associated microbes
Mesozooplankton and their associated microbial communities play key roles in pelagic ecosystem processes, yet their responses across steep environmental gradients remain poorly understood in tropical systems. Plankton metabarcoding studies are scarce in the central Mexican Pacific, and no previous work has examined zooplankton, bacteria, and fungi together across connected coastal habitats. Here, we used multikingdom, multimarker metabarcoding cytochrome oxidase subunit I and 18S ribosomal RNA for zooplankton, internal transcribed spacer for fungi and 16S ribosomal RNA for bacteria to characterize mesozooplankton and associated microbial operational taxonomic richness along a lagoon coast offshore transect. Zooplankton exhibited clear functional zonation: meroplankton OTU richness, particularly fish and decapod larvae, peaked in the lagoon; holoplankton OTU richness, driven largely by copepods, was highest at the coastal station; and euphausiid richness was greatest offshore. Microbial responses showed both overlaps and divergences relative to zooplankton functional groups. Several particle-associated bacterial phyla showed localized increases in OTU richness in the lagoon, but these groups remained low in overall richness. In contrast, the phyla with the highest OTU richness were those consistently detected across all habitats, forming a recurrent zooplankton-associated core microbiome. Fungal OTU richness peaked offshore and was dominated by Ascomycota, Basidiomycota, and Chytridiomycota. Together, these patterns reveal contrasting spatial responses of zooplankton and associated microbial communities to connected coastal environments, demonstrating the utility of integrative metabarcoding for resolving multikingdom richness structure in tropical coastal ecosystems and establishing a baseline reference point for detecting future ecological shifts.