Sea urchin holobionts: microbiome variation across species, compartments and locations in Paracentrotus lividus and Arbacia lixula

Abstract

Understanding holobiont dynamics is essential for unraveling the complex interactions between marine hosts and their microbiota. Sea urchins play pivotal roles in shaping benthic ecosystems, yet the functional roles of their microbial symbionts remain poorly characterized. Here, we present a comparative microbiome analysis of two sympatric echinoid species, Arbacia lixula and Paracentrotus lividus which occupy contrasting trophic niches. P. lividus is primarily herbivorous, while A. lixula exhibits omnivorous and carnivorous feeding behavior. We characterized microbial communities from coelomic fluid, coelomocytes, and egested fecal pellets, collected from two biogeographic regions, the Northeastern Atlantic Ocean and the Mediterranean Sea. Applying Next-Generation sequencing of the 16S rRNA gene (V3-V4 region) and using the FAPROTAX functional annotation database to infer microbial ecological functions, we found distinct microbial signatures shaped by host species, body compartment, and location. Notably, species-specific differences may reflect dietary preferences, with P. lividus enriched in sulfur-metabolizing and phototrophic bacteria, while A. lixula displayed functional signatures potentially linked to nitrogen cycling and microbial pathogenesis. Fecal microbiota exhibited the highest diversity and functional enrichment in carbohydrate degradation and nutrient cycling. Coelomic compartment hosted microbial assemblages with potential immune host-interaction traits, including intracellular symbiosis or parasitism. Geographic variation further shaped microbiota composition, with stronger location-dependent functional shifts observed in P. lividus. These findings reveal a high degree of spatial and functional differentiation in sea urchin microbiomes, highlighting the plastic nature of sea urchin microbiomes and their potential role in host adaptation to environmental change.