Diversity and varying predation capacities of culturable Amoebozoae against opportunistic vibrios in contrasting Mediterranean coastal environments

Free-living amoebae (FLA) are ubiquitous and can be found in many environments including soil, freshwater, and marine environments. They feed on various microorganisms and can play an important role in the food web and its dynamics. We previously described that FLA belonging to the <i>Vannella</i> genus isolated from oyster farms in the Thau lagoon in France are able to establish stable interactions with <i>Vibrionaceae,</i> suggesting they can play a role in pathogen dynamics. To further investigate the ecological interactions between FLA and Vibrionaceae in Mediterranean coastal waters, we conducted monthly sampling for 1 year at three contrasting sites. FLA populations were isolated from water and sediment samples on different bacterial lawns, including <i>Escherichia coli</i> or <i>Vibrio tasmaniensis</i>, <i>Vibrio crassostreae</i>, and <i>Vibrio harveyi</i>. Diversity analysis by v4-18S barcoding revealed distinct communities between fractions and sites. The Vannellidae were found significantly enriched in the water, whereas Paramoebidae were found enriched in the sediments. Additionally, uneven distribution of Vexilliferidae, Vermistellae, and, to a lesser extent, Acanthamoebidae and Subulatomonas contrasted between sampling sites. Selection of grazers on different bacterial lawns revealed that <i>V. tasmaniensis</i> inhibits the growth of most Vannellidae, whereas <i>V. crassostreae</i> inhibits the growth of Paramoebidae. These differences were further confirmed functionally using isolates belonging to each Amoebozoa taxonomic group. Overall, our results highlight the need for more comprehensive studies of the diversity and population dynamics of Amoebozoa in marine environments and indicate that the role of these diversified grazers in shaping <i>Vibrio</i> communities is complex and still poorly characterized.IMPORTANCEAlthough they can play an important role in shaping bacterial communities and as intracellular niches for potential pathogens, the diversity and ecology of free-living amoebae (FLA) in marine environments are still poorly characterized. Very few studies have used systematic approaches to unravel the population dynamics and ecological variations of FLA in different environments. Our study in marine coastal environments highlights that FLA taxonomic groups can harbor habitat preferences and have different predation capacities, suggesting that FLA-bacteria interactions need to be considered at different taxonomic levels to uncover generalist versus specialist adaptations.