Vibrio tapetis is the causative agent of the Brown Ring Disease (BRD) on the Manila Clam, Ruditapes philippinarum, which lead to a significant decrease of the Manila clam production in Northwestern Europe. While the pathogen leads to higher BRD at 14°C, at 21°C clam immunity seems stimulated. Research on Manila clam microbiota is relatively recent and most of them have focused on the digestive gland microbiota, but none has ever compared several tissues under a microbial challenge. The objective of this study was to improve our understanding of the interactions between Manila clam microbiota, a clam pathogen and environmental factors.

In a nested-design lab experiment, we studied the potential effect of V. tapetis, temperature increase and antibiotics (ATB) on clam health and microbiota diversity. Microbiota from three tissues (digestive glands DG, extrapallial fluids EPF, and hemolymph HLPH) were analyzed over a two-month period.

During the experiment, the proportion of ill clams remained relatively low. The three tissues exhibited specific microbiota: both fluids exhibited relatively similar microbiota (dominated by α and γ-Proteobacteria, Flavobacteriales and Spirochaetales), but were very different from the DG (largely dominated by Mycoplasmatales followed by α-Proteobacteria). Despite high variability between individuals, significant impacts on β-diversity were highlighted for all the tested parameters. At 14°C, V. tapetis exposures were associated with an increase in Crocinitomicaceae, which did not persist at 21°C. Therefore, the temperature might partially mitigated some V. tapetis effects. However, temperature increase was also a structuring factor including by increasing Nitrospinales in fluids. ATB exposure modified clam microbiota and made clams more sensitive to both the V. tapetis challenge and the temperature increase.

Our results suggest that pathogens and environmental parameters can modify microbiota without influencing clam health.