Fig. 1

Overall experimental design for larval microbial exposure and reproduction of C. gigas. Biparental reproduction was performed to generate the family 32 (selected during the ANR decipher project, see [28]). The family 32 was chosen for its intermediate susceptibility to the POMS disease. The F1 generation was generated in March 2016 by full-sibmultiparental reproduction. Just after fertilization, the oyster larvae were exposed to a hatchery environment (filtered and UV-treated control seawater = control seawater, blue color) or to a natural microbe-enriched environment (microorganism-enriched seawater = ME seawater, pink color). The microorganisms used to enrich the seawater came from donor oysters that acquired their microbiota in the field during a POMS-free period (T° < 16 °C, no OsHV-1). The donor oysters were transferred from the field site to the hatchery and placed upstream of the breeding pipes (3 replicates per condition) in order to transmit their microbiota to recipient larvae via seawater flux. This exposure started 2 h after F0 gametes fecundation and lasted for 10 days. During exposure, donor oysters were renewed three times. This experimental design aimed at mimicking the microorganism-rich seawater that is met in natural environment. After 10 days, both ME-exposed and control oysters were raised in standard hatchery conditions (filtered and UV-treated hatchery seawater). Additionally, both control and ME-exposed oysters were used to perform multiparental reproduction and generate the F2 generation. The F2 progeny was raised in standard conditions with control seawater. Samples were taken all along the life of the F1 and F2 oysters for molecular biology analyses (see Additional file 1: Table 2) and for a pathogen challenge assay at juvenile stages (survival assay, 120 days after fertilization). Red stars indicate seawater sampling for 16S amplicon sequencing analysis, and blue stars indicate seawater sampling for cultivable bacterial analysis