Bacterial Communities Across the Production Chain of a Pacific Oyster (Magallana gigas) Hatchery During a Larval Mortality Event

Bacterial disease is a major constraint on Magallana gigas larval production, yet hatchery microbiology has been characterised almost exclusively through the lens of Vibrio, and rarely across the whole production chain. We tracked bacterial communities throughout an entire larval rearing cycle at a commercial hatchery in northern China. A total of 78 samples were collected from the full production chain, from water intake to larvae. Bacterial communities were characterised using 16S rRNA (V4–V5) amplicon sequencing and culture-based isolation, with larvae sampled from three replicate tanks at six developmental stages. A protracted mortality event began at the D-veliger stage, with cumulative losses of roughly 40% before sinking ceased; ostreid herpesvirus 1 was not detected. The only taxon that rose above its healthy baseline during larval mortality was a single undescribed a single undescribed amplicon sequence variant (ASV) of the family Cryomorphaceae. Its relative abundance increased to a mean of 41% (with a tank-to-tank range of 33.7–51.6%) before disappearing once the mortality event concluded. No described species exceeds 92.2% 16S rRNA gene sequence identity to it, whereas its closest environmental relatives (97–98%) are, without exception, uncultured bacteria associated with marine invertebrates. It was an order of magnitude more abundant in larvae than in the surrounding water. Vibrio rose transiently at the onset of mortality but fell below its healthy-stage abundance while larvae were still dying. Tenacibaculum, by contrast, was the dominant genus of the rearing water yet was never recovered on Vibrio-selective medium and showed no association with mortality. Chlorination of the feed-room supply removed Tenacibaculum while leaving Vibrio uncontrolled. These findings reveal the limitations of the Vibrio-targeted, culture-based paradigm that has long dominated hatchery microbiology, as it overlooks both prevailing water-column organisms and mortality-linked taxa. Our results highlight the need for whole-community, culture-independent surveillance to better understand larval disease.