Aquacultured animals are reared in water hosting various microorganisms with which they are in close interactions as these microorganisms can be involved in the animal development, physiology or health during their whole lifecycle. Consequently, it is important to understand the relationships between the rearing water microbiota and the larval stage and health status; notably in New Caledonia, where the rearing of Penaeus stylirostris is one of the main economic activities. Unfortunately, this activity is strongly impacted by larval mortalities that impair the shrimp production and enhance major economic loss for the farmers and the Territory. This phenomenon, occurring at any larval stage since the past decade, is poorly understood. This study aimed to detect microbial biomarkers in the rearing water, specific of a given larval stage and health, to establish microbial proxies to monitor the rearing ecosystems and ultimately to help microbial management in the hatcheries.
We studied the daily microbial compositions of the water storage as well as those of the rearing water where both healthy larvae with a high survival rate, and unhealthy larvae with a high mortality rate, occurred during the same rearing cycle. We used the sequencing of the V4 region of the 16S rRNA gene coupled to zootechnical parameters and statistical analysis, to explore if any microbial lineages and biomarkers could be linked to a certain larval stage and mortality rate.
We highlighted that the active microbiota of the rearing water was highly dynamic whatever the larval survival rate, with various active lineages associated with a given larval stage and survival rate (Figure 1A). When compared to the microbiota of the storage waters, it appeared that several of these specific lineages were also detected in the natural seawater, highlighting the great role of the seawater microbiota (Figure 1B). The biomarker exploration allowed to spot out several microbial proxies specific of healthy or unhealthy larvae, that could be used as practice tools to test the natural seawater before the rearing and then during the first days of the larval rearing to monitor the larval health. In fine, these biomarkers might be useful to manage the rearing water microbiota and select valuable microorganisms for the larvae.