In New-Caledonia, Penaeus stylirostris is farmed in semi-intensive mode and is one of the main economic inputs for the territory. However, for the last decades, this sector has been facing huge larval mortalities occurring at all larval stages in hatcheries, for which no causes have yet been found. Dysbiosis of the microbiota of the rearing water and/or of the larvae are suggested as factors leading to larval death. Indeed, aquacultured animals are reared in water hosting various microorganisms with which they are constantly in close relationships. Microbial exchanges between the animal and the water can occur but little is known about the interactions between the shrimp larvae and their environment, especially in shrimp hatcheries Thus, detecting stage specific biomarkers of healthy and unhealthy larvae for later developing monitoring tool of the rearing might be useful to help the farmers.
To highlight specific microbial lineages and biomarkers associated with the larvae, we have studied the daily microbial compositions of the larvae reared in different conditions along with the storage waters. Illumina sequencing of the V4 region of the 16S rRNA gene coupled to zootechnical parameters and statistical analysis allowed us to link microbial lineages and biomarkers to a given larval stage and mortality rate.
Our results underline that the active microbiota associated with the larvae was highly dynamic with 3 main clusters corresponding to the different larval stages: 1) eggs and nauplii, 2) zoea and 3) mysis; irrespective of the survival rate. Deeper analysis exhibited that various active lineages were specifically associated with a given larval stage and survival rate; while several of them were shared between various conditions (Figure 1). When these taxa were compared to the storage waters microbiota, many of them were previously detected in the natural seawater; emphasizing the great role of the natural seawater on the larval microbiota. The biomarker exploration allowed to identify microbial genera that were specific of healthy or unhealthy larvae; biomarkers that might be used as monitoring tool to survey the larval health and to predict the fate of future rearing.