In New Caledonia, the Pacific blue shrimp Penaeus stylirostris, is the main food processing exporter and a key contributor to the territory’s economy. However, since 2005, this sector has faced high larval mortalities across all developmental stages in hatcheries, with the zoea stage being particularly affected. Larval microbial dysbiosis is presumed to be a key factor of these mortalities. Therefore, identifying specific microbial lineages involved in larval dysbiosis at the zoea stage, along with variations in the abundance of the core microbiota, will help to investigate the propagation of dysbiosis and emphasise the bacterial taxa that are most affected.
To highlight the specific active microbial lineages associated with the three zoea larval stages according to health status (as reflected by mortality rates), or those common to all larvae regardless of stage or health status, we studied the daily microbial composition of larvae reared under different conditions, across different seasons and from various hatcheries of the territory. Illumina sequencing of the V4 region of the 16S rRNA gene, combined with zootechnical parameters and statistical analyses, enabled us to link specific microbial lineages to given zoea larval stages and mortality rates.
Our results indicate that three lineages were specific to unhealthy zoea regardless of the sub-stage (Figure 1). Comparison of the active larval microbiota across all sub-stages and health statuses revealed the existence of a core microbiota, with the abundance of its related taxa significantly varying according to health status (Figure 1). The identification of lineages specific of the unhealthy zoea, along with variations of the core microbiota, paves the way for further studies, such as isolating and describing these species or performing genome sequencing to determine their physiological preferences, metabolism and activities, to ultimately validate their ecological functions in the larval mortalities.