Background

Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management.

Method

In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method.

Results

We found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.