Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris: possible influence of the rearing water and more

Abstract

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.

The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission

“…Furthermore, the rearing environment is known to be a key factor in the structure of the microbiota associated with fish larvae ( Giatsis et al, 2015 ; Vadstein et al, 2018 ). Contrary to what we had shown previously, in this study, the nauplius samples grouped with the tank water samples and not with the eggs ( Giraud et al, 2021 ). Indeed, when considering the microbial communities associated with the reproductive organs of the breeders, egg samples clustered with the male and the female samples ( Figure 2A ).…”

“…In a previous study that we conducted, we have also suggested that some bacterial strains could be vertically transmitted in the Pacific blue shrimp Litopenaeus stylirostris ( Giraud et al, 2021 ). Indeed, studying the active microbiota associated with the early larval stages (eggs and nauplii) of L. stylirostris as well as with their rearing environment, several bacterial families were specifically associated with the eggs and the nauplii and were not found in the environment leading us to hypothesize that they had been acquired from the breeders.…”

“…These three major bacterial classes had been previously identified in water samples collected from the water reservoirs of the Saint Vincent experimental shrimp hatchery in October and November 2018 and February 2019. However, these reservoir samples also showed high abundances of Acidimicrobiia , Cyanobacteriia , and Planctomycetes ( Giraud et al, 2021 ). Thus, differences in total microbial compositions were observed between the water in the tanks and the water used to fill the tanks.…”

“…Breeders were reared in earthen ponds before transfer to maturation tanks according to the method described in Pham et al (2012) . Tanks in the maturation and in the hatchery were filled with treated natural seawater from the Saint Vincent Bay as described in Giraud et al (2021) . Water from three different hatchery tanks was sampled after addition of ethylenediaminetetraacetic acid (EDTA; Figure 1 ).…”

“…Raw sequences were treated using the DADA2 package under RStudio ( Callahan et al, 2016 ; RStudio Team, 2020 ) as described in Giraud et al (2021) . After the obtention of the ASV table, sequences affiliated to eukaryotas, chloroplasts, and mitochondrias were removed before further analysis.…”