DOI: 10.5281/zenodo.17094627
title: Synergistic pathogenicity between Herpesvirus and Vibrio aestuarianus in killing juvenile oysters during spring in natural conditions

description: READ ME

This repositery contains all dataset that allow to reproduce this study (16S rRNA sequences in .fastq format, the R script and the informative file related with the samples regarding the oysters (samp_data.txt) or regarding the environmental parameters (env_data_full.txt). It also contains Additional material to complete the related manuscript.

1) The file "samp_data.txt" 

This file contains the informations regarding the samples. The description of the variables follows:



SampleID: The identifiant of the sample (host)

Name: The name of the samples

Compartment: The sample type (here, Oyster)

Zone: The sampling zone (here, Table)

Date: Sampling date (format, DD/MM/YYYY)

Season: Sampling season (this study has been made in France)

Status: Health status of the oyster (i.e., Alive or Moribund)

Temperature:  SST during sampling near tables (degree °C)

Mortality_count: number of dead oyster counted during the sampling on the probe rope

Cumulated_mortality: cumulated count of dead oyster counted during the sampling on the probe rope

Mortality_percent: Dead oyster/Alive oyster * 100

Log_conc_aestu: Measured concentration of Vibrio aestuarianus (qPCR) in oyster samples (log transformed)

Log_conc_herpes: Measured concentration of the herpes virus OsHV-1 (qPCR) in oyster samples (log transformed)


 

2) The file "mortality_survey.txt" 

This file contains the informations regarding the mortality survey including the environmal parameters. The description of the variables follows:



Date: Sampling date (DD/MM/YYYY)

Rope: Type of rope (control or sampled)

Mortality: dead oysters counted

Mortality_ratio: dead oysters counter/alive oysters

SST: Sea Surface Temperature measured (in °C)

Salinity: seawater salinity measured

O2_mean: mean average of the measured dioxygen (5 measures)

Chla_mean: mean average of the measured chlorophyll a (5 measures)

Chlb_mean: mean average of the measured chlorophyll b (5 measures)

Chlc_mean: mean average of the measured chlorophyll c (5 measures)

Bact_mean: mean average of bacterial counts (cytometry)

Virus_mean: mean average of viral particuled counted (cytometry)

PON_mean: mean average of Particulate Organic Nitrogen (5 measures)

POC_mean: mean average of Particulate Organic Carbon (5 measures)

SiOH4_mean: mean average of orthosilisic acid (5 measures)

NO2_mean: mean average of nitrites (5 measures)

NO3_mean: mean average of nitrates (5 measures)

NH4_mean: mean average of nitrogen (5 measures)

PO4_mean: mean average of phosphate (5 measures)


3) The file "env_data_full.txt" 

This file contains the informations regarding the environmental parameters and the host samples. The description of the variables follows:



Ref: Sampling reference

ID: Sample identification

Zone: The sampling zone

Origin: type of samples (Oyster_hatchling, Dead_hatchling, sediment, water)

Date: Sampling date DD/MM/YYYY

Season: sampling season

Temperature: Sea surface temperature measured (°c)

Salinity

Juvenile_mortality

O2: measured dioxygen in seawater

Chla: measured chlorophyll a in seawater (cytometry)

Chlb: measured chlorophyll b in seawater (cytometry)

Chlc: measured chlorophyll c in seawater (cytometry)

Bact_tot: measured bacterial particules in seawater (cytometry)

Nano_tot: measured nanoeukarya in seawater (cytometry)

Pico_tot: measured picoeukarya in seawater (cytometry)

Cyano_tot: measured cyanobacteria in seawater (cytometry)

NO2: measured nitrites in seawater or sediment

SiOH4: measured orthosilisic acid in seawater or sediment

NO3: measured nitrates in seawater or sediment

PO4: measured phosphorus in seawater or sediment

NH4: measured nitrogen in seawater or sediment

Virus: virus counts in seawater

MOP: particulate organic material measured in sediment

PON: particulate organic nitrogen measured in seawater

POC: particulate organic carbon measured in seawater


3) The file "Microlag-script.R" 

This script allows to perform all the analyses that were made for this study. It was made on R version 4.4..

3) The RData objects

We publish the R object (phyloseq object) that allows to perform all statistical analyses from the initial object "physeq_all.RData". It avoids to perform all bioinformatical steps to process the sequences.

4) The file "R1R2.tar"

This folder zip contains all sequence at fastq format. These sequences are from the V3-V4 of the 16S rRNA genes sequenced by Illumina MiSeq 2x250 bp.
description: Young oysters of Pacific oyster Magallana (Crassostrea) gigas are regularly impacted by summer mortalities since 2008, caused by the infection by the Ostreid herpesvirus 1 (OsHV-1) when seawater temperature increases in summer. Adult oysters rather suffer from a vibriosis caused by the bacterial primary pathogen Vibrio aestuarianus francensis. Although these diseases are now well described, little is known about their contribution and possible synergy in natural mortality events of juvenile oysters. Using an in-situ approach conducted in the Thau lagoon, we investigated the potential implication of Vibrio aestuarianus in the juvenile oyster’s mortality, as well as the virus OsHV-1, throughout a large sampling period from winter to late summer, after the mortality event. We further determined their respective effects on the microbial abundance and diversity on alive and moribund oysters. We demonstrated that microbiomes are dynamic throughout seasons and tend to become more similar in spring with a dominance of Mycoplasmataceae in alive oysters. Surprisingly, our data highlighted the prevalence and high loads of Vibrio aestuarianus in all moribund oysters. In contrast with the literature, we found that the microbial communities of moribund juvenile oysters were significantly influenced by both Vibrio aestuarianus and the virus OsHV-1. The moribund bacterial indicators were detected in abundance during mortalities in the surrounding environment of oyster farms and further (700m far). These results highlight the connectivity between the different compartments of the lagoon and raise questions about the potential spread of the primary pathogen Vibrio aestuarianus from adult to juvenile oysters in farming areas located in lagoons.