Synergistic pathogenicity between Herpesvirus and Vibrio aestuarianus in killing juvenile oysters during spring in natural conditions

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.