Rhythms of lysis: viral regulation of prokaryotic turnover across diel cycles
Data files
Jan 19, 2026 version files 4.22 MB
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ASV_metadata.xlsx
4.16 MB
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Dilution_experiment_data-HB.csv
2.56 KB
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Dilution_experiment_data-Synechococcus.csv
2.26 KB
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Environmental_metadata.xlsx
31 KB
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group.txt
1.51 KB
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README.md
6.86 KB
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seven_lysis_group_of_ASV.R
6.04 KB
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WGCNA-diel_ASVs.R
6.99 KB
Abstract
Diel rhythms structure microbial activity in the ocean, yet the role of viral lysis in driving short-term community dynamics remains poorly understood. Here, we combined dilution experiments, high-resolution microbiome sampling, and extracellular ribosome sequencing to investigate diel virus–host interactions in the South China Sea. Viral lysis accounted for an average of 41% of Synechococcus and 24% of heterotrophic bacterial mortality at night. Overall, 74% of amplicon sequence variants (ASVs) showed lysis signals, with many displaying significant diel fluctuations. Notably, rare taxa comprised a large fraction of diel-responsive ASVs, indicating high turnover among low-abundance populations. Synechococcales exhibited tightly coupled nighttime peaks in abundance and lysis, while SAR11 and Flavobacteriales showed delayed lysis after late-day growth. In addition, virus-mediated mortality had a stronger influence on metabolically active and diel-responsive ASVs. These findings highlight viral lysis as a temporally structured and taxon-specific force sustaining microbial turnover and diversity in oligotrophic waters.
Dataset DOI: 10.5061/dryad.4qrfj6qrg
Description of the data and file structure
Environmental_metadata.xlsx provides station, date and time, depth, latitude and longitude, hydrographic variables (temperature, salinity, dissolved oxygen), fluorescence, photosynthetically active radiation (PAR), nutrient concentrations (NO₂⁻, NO₃⁻, PO₄³⁻, SiO₃²⁻), and abundances of heterotrophic bacteria, Synechococcus and Prochlorococcus.Additional worksheets summarize the acrophases (peak times) of diel periodicity in cell abundances for different microbial groups at SEATS and SS1.
ASV_metadata.xlsx contains 16S rRNA amplicon sequence variant (ASV) tables and taxonomy; rows are ASVs and columns are samples for the rDNAcell, rRNAcell and rRNAext fractions.
Dilution experiment data.xlsx reports cell abundances of heterotrophic bacteria and Synechococcus for each dilution treatment and time point (0, 6, 12, 18, 24 h) in the modified dilution experiments at SEATS and SS1.
group.txt lists the sample group assignments (e.g. LOWDAY, LOWNIGHT, HIGHDAY, HIGHNIGHT) used in downstream analyses.
seven lysis group of ASV.R and WGCNA-diel ASVs.R are R scripts that reproduce the seven lysis-group classification, CLI calculations, WGCNA and the associated figures.
Files and variables
File: group.txt
Description: This file provides sample-level grouping information for diel analyses at the SEATS station. Each row corresponds to one sample, and the four binary indicator columns (one-hot encoding) assign the sample to one of four categories defined by sampling time (day vs. night) and water-column layer (upper vs. lower euphotic zone).
Variables
- Sample_ID: Sample identifier encoding station and sampling conditions (e.g.,
SEATS-25M-0Hindicates SEATS station, 25 m depth, 0 h sampling time). - HIGHNIGHT:Indicator (0/1). The sample was collected during daytime in the upper euphotic zone (shallower layer).
- LOWDAY: Indicator (0/1). The sample was collected during nighttime in the upper euphotic zone.
- LOWNIGHT: Indicator (0/1). The sample was collected during nighttime in the upper euphotic zone.
- HIGHDAY: Indicator (0/1). The sample was collected during daytime in the lower euphotic zone (deeper layer).
- HIGHNIGHT: Indicator (0/1). The sample was collected during nighttime in the lower euphotic zone.
File: seven_lysis_group_of_ASV.R
Description: R script used to classify ASVs into seven lysis-related groups based on their presence–absence patterns across three molecular fractions at the same station and time point: cellular DNA (rDNAcell), cellular RNA (rRNAcell), and extracellular RNA (rRNAext).
By comparing whether each ASV is detected in these three fractions, the script infers different ecological and lysis states of ASVs and assigns them to one of seven distinct groups.
File: WGCNA-diel_ASVs.R
Description: R script implementing Weighted Gene Co-expression Network Analysis (WGCNA) on diel ASV abundance and lysis-related indicators. The script constructs co-occurrence modules and evaluates their relationships with environmental variables and diel phases.
File: Environmental_metadata.xlsx
Description: Environmental_metadata.xlsx provides station, date and time, depth, latitude and longitude, hydrographic variables (temperature, salinity, dissolved oxygen), fluorescence, photosynthetically active radiation (PAR), nutrient concentrations (NO₂⁻, NO₃⁻, PO₄³⁻, SiO₃²⁻), and abundances of heterotrophic bacteria, Synechococcus and Prochlorococcus.Additional worksheets summarize the acrophases (peak times) of diel periodicity in cell abundances for different microbial groups at SEATS and SS1.
File: ASV_metadata.xlsx
Description: ASV_metadata.xlsx contains 16S rRNA amplicon sequence variant (ASV) tables and taxonomy; rows are ASVs and columns are samples for the rDNAcell, rRNAcell and rRNAext fractions.
File: Dilution_experiment_data-HB.csv
Description: Cell abundances of heterotrophic bacteria measured during dilution experiments conducted at the SEATS station. Measurements were taken at multiple diel time points to quantify bacterial growth, grazing mortality, and virus-mediated lysis rates.
- 0h: Cell abundance at the start of incubation (cells mL⁻¹).
- 6h: Cell abundance after 6 hours of incubation.
- 12h: Cell abundance after 12 hours of incubation.
- 18h: Cell abundance after 18 hours of incubation.
- 24h: Cell abundance after 24 hours of incubation.
File: Dilution_experiment_data-Synechococcus.csv
Description: Cell abundances of Synechococcus measured during dilution experiments at the SEATS station across diel cycles. These data were used to evaluate top-down controls, including protist grazing and viral lysis, on picocyanobacterial populations.
Variables
- 0h: Cell abundance at the start of incubation (cells mL⁻¹).
- 6h: Cell abundance after 6 hours of incubation.
- 12h: Cell abundance after 12 hours of incubation.
- 18h: Cell abundance after 18 hours of incubation.
- 24h: Cell abundance after 24 hours of incubation.
Code/software
All data files can be viewed and processed using free and open-source software.
The analyses and data processing were primarily conducted using R (version ≥ 4.2.0) on a Linux-based computing environment.
The following R packages were used: tidyverse, vegan, WGCNA, reshape2, ggplot2. All packages are freely available from CRAN or Bioconductor.
The submission includes several R scripts used for data processing, classification, and statistical analysis:
seven_lysis_group_of_ASV.R
Script used to classify ASVs into seven lysis-related groups based on their presence–absence patterns across three molecular fractions at the same station and time point: intracellular DNA (rDNAcell), intracellular RNA (rRNAcell), and extracellular RNA (rRNAext).
WGCNA-diel_ASVs.R
Script implementing Weighted Gene Co-expression Network Analysis (WGCNA) to identify co-occurring ASV modules and to assess their relationships with environmental variables and diel ph
Access information
Other publicly accessible locations of the data:
- Sequencing data from this study are available in the NCBI Sequence Read Archive (SRA) associated the BioProject accession number PRJNA1304870 (SRA accession numbers SRR34967866 to SRR34968069).
Data was derived from the following sources:
- This dataset was generated from original field sampling and laboratory experiments conducted at the SEATS station and was not derived from previously published datasets.