DOI: 10.5061/dryad.4qrfj6qrg
title: Rhythms of lysis: viral regulation of prokaryotic turnover across diel cycles

description: 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.
description: # Rhythms of lysis: viral regulation of prokaryotic turnover across diel
 cycles Dataset DOI:
 [10.5061/dryad.4qrfj6qrg](https://doi.org/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 rDNA~cell~,
 rRNA~cell~ and rRNA~ext~ 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-0H` indicates 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 rDNA~cell~, rRNA~cell~ and rRNA~ext~ 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.