Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'

Wu, Ruonan; McClure, Ryan; Nelson, William; Hofmockel, Kirsten

doi:10.25584/1922085

Title: Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'

Dataset
Other Related Research

Abstract

Soil moisture shifts have largely unknown impacts on soil virus-host interactions. Here, we applied high-throughput chromosomal confirmation capture (Hi-C) metagenomics to link phage with their hosts in soils under wet and dry conditions. Bulk metagenomes and metatranscriptomes were analyzed from the same soil incubations. Host-associated phage diversity and the number of viruses per host increased following soil desiccation. Under wet conditions, the viral enrichment and host abundances were significantly negatively correlated, but the transcriptional activities of the phage were higher. Together, these results suggest that there was a general transition of phage from lytic to lysogenic during drying and that viral infection was higher under dry conditions. Soil desiccation also caused shifts in phage hosts and some of these were central in microbial co-occurrence networks, highlighting the impact of soil phages on microbiome structure. This study provides the first empirical evidence of phage-mediated bacterial dynamics during soil desiccation.

Authors:

;

Battelle Pacific Northwest Labs., Richland, WA (United States); Pacific Northwest National Laboratory
Battelle Pacific Northwest Labs., Richland, WA (United States)

Publication Date:: Wed Jan 25 23:00:00 EST 2023

DOE Contract Number:: AC05-76RL01830

Research Org.:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Subject:: 59 BASIC BIOLOGICAL SCIENCES

OSTI Identifier:: 1922085

DOI:: https://doi.org/10.25584/1922085

Citation Formats


                    Wu, Ruonan, McClure, Ryan, Nelson, William, and Hofmockel, Kirsten. Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'.  United States: N. p., 2023. 
        Web.  doi:10.25584/1922085.

Copy to clipboard


                    Wu, Ruonan, McClure, Ryan, Nelson, William, & Hofmockel, Kirsten. Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'.  United States.  doi:https://doi.org/10.25584/1922085

Copy to clipboard


                    Wu, Ruonan, McClure, Ryan, Nelson, William, and Hofmockel, Kirsten. 2023.  
"Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'".  United States.  doi:https://doi.org/10.25584/1922085.  https://www.osti.gov/servlets/purl/1922085. Pub date:Wed Jan 25 23:00:00 EST 2023

Copy to clipboard


                    
@article{osti_1922085,

  title        = {Datasets used in manuscript, 'High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions'},

  author       = {Wu, Ruonan and McClure, Ryan and Nelson, William and Hofmockel, Kirsten},

  abstractNote = {Soil moisture shifts have largely unknown impacts on soil virus-host interactions. Here, we applied high-throughput chromosomal confirmation capture (Hi-C) metagenomics to link phage with their hosts in soils under wet and dry conditions. Bulk metagenomes and metatranscriptomes were analyzed from the same soil incubations. Host-associated phage diversity and the number of viruses per host increased following soil desiccation. Under wet conditions, the viral enrichment and host abundances were significantly negatively correlated, but the transcriptional activities of the phage were higher. Together, these results suggest that there was a general transition of phage from lytic to lysogenic during drying and that viral infection was higher under dry conditions. Soil desiccation also caused shifts in phage hosts and some of these were central in microbial co-occurrence networks, highlighting the impact of soil phages on microbiome structure. This study provides the first empirical evidence of phage-mediated bacterial dynamics during soil desiccation.},

  doi          = {10.25584/1922085},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Jan 25 23:00:00 EST 2023},

  month        = {Wed Jan 25 23:00:00 EST 2023}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.25584/1922085

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

Hi-C metagenome sequencing reveals soil phage–host interactions

Journal Article Wu, Ruonan ; Davison, Michelle R. ; Nelson, William C. ; ... - Nature Communications

Abstract Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates moremore »« less
Hi-C metagenome sequencing reveals soil phage–host interactions

Journal Article Wu, Ruonan ; Davison, Michelle R. ; Nelson, William C. ; ... - Nature Communications

Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lyticmore »« less
Hi-C Viral Host Links

Dataset Wu, Ruonan ; McClure, Ryan ; Nelson, William ; ...

Hi-C Viral Host Links: virus-host associations indicated by Hi-C sequencing were processed by Phase Genomics by folowing the protocal, https://www.biorxiv.org/content/10.1101/2021.06.14.448389v1.full
HiC manuscript: bulk metagenomic data_MG_raw Upload

Dataset Wu, Ruonan ; McClure, Ryan ; Nelson, William ; ...

The raw bulk metagenomic data were trimmed and de-novo assembled. The assemblies were screened for viral contigs (by virsorter2, Deepvirfinder, VIBRANT, checkV) and binned to generate MAGs that were further refined by Hi-C read links.
Dataset for the Danczak et al., 2025 manuscript about bacterial-fungal interactions

Dataset Danczak, Robert E. ; Bell, Sheryl L. ; Warburton, Evan J. ; ...

We generated genome-resolved multiomics data from a series of metagenomic and metatranscriptomic sequencing. Specifically, we acquired, functionally annotated, and taxonomically classified both bacterial and eukaryotic metagenome assembled genomes (MAGs). For bacterial MAGs, we assembled eukaryotic float metagenomic sequencing data from JGI using MEGAHIT, binned and refined MAGs using MetaWRAP and dRep, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy using GTDB-tk. For eukaryotic MAGs, we first identified potentially eukaryotic contigs from a coassembly of eukaryotic float metagenomic sequencing data from JGI using EukRep and Whokaryote, binned MAGs using MetaBAT2, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy usingmore »« less

Similar Records