DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

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"DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes" 

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

 

Terabase soil metagenome samples were collected from Washington State University’s Irrigated Agriculture Research and Extension Center (IAREC), Konza Prairie Biological Station (KPBS), and Iowa State University’s Comparison of Biofuel Systems (COBS). Soil samples were collected from the same independent soil site collection tubes as the first Terabase Metagenome release, however were not pooled prior to sequencing as referenced in versions 1.0 for all three sites. The versions described in this paper are the second version (2.0), for which dataset downloads contain raw read sequencing files, assembly files, functional annotations, MIMS.me.soil.5.0 metadata information, and a dataset download “Read Me” file.

 

KEYWORDS: lysogeny, auxiliary metabolic gene, grassland soil, metagenome, soil bacteriophage, soil virus

 

Wu R, Davison MR, Nelson WC, Graham EB, Fansler SJ, Farris Y, Bell SL, Godinez I, Mcdermott JE, Hofmockel KS, Jansson JK. DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. mBio. 2021 Nov 2;12(6):e0259521. 10.1128/mBio.02595-21

 

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The Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project (Soil Microbiome) at Pacific Northwest National Laboratory is a Genomic Sciences Program Science Focus Area (SFA) Project operating under the Environmental Microbiome Science Research Area. The Soil Microbiome SFA...

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Staff Scientist at Pacific Northwest National Laboratory

Michelle Davison is a microbiologist with a love of challenging, creative, and multidisciplinary projects. She is interested in the role phage play in environmental systems, as well as the myriad ways they can be harnessed as tools. She has experience isolating, developing and working with non-model...

Dr. Nelson’s background is in genomic analysis of microbial organisms. He spent 10 years at The Institute for Genomic Research (TIGR), first as a data analyst and then as the team lead for Microbial Annotation. He was involved in some of the earliest bacterial genome sequencing projects, including...

Earth Scientist Emily Graham is an quantitative ecosystem ecologist in the Biological Sciences Group at PNNL and is part of the Ecosystem Science Team. She is co-principal investigator of the Subsurface Biogeochemical Research Science Focus Area (SFA) and a key member of PNNL’s soil microbiome SFA...

Publications: 2018 Stegen JC, TC Johnson, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, SJ Fansler, EB Graham, DW Kennedy, CT Resch, MM Tfaily, and JM Zachara. 2018. "Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial...

PNNL Publications 2020 Ogden A.J., T.W. Wietsma, T.E. Winkler, Y. Farris, G.L. Myers, and A. Ahkami. 2020. "Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System." Scientific Reports 10. PNNL-SA-145907. doi:10.1038/s41598-020-63224-z 2019 Boiteau R.M., S.J...

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data...

As Integrative Research Scientist, Dr. Hofmockel develops the overall science and technology strategy for EMSL in collaboration with the Deputy Directors. Responsible for EMSL’s Strategic Science Area in collaboration with the Deputy Directors. Is the interface with BER and the user community for...

Janet Jansson is Chief Scientist for Biology in the Biological Sciences Division and a Laboratory Fellow at the Pacific Northwest National Laboratory (PNNL). Jansson has more than 30 years of experience in microbial ecology. Jansson earned an M.S.in Soil Microbiology at Colorado State University...

Earth Scientist at PNNL Disciplines and Skills: Biogeochemical Cycles Carbon Cycle Isotopes Microbial Communities Microbial Ecology Microbiology Microbiome Science Nitrogen Education: Morningside College: Bachelor of Science, Biology

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Dr William C Nelson
Lindsey N. Anderson
Janet K. Jansson
Ruonan Wu
Jason McDermott
Sheryl L. Bell
Ari Jumpponen
Sarah J. Fansler
Kimberly J. Tyrrell
Yuliya Farris
Kirsten Hofmockel
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