Impact of Soil Viruses on Microbial Compositions and Functions
Ruonan Wu*1 (firstname.lastname@example.org), Clyde A. Smith2, Garry W. Buchko1, Ian K. Blaby3, Nikos Kyrpides3, Yasuo Yoshikuni3, John R. Cort1, Michelle R. Davison1, William C. Nelson1, Yuqian Gao1, Kristin E. Burnum-Johnson1, Smith L. Montana1, Mary S. Lipton1, Ryan S. McClure1, Jason E. McDermott1, Janet K. Jansson1 and Kirsten S. Hofmockel1
1Pacific Northwest National Laboratory; 2Stanford University; and 3Joint Genome Institute
PNNL’s Phenotypic Response of Soil Microbiomes Science Focus Area aims to achieve a systems-level understanding of the soil microbiome’s phenotypic response to changing moisture. Researchers perform multi-scale examinations of molecular and ecological interactions occurring within and between members of microbial consortia during organic carbon decomposition, using chitin as a model compound. Integrated experiments address spatial and inter-kingdom interactions among bacteria, fungi, viruses, and plants that regulate community functions throughout the soil profile. Data are used to parametrize individual- and population- based models for predicting interspecies and inter-kingdom interactions. Predictions are tested in laboratory and field experiments to reveal individual and community microbial phenotypes. Knowledge gained provides fundamental understanding of how soil microbes interact to decompose and sequester organic carbon and enables prediction of how biochemical reaction networks shift in response to changing moisture regimes.
Soil is known to harbor diverse and abundant viruses, but most soil viruses are uncharacterized. The ecological impacts of soil viruses and their responses to climate change remain understudied. To address these knowledge gaps, researchers launched a cross-scale study, from viral genes of interest to viral communities in soil microcosms and field experiments. Viruses carry auxiliary metabolic genes (AMGs) that potentially contribute to soil metabolic processes while tuning the host machinery towards their own replication (Jansson and Wu 2022). We, therefore, first focused on AMGs as viral genes of interest. In collaboration with the Joint Genome Institute (JGI), the Environmental Molecular Sciences Laboratory (EMSL) and the Stanford Synchrotron Radiation Lightsource (SSRL), researchers verified the activity of a chitosanase encoded by a soil viral AMG and determined the first protein structure within the all-chitosanase family GH75 at ultra-high resolution (<0.9 Å; Wu et al. 2022). Co-crystal structures with site-directed mutants and chitohexaose further elucidated the catalytic mechanism of the viral chitosanase. This study provides more molecular evidence that soil viruses may aid their hosts in organic carbon decomposition. To quantify the metabolic contribution of soil viruses at the community level, researchers next investigated viral population dynamics under the impact of environmental perturbation.
Using three contrasting field experiments, researchers tested the viral response to changes in soil moisture, studied viral communities in a range of grassland soils with different historical precipitation patterns (Wu et al. 2021), and then generated hypotheses to test in a soil incubation experiment (Wu et al. 2021). In collaboration with the National Energy Research Scientific Computing Center (NERSC), researchers assembled the deeply sequenced soil metagenomes (>1 Tb each; Nelson et al. 2020) and recovered a total of 2,631 viral contigs including 14 complete circular viral genomes (Wu et al. 2021). Researchers found that soil with a lower historical moisture content harbored significantly higher viral diversity and abundance, while displaying less evidence of virus-host interactions, suggesting a predominance of lysogenic viruses in drier soils. The detection of AMGs involved in 18 metabolic pathways further supports the finding of viral contributions to carbon metabolism in soil (Wu et al. 2022). Researchers then selected the grassland soil exposed to an intermediate historical precipitation, and either experimentally wetted the soil to saturation or air-dried the soil to represent experimental wet and dry treatments, respectively (Wu et al. 2021). Researchers observed a lower overall level of transcription in drier soil, but across more diverse DNA viruses. A higher fraction of non-coding RNAs and more transcripts of lysogenic markers (i.e., integrases and excisionases) were detected in drier soil, further supporting a higher prevalence of lysogenic viruses in drier soils as shown in the field study.
To demonstrate the direct viral impact on soil microbiome with changing soil moisture, researchers applied High-Throughput Chromosomal Confirmation Capture (Hi-C) metagenomics to capture and identify viruses that were infecting hosts at the time of sampling and metatranscriptomics to detect the transcriptional activity of the host-associated viruses (Wu et al., submitted). Although the host-associated viruses accounted for only 5.3% to 15.0% of the total viral sequence abundance, they shared similar patterns that were previously detected in the whole viral communities (Wu et al. 2021; Wu et al. 2021). The host-associated viruses in wetter soils had higher transcriptional levels and were inversely correlated with abundances of their hosts (p < 0.05). The richness (number of different types of virus) of the host-associated viruses and the average viral copies per host (VPH), however, were higher in drier soils. These results suggest that viral infections were mostly lytic under wet conditions while more prevalent and lysogenic under dry conditions. The hosts infected by soil viruses were found to be central in community co-occurrence networks, highlighting the impact of viral infections on soil microbiome structure. This study is the first to target the detection of host-associated viruses in soil and reveals the impact of soil viruses on microbial composition with changing soil moisture.
Future work aims to bridge the findings across scales by leveraging the modeling capabilities (e.g., mechanistic modeling to simulate viral predation in porous systems) to test and generate a more comprehensive and transferable understanding of soil viruses. The cross-scale framework will continue to provide new information of the influence of changing soil moisture on viruses and their potential ecological impacts on soil microbiomes.
Jansson, J. K, and R. Wu. 2022. “Soil Viral Diversity, Ecology and Climate Change.” Nature Reviews Microbiology, 1–16.
Wu, R., et al. 2022. “Structural Characterization of a Soil Viral Auxiliary Metabolic Gene Product–a Functional Chitosanase.” Nature Communications 13(1), 1–14.
Wu, R., et al. 2021. “DNA Viral Diversity, Abundance, and Functional Potential Vary Across Grassland Soils with a Range of Historical Moisture Regimes.” mBio 12(6), e02595-21.
Wu, R., et al. 2021. “Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses.” Communications Biology 4(1), 1–11.
Nelson, W. C., et al. 2020. “Terabase Metagenome Sequencing of Grassland Soil Microbiomes.” Microbiology Resource Announcements 9(32).
Wu, R., et al. Submitted. “High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Soil Moisture Impacts on Phage-Host Interactions.”
PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO 1830. This program is supported by the U. S. Department of Energy, Office of Science, through the Genomic Science program, Office of Biological and Environmental Research, under FWP 70880.