Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
Microbiome(2022)
Abstract
Background The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.
Results Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape ( Brassica napus L.). By recovering 1,059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of “Kill-the-Winner” dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of “viral priming”, which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.
Conclusions Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.
### Competing Interest Statement
The authors have declared no competing interest.
* Abbreviations
:
AMG
: Auxiliary Metabolic Gene
ANI
: Average Nucleotide Identity
ANOVA
: ANalysis Of Variances
Bp
: base pairs
CPM
: Counts Per Million
dsDNA
: double-stranded DNA
HSD
: Honestly Significant Differences
Kb
: kilobases
NMDS
: Non-metric Multi-Dimensional Scaling
OTU
: Operational Taxonomic Unit
PERMANOVA
: PERmutational Multivariate ANalysis Of Variances
ssRNA
: single-stranded RNA
VC
: Viral Cluster
vOTU
: Viral Operational Taxonomic Unit.
MoreTranslated text
AI Read Science
Must-Reading Tree
Example
![](https://originalfileserver.aminer.cn/sys/aminer/pubs/mrt_preview.jpeg)
Generate MRT to find the research sequence of this paper
Chat Paper
Summary is being generated by the instructions you defined