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Elucidating the role of bacteriophage lifestyle strategy in Microbially-Mediated Perennial Rhizosphere Nitrogen Transformations

ABSTRACT: Illumination of the interplay between viral community lifestyle strategy (lytic vs. temperate) and the impact of these interactions on microbial population dynamics and metabolic functioning in soil is critical to our understanding of bioenergy crop productivity as well as carbon and nitrogen cycling more broadly. We will leverage an existing set of samples from switchgrass growing on marginal lands that were collected in a 2-week interval time-series over two years with comprehensive data on soil nitrogen pools, plant growth, and existing 16S-focused data on rhizosphere bacteria. We will investigate the role of phage in microbiome dynamics and nitrogen cycling in this system. Ecological and evolutionary trade-offs for bacteria and their bacteriophage are predicted to lead to shifts in viral lifestyle over the growing season and in response to shifts in nutrient availability. In particular, lytic phage are hypothesized to be more dominant during periods of rapid bacterial growth. Furthermore, temperate phage are hypothesized to be triggered into lysis by root exudates or microbial metabolites in soil. Lysis events are predicted to underlie variation in biogeochemical cycling, since the death of bacteria through viral lysis will liberate carbon and nitrogen compounds, contributing to the fluctuations in these compounds that our temporal dataset has documented. The work (proposal:https://doi.org/10.46936/10.25585/60001368) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Soil Microbiome

SUBMITTER: Rick White

PROVIDER: MSV000097724 | MassIVE | Thu Apr 24 13:49:00 BST 2025

REPOSITORIES: MassIVE

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Project description:We used microarray analysis to investigate whole genome transcriptome dynamics of the marine cyanobacterium Prochlorococcus sp. strain MED4 and the T7-like podovirus P-SSP7 over a time course during the 8 hour latent period of lytic infection prior to cell lysis. Manuscript Summary: Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process1-5. Phage-mediated transfer of host genes – often located in genome islands – has had a major impact on microbial evolution1, 4, 6. Furthermore, phage genomes have clearly been shaped by the acquisition of genes from their hosts2, 3, 5. Here we investigate whole-genome expression of a host and phage, the marine cyanobacterium Prochlorococcus and a T7-like cyanophage during lytic infection, to gain insight into these co-evolutionary processes. While most of the phage genome was linearly transcribed over the course of infection, 4 phage-encoded bacterial metabolism genes were part of the same expression cluster, even though they are physically separated on the genome. These genes — encoding photosystem II D1 (psbA), high-light inducible protein (hli), transaldolase (talC) and ribonucleotide reductase (nrd) — are transcribed together with phage DNA replication genes and appear to make up a functional unit involved in energy and deoxynucleotide production needed for phage replication in resource-poor oceans. Also unique to this system was the upregulation of numerous genes in the host during infection. These may be host stress response genes, and/or genes induced by the phage. Many of these host genes are located in genome islands and have homologues in cyanophage genomes. We hypothesize that phage have evolved to utilize upregulated host genes, leading to their stable incorporation into phage genomes and their subsequent transfer back to hosts in genome islands. Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes. Keywords: time course, viral infection, marine cyanobacteria, podovirus, bacteriophage, stress response

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Elucidating the role of bacteriophage lifestyle strategy in Microbially-Mediated Perennial Rhizosphere Nitrogen Transformations

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