In Nutrient-Limited Environments, Marine Bacteria Reprogram Their Metabolism After Viral Infection

The Science 

Viruses affect prevalent microbial systems by transferring genes laterally, altering cellular metabolism, and killing hosts, all of which affect the microbes involved in carbon/nitrogen cycling in nature. A virus-infected cell, or “virocell,” is distinct from its uninfected sister cell because the virus controls cellular metabolism to produce viruses rather than the cell itself. Yet, how virocells respond to nutrient-limited conditions, such as those found in the oceans, is poorly understood. In a recent study, a multi-institutional team of researchers infected marine bacteria Pseudoalteromonas with two different viruses and monitored their metabolism changes under different phosphate levels (a critical nutrient). This systems biology approach revealed that when nutrients are limited in nature, virocells opt for replication over managing available resource and energy needs.

The Impact 

These results suggest that although environmental conditions shape the metabolic responses of microbes in common ways regardless of viral infection, virocell-specific strategies exist to support viral replication during nutrient limitation. A framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

Summary 

Viruses play various roles in nature, and their actions inside of host bacterial cells are critical in nutrient by bacteria, especially in marine environments. Virocells, or virus-infected bacterial cells, have distinctly different metabolisms than their uninfected sister bacterial cells. A multi-institutional team of researchers used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and metabolomics, the team assessed how low phosphate (low-P) conditions affected virocells of a marine bacteria host, Pseudoalteromonas, when independently infected by two unrelated viruses. Based on observations, researchers found that a low-P environment elicited a combination of common and infection-specific responses, and in some cases, even different responses from the two different virus types for their replications. This new knowledge allowed researchers to create a framework in which to more easily identify metabolic strategies of virocells in nature when nutrients are limited.

Contacts 

Melissa Duhaime, University of Michigan, duhaimem@umich.edu 

Matthew Sullivan, The Ohio State University, sullivan.948@osu.edu 

Joshua Adkins, Pacific Northwest National Laboratory, joshua.adkins@pnnl.gov 

Young-Mo Kim, Pacific Northwest National Laboratory, young-mo.kim@pnnl.gov 

Funding 

A portion of the research was performed as part of a Facilities Integrating Collaborations for User Science award through the Joint Genome Institute and EMSL, both Department of Energy Office of Science user facilities. This work was also funded by the Gordon and Betty Moore Foundation, the National Science Foundation, the National Institutes of Health, and the University of Michigan.

Publication 

C. Howard-Varona, et al. “Environment-specific virocell metabolic reprogramming.” The ISME Journal, 18(1), wrae055 (2024). [DOI: 10.1093/ismejo/wrae055]