The resulting evolutionary arms race between bacteria modifying themselves and viruses fighting back raises questions: What does it cost a cell to resist infections, and how does that alter how ecosystems function?
In a new study, researchers have explored the mechanisms of phage resistance and its effects on the ecological jobs done by ocean bacteria. The team found that some of the mutations studied don’t interfere with – and may even enhance – the bacteria’s ability to carry out their job of capturing and sinking carbon to the ocean floor, thanks to giving the cells a “sticky” quality.
The study also revealed two kinds of mutations: the more standard surface mutations that don’t let phages in at all, and another type of metabolic mutations found inside the bacteria. These are much less studied, and would indicate a virus could enter the cell but couldn’t successfully make more viruses.
“We found that both metabolic and surface mutations caused the bacteria to get stickier, but only in surface mutants did those changes cause the cells to sink much more readily. That was very, very obvious,” said Marion Urvoy, co-first author of the study and a postdoctoral research associate in microbiology at The Ohio State University.
“And that’s kind of cool when you think about it, because carbon export in the ocean is important. From past papers, we know that virus abundance is the best predictor of carbon export, more so than any other organism, but we don’t know all the mechanisms behind this. It’s possible that the selection of surface mutants through infection, which promotes the sinking of bacteria, is one explanation.”
The research was published recently in Nature Microbiology.
The study focused on 13 phage-resistant mutants evolved from Cellulophaga baltica bacteria against two types of phages, representing ecologically relevant model systems.
After infecting the bacteria with these phages and isolating the phage-resistant mutated cells, researchers ran experiments and created computational models to see how the mutants behaved. Results showed the classic surface mutations that blocked phage entry were completely resistant to several phages, but the internal metabolic mutations provided specific resistance to only one phage at a time.
The team was able to tease out the effects of one of the two intracellular changes they observed. This mutation altered the process behind the production of a single amino acid that helps in synthesizing several lipids – fatty molecules inside the cell that store energy, form membranes and send signals, among other functions.
“The mutation impacted the pool of lipids, which prevented phage replication,” Urvoy said. “Our working theory is that because the phage needs these lipids to assemble new virus particles, it is not able to assemble at the end of the replication cycle because one of the key parts is missing.”
Turning to the ecological aspects of phage resistance mutations, the study showed mutations came with a cost to the bacteria and, potentially, to the microbial community.
“We showed for all of these mutations, whether they affect the cell surface or its metabolism, there’s a cost in terms of growth rates. That is to say the cells are growing slower, and if you affect the growth rate of an organism, you’re bound to affect other members of the community,” Urvoy said. “We found this decreasing growth was more pronounced for the surface mutants – so they’re more resistant to more phages, but it comes at the cost of growing slower in general.”
But the stickiness and sinking activity of surface mutants stood out as a critical finding when it comes to the marine biological pump that helps sink carbon to the deep sea.
The finding builds upon earlier work led by co-first author Cristina Howard-Varona, a research scientist in microbiology at Ohio State, showing that cyanobacteria that perform photosynthesis in the ocean, when simultaneously infected by phages and stressed by nearby hungry predator microbes, might take in more carbon.
Howard-Varona plans to pursue further study of the mechanisms underlying metabolic mutations against phages.
“This really opens the gate to wanting to examine more intracellular resistance because it’s so understudied,” she said. “If we add more types of phages, do you get more mutations and more types of mechanisms that we don’t know about? This is really just the tip of the iceberg.”
Urvoy and Howard-Varona work in the lab of senior study author Matthew Sullivan, professor of microbiology and civil, environmental and geodetic engineering and director of the Center of Microbiome Science at Ohio State, whose research program focuses on how viruses impact microbiomes in complex ocean, soil and human systems, including pioneering many experimental and bioinformatic approaches to “see” these impacts. Within that context, his lab is investigating how carbon cycling works in the oceans and the role viruses play.
“It’s important to understand what happens in the ocean because it affects climate globally. For microorganisms, we need to understand their impacts on carbon because they dictate whether carbon sinks or gets released into the atmosphere, and that outcome impacts our lives,” Urvoy said. “Our work and other work is now showing that viruses, as a component of the marine microbiome, also play roles, perhaps quite centrally, and we need to understand how they affect bacteria and how that fits into the whole picture.”
This work was supported by the U.S. National Science Foundation, the U.S. Department of Energy and the Swedish Research Council.
Additional co-authors are Carlos Osusu-Ansah, Marie Burris, Natalie Solonenko and Karna Gowda of Ohio State; Andrew Stai and Robert Hettich of Oak Ridge National Laboratory; John Bouranis and Malak Tfaily of the University of Arizona; and Karin Holmfeldt of Linnaeus University in Sweden.
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Contact: Marion Urvoy, Urvoy.1@osu.edu
Written by Emily Caldwell, Caldwell.151@osu.edu; 614-292-8152
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