"Pink Berries" Blossom into a Model System in the MBL Microbial Diversity Course

Since the early 1970s, students in the Microbial Diversity course at the Marine Biological Laboratory have plunged through the muck in the nearby Sippewissett salt marsh to collect samples of its tiniest inhabitants to study. Over the years, the marsh has been a birthplace of dissertation projects, a launchpad of microbiology careers, and the starting line for many collaborations between course instructors and participants.

Among the more colorful marsh residents are the “pink berries,” bright-pink aggregates of marine bacteria and the viruses that infect them. And over the course of years beginning in 2018, Microbial Diversity participants Danielle Campbell of Washington University in St. Louis and Elizabeth Wilbanks of University of California, Santa Barbara, have discovered that the pink berries make an ideal model system to study the coevolution of bacteria and their infecting viruses (phages).

The team, along with fellow course participants James Kosmopoulos and Rachel Whitaker, recently published their findings on the coevolutionary “arms race” in pink berries in Applied and Environmental Microbiology.

The pools where pink berries reside in Sippewissett Marsh. The buoy in the first pond is linked to a temperature / dissolved O2 sensor. The tubing is sampling water to collect viruses, which will be compared with pink berry viruses. Credit: E. Wilbanks

Unlike many microbial ecosystems, the pink berries only contain a few species of bacteria, mainly a purple sulfur bacterium and its symbionts. This simplicity makes the pink berries well suited for a model system for virus-bacteria interactions in a natural environment.

“They’re this really beautiful mix between something that is very truly wild and something you can also manipulate in the lab, like you would manipulate a bacterial colony,” says Wilbanks, who was also an MBL Whitman Fellow from 2018-21.

The scientists identified eight phages from the pink berries that Campbell had collected in 2018, mapped the phages to their bacterial hosts, and examined their genomes for signs of evolution. Since Wilbanks had also sampled pink berries as part of the 2011 Microbial Diversity course, they were able to compare how the phage genomes had changed over time.

Two phages persisted over seven years with few changes to their genetic sequences, but the other six phages were not present in the 2011 sample. This suggests that although the bacterial communities are fairly stable, the phage populations are highly variable over time. However, it’s still unclear what determines whether a phage persists or is lost within the pink berry.

Microbial Diversity participants (left to right) Alice Little, Eliot McCloskey, and James Kosmopoulos sampling in Sippewissett Marsh. Credit: Rachel Whitaker

Evidence of phage variation and transience can be found in the bacteria’s CRISPR system. This system captures DNA sequences from invading phages and incorporates them into the bacterial genome. These sequences serve as a memory of past viral encounters and are used to block subsequent infections. From three bacterial genomes from the pink berries, they identified 2,731 unique CRISPR spacer sequences derived from phages. However, only 6% of these sequences matched the eight phages they had identified in the pink berry clusters, indicating the bacteria had had numerous other encounters with transient viruses.

In addition to documenting a history of phage encounters, CRISPR systems shape phage evolution in pink berries by targeting specific phage genes. For example, the capsid gene, which encodes the virus’s outer protein that interacts with the host cell surface, contained the most variation over time as compared to the rest of the phage genome.

Pink berries at sediment-water interface in Sippewissett Marsh. Credit: Elizabeth Wilbanks

CRISPRs are not the only antiviral system encoded by the pink berries.“The purple sulfur bacteria, the dominant organism in the pink berries, are bristling with phage defenses,” says Wilbanks. These defenses, such as restriction-modification systems and programmed cell death, can drive the evolution of the phages. The phages that are able to dodge bacterial defenses are more likely to survive than those that cannot.

The team also found that the phage lysin gene was transferred into its bacterial host genome. Although it’s unclear whether this gene is functional, this finding paves the way for future experiments on how gene transfers shape bacterial genomes over time.

Campbell describes this Microbial Diversity collaboration as “the most intensely cooperative experience” she’s ever had. Although the course is not focused on generating publications, they sometimes arise as a result of long-lasting collaboration and enthusiasm for the ecosystems around the MBL.

Citation:

James C. Kosmopoulos, Danielle E. Campbell, Rachel J. Whitaker, Elizabeth G. Wilbanks (2023) Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in “Pink Berry” Marine Microbial Aggregates. Appl. & Env. Microbiol., DOI: 10.1128/aem.00177-23

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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.