Astrobiology

Our lab discovered that viruses that infect purple and green sulfur bacteria have the genomic information to modulate the metabolism of the cells they infect. These ancient bacteria now thrive only in anoxic lakes, but were once dominant in the oceans when oxygen was scarce on the planet. Geologists can use the biosignatures produced by these bacteria to understand these past Earth environments. Therefore, understanding how viruses affect these biosignatures is essential to understanding early life on our planet and detecting signs of life on other planets where microbial life may have emerged.
​Our Lab is partnering with geochemists at the University of Pittsburgh, Indiana University-Purdue University Indianapolis, and the University of Lausanne in a NASA-funded project to investigate how viruses affect the biosignatures of purple and green sulfur bacteria and help interpret them in ancient Earth rocks and, in the future, on other planets.
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Check our publications:
Hesketh-Best et al., 2023
Varona et al., 2024
Walker, Varona, et al., 2026

Coral reefs

Coral reefs are among the most diverse ecosystems on the planet, and viruses are the most diverse biological entities in these environments. ​Our lab is studying how viruses that infect bacteria can act as double-edged swords for coral reef health: they can help corals by killing pathogenic bacteria or, instead, form alliances with their bacterial hosts that harm corals. We have developed methods that allow deep genomic analysis of coral-associated viruses (Varona et al., 2023; Wallace et al., 2024) and have built a global-scale genomic catalog of coral viromes, the Global Coral Virus Database (Wallace et al., 2024b).

Viral abundance and predation pressure are associated with higher coral cover on over 100 reefs in the Pacific, suggesting that by killing bacteria, viruses help maintain bacterial biomass, as is characteristic of a healthy reef environment (Silveira et al., 2023; Varona et al., 2024).

Aligned with the idea that viruses can contribute to coral resilience, we discovered that the coral Madracis mirabilis, which has been incredibly resilient in the Caribbean while most species are dying, has a more diverse microbiome that is enriched in prophages, viral genomes integrated into the genomes of bacteria. These viruses contribute to genome diversification and functional redundancy, which may be adaptive traits contributing to this coral's success (Wallace et al., 2025). 

In contrast, corals affected by stony coral tissue loss disease (SCTLD) are also enriched in prophages that carry virulence genes capable of enhancing bacterial pathogenicity. SCTLD has devastated Caribbean reefs since it emerged in 2014, but the pathogen remains unknown. While our findings cannot ascertain that viral infection is the root cause, it can certainly contribute to disease progression (Wallace et al. 2026). 

Between 2026 and 2027, our lab will join the Tara Coral Consortium to investigate the basis of coral resilience in the Coral Triangle. This region of the Indo-Pacific has shown higher resilience against global thermal stress compared to other reefs. The goal of Tara Coral is to reveal the genetic, physiological, and ecological basis of this resilience. Our lab brings over 15 years of experience in coral reef viruses to probe whether viral communities might contribute to corals thermal stress response. We will sample reefs in Papua New Guinea, the Philippines, Indonesia, Palau, and other countries that host the most diverse coral reefs in the planet!

Sargassum

The brown algae Sargassum grows naturally in the Sargasso Sea, where it provides habitat for fish, turtles, and other marine life. However, in the past 15 years, Sargassum has dramatically expanded its distribution, and its overgrowth is now an economic and a health problem for the Caribbean, Gulf, and East US coast. Sargassum has been suggested as a carbon sequestration opportunity by sinking it into the deep ocean, but Sargassum's contribution to the Atlantic carbon budget is unknown. 

Our lab has revealed the structure of the microbial and viral communities associated with Sargassum and their potential for contributing to Sargassum growth by metabolizing nutrients (Stiffler et al., 2024). The Sargassum microbiome is highly enriched in prophages integrated into bacterial genomes, and prophage activation can interfere with bacterial biofilm formation. This process can select members of the Sargassum microbiome and ultimately determine which bacteria grow on the algae's surface: those that contribute to the algae's growth or opportunistic bacteria that may include potential pathogens (Stiffler et al., 2026).

The massive presence of Sargassum on the beaches of Florida and the Caribbean produces toxic gases and has sparked fears about public health risks. One such risk raised in the past few years is the presence of opportunistic pathogenic bacteria of the genus Vibrio, sometimes called "flesh-eating bacteria". Our lab performed an in-depth microbiological survey of Sargassum in Miami and found no such bacteria. Rather, the vibrios associated with Sargassum mostly came from the surrounding environment and likely take advantage of the algae's photosynthetic products for growth. These results are under peer review.