Principal Investigators

  • Forest RohwerBeing a marine microbial ecologist, Dr. Forest Rohwer sees a coral reef as a finely-tuned community in which the microbes and viruses are major players. Recognizing their importance, he pioneered the use of metagenomics as a means to characterize these previously inscrutable organisms and to investigate their role in coral reef health and disease.

    For his scientific contributions, he has received numerous awards including the prestigious Young Investigators Award of the International Society of Microbial Ecology and the Marine Microbiology Initiative Investigator Award from the Gordon and Betty Moore Foundation.

  • Linda Wegley-Kelly Dr. Wegley Kelly and Dr. Rohwer have been working together since 2001. She has directed research projects on everything from fluorescent-labeled phage to large-scale metagenomic from deep mines, salterns, and coral reefs to ammonium oxidizing Archaea.

    Linda's research group mostly works on coral-associated microbes. She uses a combination of large-scale DNA sequencing (e.g., metagenomics), analytical chemistry, and microbiology to study how the coral holobiont changes in response to local and global stressors. Linda recently showed that shipwrecks cause devastating outbreaks of algal-microbial mats the kill kilometers of coral reefs in the iron-poor parts of the central Pacific.

Merging Art and Science for CoVID-19 education

The Rohwer lab and artist Lili Todd are collaborating to create a poster series that will provide clear and concise scientific explanations for exactly how masks, the virus, and the vaccine work. Learn more about this work at

The Lab

  • Lab Members

    We have a diverse group of researchers in the lab that include undergraduate volunteers, graduate students (MS & PhD), post-docs, and visiting scientists.

  • Join the Lab

    Our lab offers research and training opportunities for students (undergraduate, MS, PhD), postdocs, and scientists.

  • Lab Training & Methods

    Learn how to build the tools that we use to explore diverse ecosystems.


  • CoralCoral Research
    Coral reefs worldwide are in decline. The dramatic rise in incidences of coral disease over the last two decades has been instrumental in this process. We have hypothesized that most of these diseases are actually opportunistic infections instigated by anthropogenic stressors. Our research is focused around understanding the interactions between the microbial world and coral reefs, and how these systems change following perturbation.

  • CFHuman Research
    We are currently investigating the dynamics of bacteria, phage, and eukaryotic viruses in the respiratory tracts of individuals with and without Cystic Fibrosis. Characterization of viral communities coupled with microbial transcriptomics and viral metagenomics will allow a better understanding of how the unique environment of the CF airway drives microbial and viral specialization and vice versa.

  • Phage OutreachPhage Outreach Program
    Our mission is to interest high school students in the study of the Phage Virus and attract them to the field of science in the future. We will do this by sharing the most interesting aspects about the phage virus along with an educational foundation, a fun art contest, and an in-depth field trip. Additionally, 3-5 motivated students will be offered a summer internship at our lab researching the Phage Virus.


  • Life in Our Phage World book coverLife in Our Phage World
    To celebrate a century of phage exploration, we invite you to get intimate with 30 diverse phages in this premier phage field guide. In these 404 pages you'll learn who these phages are, where on Earth they've been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences in pursuit of their quarry.

    The book is available in electronic (PDF) format for free. It can be downloaded as a high-resolution (323 Mb) or lower resolution (75 Mb) file. For optimal viewing, display the pages with the two-page view that includes the cover.

    Electronic Book Downloads

    Sampler (3 Mb)
    Low-resolution (75 Mb)
    High-resolution (323 Mb)

    Hardcover Book Purchases

    Buy at Amazon
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    Buy at Powell's

  • Forest Rohwer - Coral BookCoral Reefs in the Microbial Seas
    For millennia, coral reefs have flourished as not only one of the planet's most magnificent ecosystems, but also as its most biodiverse. However, since the 1980s the corals have been struggling. Both coral bleaching and disease have spread globally. During recent research expeditions to the remote Line Islands, microbial ecologist Forest Rohwer and his colleagues found that the large-scale changes to the reefs in recent decades are the work of the microbes as they respond to various human impacts.

    Coral Reefs in the Microbial Seas is the first book to recount this story, complete with introductions to the coral reef ecosystem, 21st century metagenomic research tools, and the coral's microbial and viral partners. An engaging book, its science is liberally spiced with artistic illustrations and playful stories from the research expeditions.

    Book Downloads

    Sampler (1.5 MB)
    Buy at Amazon

Lab News & Events

Coral Reef Arks

Feb 04, 2021

Coral Reef Arks

Coral Reef Arks, or “Arks,” were conceived to address the global demand for new technologies that combat the widespread degradation of coral reefs. By translocating corals into the water column above or afar, ample distance is provided from degraded substrates, along with improved access to light, flow, and Drawings of divers deploying ARKS here nutrients. Through the process of migrating corals and surrounding reef organisms to promote their health, Arks will create thriving “mini-reef” communities to support conservation and restoration goals.

Divers deploying ARKS
Divers deploying ARKS

Rohwer lab doctoral student Jason Baer spent the past year building and testing Arks structures off the San Diego coast. Albeit the non-tropical San Diego region does not exhibit reef-building corals, the colder, temperate waters are rich with life, and the violentcoastal waters offer a perfect opportunity to test the durability of the Arks structures. To Jason’s surprise, it only took a few short weeks for the Ark to become completely colonized by a diverse community of hydrozoans,nudibranchs, fish, urchins, bryozoans, crabs and more. Although travelrestrictions are still in effect due to the CoVID-19 pandemic, Jason will continue to test how the Arks influence and are influenced by the environment around them before taking Arks to the Caribbean to deploy them on coral reefs.

The benefits of a global network of Arks include expansion of coral reefs to new sites, creation of fisheries, and preservation of coral reef functions and biodiversity. For this project, the Rohwer Lab has raised nearly $10 million dollars for this cross-disciplinary project which includes scientists, artists, engineers, lawyers, and businesspeople with one common goal: conservation and restoration of coral reefs

To read more about this project, check out our associated site: and follow our site and social medias for updates.

The artwork included was created by local artist Ben Darby. Please read our recent post about him to learn more!


Artist Ben Darby uses illustration to communicate important scientific findings and ideas

Jan 27, 2021

Ben Darby, a local San Diego artist, has worked with Dr. Rohwer for 10 years by providing illustrations and creative expertise for various projects. His art has been featured in Dr. Rohwer’s textbook “Life in Our Phage World,” the CoVID-19 environmental sampling project, as well as Dr. Rohwer’s upcoming book, “P.H.A.G.E.S”. Using mainly pen and ink, Ben creates art that communicates important scientific findings or ideas to scientists as well as citizens. He enjoys the freedom he is given by Dr. Rohwer to interpret scientific icons or processes and create visually appealing pieces that aid in breaking down complex ideas. He hopes that his illustrations will aid in cementing the points that scientists are trying to convey. Not only does he put pen to paper, but he takes the time to educate himself on the research and topics he works on, which he refers to as “private tutoring.” Ben says the biggest reward for doing this work is contributing to meaningful scientific contributions and helping others understand and visualize these findings.

Scientific art pieces by Ben Darby will be featured routinely on this site and can also be found on his website: Below are pieces created by Ben for the CoVID-19 project the Rohwer Lab is currently working on. The first is a drawing he produced of the SARS-CoV-2 virus with its envelope and spike proteins. Other drawings are of animal species that have been thought to play important roles in the transmission of this, and other, SARS-viruses, such as a Pangolin, a Camel, and a Bat.

Check back again for more features of Ben Darby’s art, including pieces from Dr. Rohwer’s upcoming book, “P.H.A.G.E.S”.

Ben Darby artwork Ben Darby artworkBen Darby artwork Ben Darby artwork