By JCVI Staff

JCVI Researchers Help Advance Our Understanding of Ocean Microbes, Developing New Tools and Protocols Through Large-Scale Study

The oceans cover over two-thirds of the Earth’s surface and contain an abundance of life including diverse populations of marine microbes.  Studying the  genetics, biochemistry and metabolism of these microbes has been one of JCVI’s long standing research initiatives and is crucial in better understanding how they function as the base of all marine ecosystems. These unseen legions can also potentially solve some of the planet’s growing environmental issues, including climate change.

Sixteen years ago, the Gordon and Betty Moore Foundation launched a Marine Microbiology Initiative to help expand this knowledge and advance research related to the evolution and genomics of marine microbes. While scientists have come a long way, genetic tractability has still been limited to a few species. 

Recently, the Marine Microbiology Initiative launched  a new targeted investment to  develop experimental model systems for marine microeukaryotes (protists). Protists are a polyphyletic group of organisms, meaning they derived from more than one common evolutionary ancestor, making them some of the most diverse marine microbes. They play major roles in the ecology and biogeochemistry of the oceans, including performing much of Earth's photosynthesis and driving the carbon, nitrogen, and silicon cycles. While protists are well studied, very few can be genetically modified using technologies such as CRISPR-Cas9, so are poorly understood. 

With the help of the Moore Foundation, a group of 113 scientists from 53 institutions across 14 countries set out to change this and on April 6th, 2020, published their research in the journal Nature Methods. Their paper, titled Genetic tool development in marine protists: emerging model organisms for experimental cell biology, covers the breadth of work spanning from novel model systems to the detailed protocols that were developed specifically for marine protists.

Two graduate students working with JCVI Professor, Andrew Allen, PhD, made major contributions to this paper. Mark Moosburner, a graduate student at Scripps Institution of Oceanography, conducting his PhD research at JCVI, developed a protocol to deliver the CRISPR-Cas9 gene editing system to a model marine diatom species, Phaeodactylum tricornutum. The protocol is based on delivery of CRISPR-Cas9 technology to an artificial diatom chromosome, or episome, through a genetic transformation process called conjugation. His methods are now commonly used in Dr. Allen’s laboratory to investigate and deactivate individual genes in Phaeodactylum tricornutum that are involved in growth and metabolism.  The Nature Methods study reports on the details associated with successful genetic transformation techniques on Phaeodactylum tricornutum, as well as how they were used on other marine protists such as dinoflagellates, ciliates, green algae and more.

Jernej Turnsek, PhD, a recent graduate of Harvard University and researcher in Dr. Allen’s lab, contributed his work on Thalassiosira pseudonana, a marine diatom that is crucial  for studying cellular mechanisms related to planetary carbon and silicon biogeochemical cycles.  Diatoms metabolize silicon, the second most abundant element in Earth’s crust, and use it to construct their elaborate silicified cell walls. This is a hallmark feature of these microorganisms and is one of the reasons for their dominance in global oceans, but how they do this silicon metabolism has been a central question in the research community for decades. In this study, Dr. Turnsek used bacterial conjugation to localize a biosilica-associated protein in T. pseudonana. This work sets the stage to use bacterial conjugation to study biomineralization processes in T. pseudonana, other silicified diatoms, and also non-diatom silicified species.

All reported protocols developed and used in this influential research portfolio are now available through a community group called Protist Research to Optimize Tools in Genetics (PROT-G) on the protocol-hosting website protocols.io. The guidance available in this new tool has the potential to accelerate genetic tool development in marine protists and provide a deeper look into the mysteries of marine ecosystems.