New genetic tools expand capacity to investigate microbes

The vast resource created by the team comprises a major compilation of new techniques for performing genetic experiments on marine microbes. A persistent bottleneck in microbial oceanography is the lack of experimental model systems -- well-studied organisms that can be genetically manipulated to reveal gene functions, as well as clarify how microbes contribute to ecosystem processes.

"There is an incredible diversity of microbes that we've never had the tools to truly explore, and it represents an untapped resource of knowledge and biotechnology potential," said José Antonio Fernández Robledo, a senior research scientist at Bigelow Laboratory for Ocean Sciences and one of the lead authors of the paper. "This project catalyzed development of the genetic tools that we need to interrogate these organisms, and it has opened the door for engineering them to provide new products for the biomedical and food supplement industry."

Funded by the Gordon and Betty Moore Foundation, the initiative supported development of genetic tools for a group of microbes called protists. These microscopic, single-celled organisms are among the most diverse yet least understood marine microbes. The tools created by Fernández Robledo and his coauthors set the stage for other researchers to develop protists as experimental model systems that can revealing the inner workings of the ocean and microbial life.

Fernández Robledo used advanced molecular techniques to develop a new approach to studying Crypthecodinium, a microalgae that produces a beneficial fatty acid used as food supplement. He developed a technique to insert DNA into the organism. This is the first essential step toward identifying the roles of individual Crypthecodinium genes, and ultimately being able to ask specific questions of its genome.

Fernández Robledo obtained Crypthecodinium samples from the National Center for Marine Algae and Microbiota at Bigelow Laboratory, and he was assisted by an undergraduate from Colby College as well as a master's student with this research. The protocols the team established, as well as all others described in the paper, are freely available online to help other scientists benefit from this effort.

"The process of tool development inherently includes failures as well as successes, and the challenge to secure funding for this type of work has previously restricted scientists from making progress in this area," Fernández Robledo said. "The Moore Foundation deserves a lot of credit for recognizing that the most interesting science happens at new frontiers, and that all results are valuable and sharing them helps to move the field forward."

In addition to Fernández Robledo, several other research teams succeeded in introducing DNA into marine protists. They are now working to employ genetic techniques such as CRISPR/Cas9 to interrogate these microbial genomes, a critical step that will allow scientists to identify the functions of specific genes and potentially harness them to develop beneficial applications.

The Nature Methods paper brings together 113 coauthors from 53 institutions across 14 countries, and it offers a wealth of methods for conducting genetic research in marine protists. The project efforts were accelerated by active communication and collaboration among the researchers, who have shared their protocols in a dedicated community group called Protist Research to Optimize Tools in Genetics (PROT-G) on the protocol-hosting website protocols.io.

"This paper is a landmark achievement after several years of hard work to solve numerous technical challenges in the laboratory," said Adam Jones, program officer at the Gordon and Betty Moore Foundation. "We look forward to seeing how the protocols and guidance offered by the scientists in this newly available resource accelerate genetic tool development in marine protists."