In 1986, Yiu-Kwok Chan from Agriculture Canada identified a new bacterial species. Following standard protocol, he deposited it in the American Type Culture Collection (ATCC), a repository where scientists store novel microbial strains. It sat there for decades until 2020 when it was noticed by Roland Wilhelm, a postdoctoral researcher at Cornell University, for bearing a striking resemblance to a different group of bacteria. Wilhelm obtained a vial of Chan’s strain from the ATCC and used newer DNA sequencing technology to confirm that the 1986 strain was actually a species of the Paraburkholderia bacteria he was currently studying. This revelation was only possible because of the bacterial archive, which served as a pivotal connection between these two researchers across different eras of science.
Keeping track of global microbial evolution is a challenging task. Microbes form new species faster than humans and many other sexually reproducing animals do, and the number of microbial species scientists have discovered has been steadily growing over the years. However, some estimates suggest that bacterial extinction rates are so close to the new species formation rate that most bacterial lineages that ever existed are now extinct. Microbes are known to be essential for nutrient cycling, agricultural productivity and soil health, producing antibiotics and anticancer compounds and protecting our gut health and immune systems. However, we are still exploring and learning about the microbial world, which makes it all the more important to think about microbial conservation.
Culture collections preserve microbial diversity, just as a seed bank preserves plant genetic diversity. The World Data Center for Microorganisms reports a microbial culture collection in almost every part of the world and together, they contain over two million bacterial, fungal and viral cultures. This number is but a small fraction of the Earth’s prolific microbial diversity.
Microbial culture collections can receive samples from anywhere in the world, but some locations yield more microbes than others. The Jena Microbial Resource Collection receives cultures from all over the world but particularly from Asian countries, according to Michael Ramm, staff member at the JMRC. Some countries or institutions are current hotspots of microbial discovery and are home to large-scale isolation efforts. We often hear about biodiversity hotspots and cautionary extinction stories like the dodo bird’s, but microbial conservation is seldom part of the public conversation.
One reason we don’t think about microbial conservation is that most microbes are invisible to the naked eye and hard to grow outside their natural habitats; fewer than 2 percent of environmental bacteria can be grown in the lab. This makes storing and culturing microbes a tricky process that requires finding an elusive combination of nutrients, salts and atmospheric conditions. It can take months or even years for scientists to tease a microbe out from its habitat.
Researchers need repositories like global culture collections to ensure the long-term preservation of the precious cultures that can be cultivated. Kirk Broders, curator of the NRRL Culture Collection in Peoria, Ill., is excited about the potential of such collections. “Connecting with, and providing resources for, researchers from around the world who are conducting cool research … is the most exciting part of my job. There is also the simple joy of cultivating, growing and admiring the colorful menagerie of beautiful fungi and bacteria.”
On the surface, it might seem like these collections are cataloging cultures much like a microbial museum. However, the true value of these repositories lies in their potential for science; the next novel antibiotic, a compound that cures cancer, or a microbe that reduces greenhouse gas emissions could be hiding in those vials. “In science, it can be hard to predict what biological strains may become clinically significant,” says Sarah Alexander, curator of the National Collection of Type Cultures (NCTC). “When a scientist deposits strains, this material is available to the next generation of scientists and will always be retrievable.”
Collections allow scientists to make sure that the strain they are working with today is the same one that was used in a study 30 years ago, as in Wilhelm’s story. This is why many culture collections are starting to tighten the restrictions for a submitted strain to be recognized as an official member of the collection. In the past, microscopic examination of a culture might have proved sufficient but repositories like the NRRL are now starting to require an additional security measure that prevents contamination: the gene sequence of the submitted strain must match what the scientist found in the lab. Many microbes can also evolve very quickly, and even a few months of living in the lab can make a strain look different from when it was first identified. Once a microbiologist verifies that the gene sequences match, the strains are stored by cryopreservation, the process of long-term storage using ultracold temperatures or flash freezing with liquid nitrogen.
Culture collections are clearly critical entities that help make science more open, collaborative and reproducible. They preserve Earth’s current microbial diversity and may hold the microscopic keys to solving many pressing global challenges. They are also the libraries of the microbial world and every strain has a unique story; the first bacterial isolate in the NCTC was isolated from a World War I soldier and is being used to fight dysentery. Alexander is cognizant of the history and promise of the strains. “Maintaining, preserving, and growing the collection that contains over 6,000 strains from over 900 different bacterial species is a privilege. A culture collection is a biological repository … whereby we can preserve these living exhibits to ensure they are available to research.”