While in college, Koskella secured a research job where she witnessed a population of fungi evolve in front of her eyes. She was hooked.
Koskella, now an associate professor of evolutionary biology, captivated the alums with stories of her lab’s work to safeguard the food supply from the pests and pathogens that reduce global agricultural production by 30 percent. With the world’s population expected to surpass 10 billion people by the middle of the century, nutritional concerns have become much more pressing.
The Koskella Lab hosts many talented undergraduates, Ph.D. students, and postdocs who are searching for sustainable treatments for various diseases impacting farmers’ crops. To do so, Koskella and her researchers are looking closely at bacteria.
Modern agriculture removes plants from their natural environment to control risk and achieve economic efficiencies. Yet these carefully managed settings may unwittingly lose the symbiotic benefits of a rich microbial community that includes bacteria, fungi, parasites, and viruses. This diverse array of microscopic organisms helps plants break down organic matter, adapt to changing conditions, and resist diseases.
Koskella is bullish on the microbiome. Bacteria outnumber the number of human cells in the human body, which does indeed sound gross. But those bacteria help our body operate: Think of the gut microbiome, with hundreds of types of bacteria that collectively help digest your meals. Plants rely on their microbes in a similar way.
Koskella’s lab is experimenting with a new product, PhylloStart, that flips the conventional wisdom. Instead of removing all bacteria — both good and bad — PhylloStart recreates the natural environment by providing a group of probiotic bacteria representative of those found on the wild ancestors of commercial tomatoes. Early results are promising: treated tomato plants produce more fruit and resist more pathogens.
Second-year Ph.D. student Asa Conover said the lab used to test the PhylloStart bacteria mix on Moneymaker tomatoes, which are popular with growers, but the plants would reach the greenhouse ceiling and require a ladder to survey. They’ve since switched to MicroToms, which grow only a few inches tall.
The entrance to the Koskella Lab. (UC Berkeley photo by Alexander Rony)
All these test plants are arranged in neat rows at an experimental greenhouse across the street from campus. The facility has been a valuable resource for plant biologists and their students, who are able to combine fieldwork with lab work to hasten their discoveries. The resulting studies and patents may provide farmers with viable alternatives to pesticides and fertilizers.
On the way to the greenhouse, postdoctoral researcher Dominique Holtappels pointed out Bradford pear trees growing on and around campus. Holtappels explained that Americans originally planted the attractive, flowering species under the mistaken belief that the trees were sterile and disease resistant. Nowadays, many governments consider the cross-pollinating trees an invasive species, and the trees are often wracked by diseases known as blossom and fire blight.
Holtappels paused the tour to cut some clippings and pass them around. One branch had a cluster of leaves that had wilted and turned brown. It was too early to tell what disease was affecting this section, but a separate branch showed clear signs of fire blight: blackened and twisted leaves that looked like they had been burnt.
The diseases aren’t merely concerns confined to the ornamental Bradford pear tree. First, the blights have been found to spread to other plants in Berkeley, and second, other apple and pear trees are experiencing similar issues. The on-campus trees are a living laboratory that provides Berkeley researchers with close access to specimens for further study.
Both blights are caused by bacterial pathogens, which are themselves host to bacteriophages that infect and replicate within the bacteria, killing their host in the process. This has renewed interest in using bacteriophages as a treatment against disease.
Postdoctoral researcher Dominique Holtappels reaches up to clip part of a tree impacted by blight. (UC Berkeley photo by Alexander Rony)
Phages look like spiders from the movie The Matrix, with prismatic towers rising up from six legs. Koskella Lab researchers spend a lot of time looking at these unliving horrors. Yet, Serey Nouth, a recent graduate in microbial biology who completed her honors thesis in the Koskella Lab, confirmed the exuberance that accompanies an undergraduate student’s first successful phage hunt.
"There are estimates that there are more than 1031 viruses on Earth,” said Holtappels. “That is more than there are stars in the sky." It is an intimidating figure for scientists combating emerging diseases.
Blue and white lab coats hang on a coat rack. (UC Berkeley photo by Alexander Rony)
Holtappels advised Nouth on a project to understand the environmental effects of phage distribution in pear trees across Berkeley, just one example of how postdoctoral and graduate students serve as the vital bridge connecting research to education and mentorship. As living expenses in the Bay Area continue to rise, graduate student funding is in particularly high demand. The Undergraduate Research Apprentice Program and Summer Undergraduate Research Fellowships provide additional opportunities for students to develop their skills in the immersive learning environment that the lab, greenhouse, and campus surroundings have to offer.
The Koskella Lab is also concerned with the agricultural conundrum of citrus greening disease, where sick trees produce inedible, lopsided fruit. The bacteria-borne disease has emerged as a major threat to citrus growers and currently has no cure. The situation is so dire that the growers have resorted to spraying entire orchards with antibiotics.
Koskella and Holtappels were skeptical of such an indirect and untargeted tactic that kills bad bacteria as well as good, collateral damage in a biochemical tug-of-war. There is also the danger that mass applications could increase antibiotic resistance, threatening public health. The researchers hope to find another option that is more effective and environmentally sustainable.
Koskella noted how microbial evolution offers a key advantage in the Anthropocene, the current geological epoch that is defined by humanity’s impact and climate change. While large species like trees evolve slowly, the tiny microbes in and around them can do so on a vastly shortened timescale, transferring those benefits back to the larger organisms and hastening adaptation.
To advance our understanding of these issues, Koskella serves as co-director of the Joint Berkeley Initiative for Microbiome Sciences. The academic consortium convenes interdisciplinary gatherings where Berkeley researchers discuss their latest research.
"Plant people and animal people generally don't talk to each other,” said Koskella. She explained that the two groups of scientists rarely collaborate or cite each other — they’ll even rediscover each other's findings. It’s inefficient, but fortunately, it’s usually unintentional. When these ecologists and biologists get together, they often find out there is much to learn from each other’s work.
The enhanced cooperation that Koskella is helping to lead offers hope in tackling many ecological challenges — from climate change to pollution to food system breakdown. Yet, humans struggling with the vastness of these issues need only look to the microbiome. After all, if a collective of microscopic organisms can have a massive impact on the planet, so can we.
Papers published by the lab's researchers are pinned to a board in the hallway. (UC Berkeley photo by Alexander Rony)
