Dr. Kyria Boundy-Mills, curator of the Phaff Yeast Culture Collection,
views yeast cells under the microscope
Photo by Dr. Irnayuli Sitepu
Today we are sitting down with Dr. Kyria Boundy-Mills,
curator of the Phaff Yeast Culture Collection, to find out what it’s like to
manage a prominent yeast collection.
Q: What is the most fun part of your job?
A: Thanks for asking that first! There are many less than
fun parts, such as managing budgets, remembering passwords, figuring out how to
comply with new regulations and other paperwork… But, the fun parts more than
make up for that. The most satisfying part of my job is learning all the creative
ways that people are using yeasts from the Phaff Yeast Culture Collection. We have
provided yeasts for several massive genome sequencing projects such as the Thousand
Fungal Genomes project. Biotechnology companies use Phaff collection yeasts or their genes to
develop better production strains to make bulk and fine chemicals for food,
health, agriculture, and many other fields. Academic researchers around the
world use our yeasts to describe new species, and to study genomics,
metabolomics, physiology, and reproduction of yeasts. Several years ago, we even had an artist use Phaff collection yeasts to make art for an art exhibit.
One of my favorite stories: In 2013, Boston Beer Company (makers of Samuel Adams) wanted to
re-create a well-known historic beer using brewer Jack McAuliffe's vintage recipe from the 1970s. New
Albion Brewery was one of the first craft breweries in the modern era in the US, but went
out of business in the 1970s. New Albion acquired yeast strain 36C4 from Wallerstein
Brewing Labs, but that company had also gone out of business long ago. BUT, back in
1977 there was a student intern at New Albion named Don Barkley who also worked with the yeast
collection at UC Davis, and preserved yeast 36C4 in the Davis
collection. So, the Phaff collection was able to provide the ORIGINAL yeast
strain to Boston Beer Company 36 years later.
All these creative uses of Phaff collection yeasts are
possible because my predecessors gathered, characterized, organized and preserved
thousands of yeast strains, and because UC Davis supported the collection
through thick and thin.
Q: Tell us more about the yeast collection.
A: The Phaff Yeast Culture Collection was named after Herman
Phaff (1913-2001), who spent over 50 years traveling around the world
collecting yeasts for his research on yeast taxonomy and ecology. He isolated
yeasts from specific habitats he was studying at the time: foods such as dried
fruit, bark beetles in infested trees, Drosophila
flies in tree fluxes. He spent about 20 years studying yeast in Drosophila-infested decaying cactus,
work that revealed some of the basic concepts of yeast ecology. The collection
has over 6,000 yeasts that he gathered (about 2,000 of these from cactus), plus
yeasts from other researchers and collections, plus yeasts collected by me and
other UC Davis researchers. We have over, 7,500 strains in the public catalog,
including over 1,000 of the 2,000 known yeast species, plus dozens of new species that
don’t have names yet. We distribute yeasts to researchers at universities, government
agencies, and companies around the world, and also use yeasts in our own
research. These yeasts that were isolated decades ago for ecology research are
now being used for totally different research fields.
Q: What is so special about this collection?
A: This is one of the largest public collections of wild yeasts in the world. (We are currently #4, after NRRL, ATCC and CBS.) PLUS, most of the yeasts were isolated as part of UC Davis research projects, and not deposited in other collections, so about 80% of the yeast strains are not available from any other source. PLUS, we also have tons of physiological data about these yeasts, because they were identified through a very laborious procedure before ribosomal sequencing was a thing: up to 80 characterization tests. PLUS, there are dozens of new species that don’t have names yet – we have the only known representatives of these yeast species in any collection in the world.
A: This is one of the largest public collections of wild yeasts in the world. (We are currently #4, after NRRL, ATCC and CBS.) PLUS, most of the yeasts were isolated as part of UC Davis research projects, and not deposited in other collections, so about 80% of the yeast strains are not available from any other source. PLUS, we also have tons of physiological data about these yeasts, because they were identified through a very laborious procedure before ribosomal sequencing was a thing: up to 80 characterization tests. PLUS, there are dozens of new species that don’t have names yet – we have the only known representatives of these yeast species in any collection in the world.
Q: What is the largest order you ever distributed?
A: In 2008, University of Wisconsin researchers were working on a Department of Energy-funded project as part of the Great Lakes Bioenergy Research Center. They requested over 2,000 yeast strains, which they used to compare properties of yeasts that are useful for conversion of plant materials such as corn stalks to biofuels.
A: In 2008, University of Wisconsin researchers were working on a Department of Energy-funded project as part of the Great Lakes Bioenergy Research Center. They requested over 2,000 yeast strains, which they used to compare properties of yeasts that are useful for conversion of plant materials such as corn stalks to biofuels.
Q: What yeast strains are used the most?
A: I have two answers for you. We both distribute yeasts to
outside researchers, and use yeasts in our own research program. For in-house
research projects, we prefer to use commonly studied yeast species as controls,
and the type strain if possible. So, the strain we have used most often
in-house is the type strain of well-known yeast species Saccharomyces cerevisiae UCDFST 01-158. This strain has been used
in 27 separate in-house experiments since 2001, including studies of cellulase
activities, antimicrobial activity, lipid content, pectinase activity, xylose
assimilation, growth on lignocellulosic hydrolysates, and yeast cell wall
composition.
This same strain is one of the most commonly distributed to
outside researchers, who have used it to develop microbiome analysis methods,
study the genome diversity of the species, characterize industrial strains, etc.
Q: What is your favorite yeast strain?
A: Easy: Strain number UCSDFST 81-84. A few years ago, my grad student Tonio Garay and project scientist Irna Sitepu were studying oleaginous yeasts, which are high oil yeasts: they can eat sugar and convert it into oil, and store it inside the yeast cell. A few dozen yeast species can accumulate over 60% oil. Yeast oil is similar to vegetable oil, but can be produced faster – many crops per month, vs. one crop per year for plants. So, if we can bring the production cost down, yeast oil could theoretically substitute for petroleum and vegetable oil for some food, feed, fuels and chemicals. We found that yeast strain 81-84 stored lots of oil inside the cell, PLUS started secreting a weird sticky goo outside the cell. This weird goo turned out to be a new type of lipid – a glycolipid that we named Polyol Esters of Fatty Acids (PEFA). We found several other strains in the Phaff collection belonging to species in the genus Rhodotorula that make PEFA. So, why is 81-84 my favorite? In addition to making the most PEFA of any strains we studied, it encapsulates to the history and nature of the Phaff collection: This yeast was isolated in 1981 from a cactus as part of a study of yeast ecology. AND, it is a novel species that doesn’t have a name yet. No other public collection has any strains of this species.
A: Easy: Strain number UCSDFST 81-84. A few years ago, my grad student Tonio Garay and project scientist Irna Sitepu were studying oleaginous yeasts, which are high oil yeasts: they can eat sugar and convert it into oil, and store it inside the yeast cell. A few dozen yeast species can accumulate over 60% oil. Yeast oil is similar to vegetable oil, but can be produced faster – many crops per month, vs. one crop per year for plants. So, if we can bring the production cost down, yeast oil could theoretically substitute for petroleum and vegetable oil for some food, feed, fuels and chemicals. We found that yeast strain 81-84 stored lots of oil inside the cell, PLUS started secreting a weird sticky goo outside the cell. This weird goo turned out to be a new type of lipid – a glycolipid that we named Polyol Esters of Fatty Acids (PEFA). We found several other strains in the Phaff collection belonging to species in the genus Rhodotorula that make PEFA. So, why is 81-84 my favorite? In addition to making the most PEFA of any strains we studied, it encapsulates to the history and nature of the Phaff collection: This yeast was isolated in 1981 from a cactus as part of a study of yeast ecology. AND, it is a novel species that doesn’t have a name yet. No other public collection has any strains of this species.
This discovery was possible because
my predecessors preserved thousands of yeasts for unknown future uses. I now work
diligently to preserve these yeasts for the researchers of tomorrow.
___________________________________
(full disclosure: Kyria interviewed Kyria...)
Dr. Kyria Boundy-Mills worked with Herman Phaff from 1999 to 2001, and has been the curator of the Phaff Yeast Culture Collection at UC Davis (http://phaffcollection.ucdavis.edu) since Herman Phaff passed away in 2001. She is active in the US Culture Collection Network (http://www.usccn.org), and on the executive board of the World Federation for Culture Collections (http://www.wfcc.info/).
