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The largest collection of wild yeasts in the world fits inside a single beige chest freezer, humming quietly at the back of a busy lab in the University of California at Davis's shiny new Robert Mondavi Institute for Wine and Food Science.



The Phaff Yeast Culture Collection, as it's known, consists of more than 7,000 strains of 750 different species of the single-celled fungi, mixed with glycerine in cryogenically stored vials or freeze-dried into pellets. Roughly 80 percent of them are not held by any other yeast library in the world.



Kyria Boundy-Mills
, the Phaff Collection curator, knows this because last year she surveyed her global yeast-collecting colleagues, then published her findings in the Journal of Industrial Microbiology and Biotechnology. Her own yeast empire is one of several such microbial archives around the world, ranging from broad national "type" libraries to niche collections specializing in microbes from reefs, breweries, and even Antarctic explorers' huts.

As Boundy-Mills showed Venue around her office and lab, she explained that the Phaff Collection's main focus is yeasts isolated from environmental habitats: gathered from sewage sludge, vanished cacti forests, cockroaches, hot springs, glaciers, human cerebrospinal fluid, and a mare's uterus.



The oldest yeast in the collection was isolated by the UC Berkeley cellarmaster in 1893. When Venue visited, Boundy-Mills was still busy processing the 150 new species of yeast she brought back from a 2011 National Institutes of Health-funded biodiversity survey expedition in Indonesia.

"Nearly half of them are new to science," she told us, which makes them a lot of work. "That’s lifetime’s worth of work there, just to describe 60 new species."

The expedition, which included entomologists, botanists, and ichythologists, cataloged such an immense richness of biodiversity that, Mills told Venue, their research site has now been proposed as a national park. "If it's passed," she said, "it will be the first national park in Indonesia to be declared based on biodiversity data—and one of the first in the world based specifically on biodiversity."

The unspoken implication here—that there could even someday be a yeast-based national park—raises the fascinating subject of scale when discussing the types of landscapes or habitats we consider worthy of preservation. Could a single, microbiologically rich room or building be biologically important enough to be declared a national park?

In any case, while other colleagues focused on collecting and identifying microbes and plants with therapeutic potential, Boundy-Mills' focus was on possible bioenergy applications. Specifically, this meant looking for new enzymes that can break down plant materials to simpler sugars, as well as new yeast varieties that can eat sugar and turn it into oil. As Boundy-Mills explained:

Most yeasts will stop eating when they’re no longer hungry. But there are a few yeast species that keep eating the sugar—and eating it and eating it—and they convert it to oil and store it. Under the microscope, you see these big, huge oil droplets inside the cells. They can be up to 60 percent oil—they’re like these obese, couch-potato yeasts.

To find enzymes that can break down plant material, Boundy-Mills and her team sampled the gut microbes of wood-feeding beetle larvae, as well as the decaying wood around them. Meanwhile, a lot of the high-oil yeasts that Boundy-Mills brought back were isolated from the surface of leaves, with some coming from the soil.


Dissected Buprestid beetle larvae, photograph by Irnayuli Sitepu (UC Davis; Ministry of Forestry, Indonesia).

Yeast cells, at only a couple of microns in length, are frequently more of a challenge to isolate for collection than plants or fish. In some cases, Boundy-Mills would just take a sterile bag, put it around a leaf, pluck it off, and pour in some sterile saline solution. After it had swished around for a while, she would put that liquid on an agar plate to culture any microbes that had been on the leaf's surface. Meanwhile, she told us with evident glee, a lot of the high-oil yeasts form ballistospores, meaning that they shoot out their spores, firing them several millimeters into the air:

This is kind of cool. For them, we smeared some Vaseline inside the lid of the Petri plate, and we stuck some pieces of leaf in the lid. If the yeast can make these ballistospores, they will shoot those down onto the agar surface and grow there. It’s called the ballistospore capture method.

Now that she has these Indonesian couch-potato yeasts back in the lab (after mountains of import and and export paperwork, and a lengthy process of purification and DNA analysis), Boundy-Mills is not only observing their oil production performance, but also studying the other by-products that could possibly come out of the yeast cell, in order to make it an economically viable biofuel production process.

As well as oils, some of her yeasts produce protein, anti-oxidants, and even flavoring ingredients. Elsewhere in the collection are yeasts that show promise in agricultural pest control or are used in food processing.

One strain, Phaffia rhodozyma, was originally isolated on a tree stump in Japan, and is now used industrially to produce a dietary supplement for farmed salmon and shrimp, to make them pinker.



In addition to her own research and the occasional yeast-hunting expedition, Boundy-Mills spends her time preparing and sending out strains to researchers who request them, and maintaining the collection—no small task, as the yeasts are far from immortal, even in the extreme cold, so each strain has to be re-cultured on agar in Petri dishes every five years.


Kyria Boundy-Mills with Herman Phaff's notebooks. Phaff, who founded the collection, focused on the ecology of yeast, recording copious contextual notes on their functionality in nature, their interaction with decaying plant material, and the insects that live alongside them.


The Yeasts: A Taxonomic Study has expanded from one volume (center) to three (left) over the past decade.

Boundy-Mills also acts as a kind of yeast consultant, screening and identifying yeasts for biotech companies. As we prepared to leave, she showed us her yeast bible: a taxonomic catalog of all known yeasts. To help us understand why she finds the field so exciting, she explained:

In 2001, when Hermann Phaff, who founded this collection, died, the Taxonomic Study was just one volume, with about six or seven hundred species. In 2011, they had to split it into three volumes, to accommodate more than 1,400 species. And there’s another couple of hundred yeast species that have come out since that was published.

Incredibly, while the known universe of yeasts is increasing exponentially, thanks primarily to DNA sequencing technology, it's estimated that less than one percent of the world's yeast species have been discovered.

"It's one of the most under-surveyed fields—microbes in general," Boundy-Mills sighed. "There are no yeasts that are on the endangered species list because we wouldn't even know if they were at risk. We’re spending all this time and effort exploring the extraterrestrial world, which is great. But we need to spend more time and effort exploring the terrestrial world, too. There’s so much on this planet that we just have not discovered yet!"
According to Jack Chambers, proprietor of the Sonoma Valley Worm Farm and a former Delta Air Lines pilot, when he got in the cockpit of a 747, "the other guys would have second homes and boats and be into golf. But I was the worm guy."


Venue visited Chambers on a sunny September afternoon, and, as he showed us around the farm, he explained that his worm obsession began, straightforwardly enough, as a gardening hobby. A friend told him about a local farmer who had earthworms for sale, and so, twenty years ago, in 1992, Chambers paid a visit to Earl Schmidt, a former mink rancher, enthusiastic angler, and bait worm farmer.

Five days and one 5 gallon bucket of Red Wigglers (Eisenia fetida) later, Chambers' home compost pile was a rich, deep black color with a crumbly texture that he'd never been able to achieve before. He started hanging out with Earl, helping out in return for a chance to learn about worms.


As they picked worms side-by-side over the next three months, Earl told Chambers that he was looking forward to retirement and finally having the time to fish. Chambers, "without really knowing what I was getting into," found himself offering to buy the place.

A crash course in all things worm quickly followed, including a carefully scheduled layover in Vigo, Spain, to attend the World Worm Conference, and conversations with vermiculture pioneer and Ohio State University professor, Clive Edwards. Trial and error also played a role, with Chambers reminiscing about the "worm volcano" he accidentally created by experimenting with cornmeal as a feed — 50,000 disgusted worms all crawled over the sides of the bin at once, in a scene worthy of a horror movie. "Now, if I'm trying something new," explained Chambers, "I only add it to quarter of the bin, to leave room for escape."

Chambers credits his pilot's appreciation for standard operating procedures and checklists for many of the technical improvements he's introduced over the past twenty years. For example, in order to pre-compost the manure source and kill any pathogens or weed seeds before feeding it to the worms, Chambers arrived at his own design for a three-bin forced-air system, complete with a rigorously optimized schedule of turning, blowing, and releasing gases. "If I've done anything with worms," he says, "it's that."


That is certainly not all, though. As we moved under the corrugated steel sheds that house the farm's four million worms, Chambers explained that he realized early on that, in fact, "the vermicompost is the big deal, not the worms." In other words, rather than simply feeding worms in order to harvest them for sale to sport fishermen and gardeners, Chambers focused on marketing their castings, particularly to the region's high-end grape-growers.

To do so, he has built four ninety-foot long continuous flow vermicomposting bins, based on an original blueprint by Clive Edwards, but improved over the years to the point that he now has a patent pending on the design.


"This is high-tech for worms," explained Chambers, as he demonstrated his most recent iteration, the VermiComposter CF40. In sixty days, pre-composted manure will make its way from top to bottom of the four-foot deep bins through a continuous conveyor-belt system of worm digestion.

The raised bins are fed from the top twice per week, and harvested from the bottom once weekly using an automatic breaker bar. A wire mesh tumbler then separates the worms from their excretions; the worms go back in the bins and the remaining black gold is sold for a dollar a pound.


Earthworms are easy to overlook, but among those who do observe their work, they seem to inspire extreme devotion, counting among their historical fans both Aristotle and Charles Darwin. Chambers is equally enthusiastic. As we dug our hands into the warm, soft compost and watched the worms we had disturbed wriggle back into the darkness, he expounded on the mysteries of worm reproduction as well as numerous studies that have shown vermicompost's beneficial impact on germination rates, disease suppression, flavor, and even yield (up to a twenty percent increase for radishes, according to Clive Edwards' colleagues at Ohio State).


Vermicompost is typically used as a potting medium — Chambers' advice is to "put one cup in the hole with your seed or transplant" — or it can be brewed at 73 degrees for 24 hours to make a "compost tea" that can be sprayed onto the soil or plant directly. Although it is between four and fourteen times more expensive than regular compost, Chambers argues that, like a high-end skin product, vermicompost's benefits and economy of use make it well worthwhile:

I tell vineyards to think of it like insurance. After all, a vine costs about $3, and some vineyards lose as many as twenty percent of their new plantings. With our vermicompost, they usually lose less than one percent.


Chambers and his wife even planted four hundred vines of their own, losing only two, and they attribute their ongoing victory over powdery mildew to regular applications of compost tea. They make a very good "Worm Farm Red," that we were lucky enough to sample and that even won a gold medal in the amateur category at the 2008 Valley of the Moon Vintage Festival.

Sonoma Valley Worm Farm already makes more than 200,000 lbs of vermicompost a year, but Chambers took early retirement from Delta last year, and has big plans for the business. The day we visited, he had just finalized the agreements for a new facility that will more than double his capacity, as well as incorporate several new improvements to his existing equipment.


As we examined the architectural plans in Google SketchUp, Chambers described his vision for the next generation VermiComposter CF 40, which will include electronic moisture and temperature monitoring and automated feeding.

While he waits for the new facility to be built, he's already experimenting with feeding the worms an extra inch of compost per week, to see whether he can increase their productivity. Meanwhile, in response to interest from California's berry giant, Driscoll's, he's started working with compost tea-kettle manufacturers on a unit that could brew up to 250,000 gallons at a time. In fact, Chambers' only concern as he scales up, he told us, was what he would do when the worms' demand outstripped the manure supply of the organic dairy farm (Straus Family Creamery) that he currently works with.


Given that, last year, the EPA estimated that thirty percent of annual landfill contents could have been recycled through composting, and that California's dairy cows produce 30 million tons of manure annually, much of which is stored in waste lagoons where it risks contaminating groundwater, it seems as though feeding four or five million new worms is not going to be much of a challenge at all. The fact that those worms will not only remove that waste from the environment, but also transform it into something that scientists are calling "pretty amazing stuff," as well as "the next frontier in biocontrol," is even better.

Chambers told us that he is convinced that "worms are going to be the next big thing in agriculture." If we're smart, it will be.
 
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