263: Make Better Wines with Bioinformatics
Tiny microbes have a big impact on wine quality. Aria Hahn, CEO and co-founder of Koonkie, Inc., discusses the exciting work her bioinformatics organization is doing in the field of metagenomics. Hahn explains the differences between genetics, genomics, and metagenomics. She shares insights from a project studying yeast populations in British Columbia's Okanagan region, revealing the diversity and distinct clades found on wine grapes. The conversation also covers the broader applications of bioinformatics in agriculture, including regenerative farming, soil health, and potential bioprotectants against wine spoilage. Hahn underscores the impact of microbiome management on wine terroir and the potential of bioinformatics in understanding and improving winemaking processes. Resources: 201: Balance Hot Climate, High Sugar Wine with Green Grape Juice aka Verjus 243: Microbial Communities in the Grapevine 251: Vine SAP Analysis to Optimize Nutrition Aria Hahn – Google Scholar Aria Hahn – LinkedIn Koonkie Make Better Wines with Bioinformatics The Microcosmos - Discover the World of Genomics Apple App Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade Vineyard Team Programs: Juan Nevarez Memorial Scholarship - Donate SIP Certified – Show your care for the people and planet Sustainable Ag Expo – The premiere winegrowing event of the year Vineyard Team – Become a Member Get More Subscribe wherever you listen so you never miss an episode on the latest science and research with the Sustainable Winegrowing Podcast. Since 1994, Vineyard Team has been your resource for workshops and field demonstrations, research, and events dedicated to the stewardship of our natural resources. Learn more at www.vineyardteam.org. Transcript [00:00:00] Beth Vukmanic: Tiny microbes have a big impact on wine quality. [00:00:09] Welcome to Sustainable Wine Growing with Vineyard Team, where we bring you the latest in science and research for the wine industry. I am Beth Vukmanic, Executive Director. [00:00:19] In today's podcast, Craig McMillan, Critical Resource Manager at Niner Wine Estates, with longtime SIP certified vineyard and the first ever SIP certified winery, speaks with Aria Hahn, CEO and co founder of Koonkie Inc. [00:00:35] She discusses the exciting work her bioinformatics organization is doing in the field of metagenomics. Hahn explains the differences between genetics, genomics, and metagenomics. [00:00:47] She shares insights from a project studying yeast populations in one of British Columbia's wine growing regions, revealing the diversity and distinct clades found on wine grapes. [00:00:58] The conversation also covers the broader applications. bioinformatics in agriculture, including regenerative farming, soil health, and potential bioprotectants against wine spoilage. [00:01:09] Hahn underscores the impact of microbiome management on wine terroir and the potential for bioinformatics in understanding and improving the winemaking process. [00:01:19] We know your customers are looking for sustainable wines. In a recent review of 30 studies, Customers reported a higher preference for eco label and social responsibility labels compared with nutrition labels. Achieving SIP certified gives you third party verification that your vineyard winery or wine has adopted and implemented stringent sustainable standards. Apply today at SIP certified. org. [00:01:46] Now let's listen [00:01:50] Craig Macmillan: Our guest today is Aria Hahn. She is the CEO and co founder of Koonkie, Inc., a bioinformatics organization, business, doing all kinds of exciting stuff. Thanks for being on the podcast, Aria. [00:02:02] Aria Hahn: Yeah, so excited to be here. Thanks for [00:02:04] Craig Macmillan: We're going to get into the thick of it But we were attracted to some work that you folks and your colleagues have done with bioinformatics and yeast, wild yeast. But I wanted to drop back. A little bit first to kind of give some context. All of this kind of comes under the umbrella of metagenomics, correct? [00:02:21] Aria Hahn: Yeah, absolutely. [00:02:22] Craig Macmillan: and what is metagenomics? [00:02:24] Aria Hahn: I'm going to take further step back and talk about genomics um, maybe the distinction between genomics and genetics. [00:02:32] So genetics is something I think most people kind of understand. They have this intuitive sense of it. um, that make up ourselves and all living creatures. But it actually turns out that in most organisms, and not bacteria, and we'll get there in a Most of your DNA is not in genes. It's in between genes. And so genomics is the study of genes and all of the things that are in between genes. So that's kind of the distinction between genetics and genomics. And then metagenomics is when we do that at the community level. [00:03:02] so you could do metagenomics of humans, but metagenomics refers to populations of bacteria, uh, microbes, archaea, viruses, things that you cannot see and I'll say interact with directly. [00:03:17] Craig Macmillan: And then bioinformatics is a subset or is a technique, is that correct? [00:03:23] Aria Hahn: Yeah, it's a technique, you know, it used to be even 10, 15 years ago that everyone kind of did their own bioinformatics. And so really what that means is when we sequence DNA or read that DNA, so it's only four letters, ATCs and Gs, we extract the DNA the sample is, could be the surface of grapes, uh, a human, anything. [00:03:42] Um, Then we put it on a sequencer. There's a bunch of different sequencing technologies right now. Um, But you end up with these like very gross files that aren't openable on regular computers and they're literally just ATCs and Gs. And so bioinformatics is the cross section of high performance computing and biology. And so we develop algorithms and processes and pipelines to really take those gross huge files of ATCs and Gs and make them human readable. make them interesting, figure out, you know, what are the genes that are there? Who is there? What are they doing? And who's doing what? [00:04:19] Craig Macmillan: Okay, and I think that's the important part here is you would take a sample from the environment. We'll talk about this one more in a second, but there are particular sequences that may be associated with a certain type of microbe or even a particular genus or particular species of microbe that can be detected. [00:04:39] Aria Hahn: Yes, absolutely. [00:04:40] So a genome is all of the DNA that makes up that organism. So you and I have distinct genomes, but of course, our genomes are going to be pretty similar to each other compared to a human genome, to a fish, to a plant, to a [00:04:55] Craig Macmillan: why the focus on microbes? [00:04:57] Aria Hahn: Yeah, that's a great question. It depends how philosophical You want to get You know, people are generally [00:05:02] familiar with the concept of like the Higgs boson particle. It's like the God particle that makes up everything and that's great and the physicists are gonna come for me. But when we think about our planet Earth, I always say like If there is a god particle on this planet that is alive and that we interact with, like, it's a microbe. [00:05:21] This is their planet. They were here long before us and they will surely be here long after us. So we think about microbes in terms of they are the destroyers of higher level populations. They keep us healthy. They make us I'm going to say it's a great example, but it wasn't a great thing. [00:05:40] So caveat that. But COVID was a great example about how this is not our planet where we had an of a virus in one location in a very particular place in the world. And all of a sudden it was across the planet. We are vectors for them. [00:05:58] You know, looking at those maps and showing the spread and how quickly it happened, I like to use that often in visual presentations to say, if you don't believe me, like, look at this. It's spread through us. [00:06:10] Craig Macmillan: Right. And I think also this gets to some other things we might talk about later on, but there are communities of microbes that are associated with certain macroorganisms. [00:06:23] Aria Hahn: uh, so are, they're everywhere, they're on your um, there's lots of research in the cosmetic industry that's looking at that. There was this crazy CEO years ago where he was I'm gonna slather this microbial laden cream on my skin and then I'm never gonna shower again and I'm not gonna smell. Not necessarily like my cup of tea, I love a good hot shower. But, you know, it can be there. The soil is the microbial diverse environment on the planet. , But your gut, like you, you as a human being, can't actually digest your food without those microbes. You can't get those vitamins and nutrients that you need without that community in your stomach. [00:07:03] Plants work the same We say charismatic macrofauna, eagles, whales, things that are very Um, They, they don't to, you the seaweed and the weeds and the grass and kind of everything in between. it's All supported by the microbiome, by these microbial communities. [00:07:20] Craig Macmillan: so let's talk about one microbiome in particular, and that would be populations of yeast that we find on wine grapes. [00:07:29] Aria Hahn: Yeah, yeah. So we've looked at yeast and bacteria and they're both cool. [00:07:34] Craig Macmillan: That is super cool. And so this one particular project where you looked at yeast on wine grapes in British Columbia Tell us a little bit about that project [00:07:41] Aria Hahn: there's, So I live in I'm, I'm right in the thick of, you know, BC wine country, which is a fantastic place to live, we were fortunate enough to work with the Wine Research Institute out of the University of British Columbia, Vivian Mease Day's group. them and They do very, very cool work, but they were trying to look at the yeast populations in wineries across the Okanagan region. [00:08:02] We know that the history of lots of commercial. Yeasts are actually from oak trees in Europe. So that's very cool. And what we wanted to see is how are the yeasts that are being used to produce wine in the Okanagan region distinct and similar to commercial yeasts and yeasts that have been characterized from across and so We did just that and we were actually able to sequence a whole bunch of yeast. And so, again, that's like reading the genome effectively there. so we found four distinct clades, um, in the Okanagan region. And a clade is they're related groups, and so it's not like you and you're a twin where you might have an identical, uh, genome to a twin. [00:08:50] It's more like you and your cousins and second cousins and second cousins twice removed and, you're, you're kind of vaguely related to each other. You kind of cluster over here, but you're not necessarily super We've kind of found four clades that the 75 yeast strains that we studied in that particular piece of work Really related to, then we looked at like what is different in their genomes. [00:09:12] So they're all the same species. That's the first thing to, to think about here. So just like you and I are the same species, they're all the same species, but just like you and I, we have different areas of, of specialties. Some people podcasters. Some people are, artists and scientists and, um, kind of everything in between. [00:09:33] And we need everybody. So, we're all the same species, but we have different specialties. And the yeasts work very similarly to that. [00:09:40] Craig Macmillan: all right, so this is interesting to me so You go out and you you said when you looked at 75 species of yeast or different types of yeast Those are ones that you, you found. It wasn't like you went in and said, I want to test for each of these 75. You got information, you got data in and said, Oh, look, here's 75 different types of [00:10:01] organism. Yes, that's a, that's a great Um, so, we And we uh, the ferment or the, the yeast skins and we extract the DNA and then we get rid of the great DNA, which could probably also be really cool, but we didn't look at it in this case. And kind of threw that into the and then said, okay, we're just going to focus on the Saccharomyces cerevisiae Latin term for a very common yeast strain, um, used in wine. And we said, we're going to look for it. [00:10:30] Aria Hahn: Then we found actually hundreds and . And then, um, and I didn't do this work, I don't do a lot of lab work myself, so, uh, this part is kind of the edge of my knowledge. But there is some ways to kind of do microsatellite clustering. And so you look, and you look for tiny differences in the genome, and you say, okay, maybe we found 500, but we actually want to look at ones that are distinct from one another. So we don't want to randomly pick 75, we want to pick 75. strains of this yeast that are different from one another. [00:11:01] And so you could use some lab techniques to make that happen. And then you take those hundreds and we say, these are the 75 that we know are different. We're going to dive deep into those 75 so that we can kind of get this breadth of genetic diversity from the region. [00:11:18] Craig Macmillan: And that was something I was thinking about. You mentioned you took samples from either fermenting wine or recently fermented wine or from skin material. How exactly is this collected so that you know that you're getting just [00:11:30] what you want? [00:11:31] Aria Hahn: Yeah. Painfully is the answer. So like when you do soil sampling, it's actually really And we tell people all the time sampling for yeast or microbes is not that complicated. I say every single time we talk to a client, I'm like, look, wash your hands with ethanol, you know, hand sanitizer, essentially between rinse your tools. And mainly you can't mess this up as long as you don't spit in the bag or bleed in the And I say this every time, and I will say one out of every few hundred samples is full of blood. Hands down like you always think we always the that and then hands down. We're like, this is full of And I think it's just like a matter of working in the field like people nick themselves They don't really realize that but really that kind of thing is really easy [00:12:15] When it comes to sampling a ferment that can also be fairly easy. [00:12:19] You have a lot of it You can kind and put it in a jar, but I will Um, Jay Marknack, who's done a lot of this work and developed a lot of these methods, he actually developed this method that is painstaking. Um, But you have like, he's got this method where he takes the grapes really carefully without touching them off of the and then washes just like very carefully with these like rinse solutions to really just get the microbes and yeast that are on that surface without touching it, without touching other surfaces. It's really just what was there in the field. And rinse all of that off. And you can imagine that's not that fun of a Um, And, and, and so, and it wasn't like he did it on his first try either. So he's now developed that we're copying and using, thank goodness. Uh, But it can be like that kind of painful where it's like washing individual grapes, collecting that rinse water, and then filtering that rinse water, like onto a physical filter, then extracting the DNA from that filter. [00:13:18] It's not fast. [00:13:19] Craig Macmillan: Nope, that's what I wanted to know. I've collected a lot of soil samples in my life for looking at soil microbiome. And you know, technique is everything. You know, contamination will mess you up pretty badly. [00:13:29] Aria Hahn: We had this one study I felt so bad, but they had collected these samples. They sent us the samples and we get the data back and it's, they're soil, they should be teeming with life, right? [00:13:38] And there's like one species basically in this thing, like there's a handful, but like one is dominating. So we go to them and we're like, what is going on here? And they're like, well, I don't see how that could have happened. , we've been storing these in a dark closet for a year. And we're like, that's why. You are studying bottle effects right here. And they're like, oh, we thought it'd be fine because it was dark and cool. And we're like, yeah, but it's not open to the air, and it doesn't have the plants and animals and bugs. You grew one guy. [00:14:07] Craig Macmillan: Yeah. We've been talking about bacteria, or the yeast. Are there other types of organisms, microorganisms, that you can use this technique with? [00:14:14] Aria Hahn: Totally. So you can use this technique on basically anything that's alive. So you could target viruses, uh, not something we've done on wineries, but could absolutely do it. You can target, , archaea, which are very similar to bacteria in that there are a single cell. But they are similar to eukaryotes. [00:14:32] So things that are bigger, um, like us, like mammals, like fish, Uh, but they are kind of small and invisible, , to the naked eye like bacteria. So those, we can, we can do that all the way up to, any animal that we can see, feel, touch, , and kind of anything in between. So it's a really powerful technique. As long as it has DNA, we can make this work. [00:14:53] Craig Macmillan: So you found these 75 types? of yeast organisms, but they fell into groups, they fell into clades. And I thought that was one of the most interesting things about this. Can you tell us a little bit about the natural history of behind these clades and kind of what that means? [00:15:09] Aria Hahn: We found these 75 different strains and they did group into four clades. So four kind of groups of more or less related organisms. So you can think of them as like clustering based on similarity. [00:15:22] The first one was one that is well known and well studied. So that's wine and European. And so those strains are more similar to these that we see in wines out of Europe and commercial strains. [00:15:35] And then the second clade we saw was the trans pacific oak. So a lot of wine yeast are very closely related to yeast that are found on oak trees. And so actually think that, , the original, , European wine yeast strains from, you know, the 1800s are from Mediterranean oak trees. And so it's not uncommon that we see these strains related to oak. [00:15:59] So that was the trans pacific oak. Then we see another group or clade that we called beer one mixed origin. And so we saw similarities to known previously studied yeast strains that are related to beer, sake, so other kind of fermented drinks. also kind of expected. [00:16:18] And then what was really exciting is that we found a new clade that we've designated the Pacific West Coast wine clade. it's always neat when you get to discover something new, of course. And so it has high nucleotide diversity. And so what that means is that even within this clade we do see a lot of genetic diversity kind of in there. [00:16:38] And what we do know is that that whole clade shares a lot of characteristics with wild North American oak strains, but, and this is kind of where like it all kind of comes full circle, but we also see that it has gene flow from the wine European and Ecuadorian clades. It can mean a couple of things. So it could mean that There is just so much selective pressure when you're, when you're trying to make good wine that these genes that are found in European wine strains, commercial wine strains, they're present in Saccharomyces cerevisiae in general, but then when we try to make good wine, we select for strains that have these, genes, , that we know produce good wine, because they produce good wine everywhere. [00:17:27] And so it could just be this process of natural selection. It also could be that most wineries , are not purists. It's not that. never in their history have other wine strains visited their their vineyards. They might have tried a commercial strain. They have wine from others, you know, people track things in, animals track things in. And so it could just be that there is this gene flow, quite literally from, from Europe, from these wine strains that just kind of comes into our population here in the Pacific West Coast. [00:18:00] And so there's kind of these, these two ways that we could have got these things, We do have some evidence to suggest that they were actually transferred in. [00:18:07] So it's called horizontal gene transfer. And my go to example on how horizontal gene transfer works is always , The Matrix, like the movie with Keanu Reeves. But what I've also learned is that if you talk to people that are like younger than me, they don't know that movie anymore, so this only lands with like a certain age of [00:18:23] Craig Macmillan: Right, I know, I know, [00:18:24] Aria Hahn: You know The Matrix where they like plug in and then they have all these new skills? [00:18:28] Bacteria can kind of do that, where you can just take genes from, , a relative, has to be like kind of closely related, and we take them and then we just put it into their genome, and in many cases, not all, but many, they're able to just kind of start making use of those genes right away. [00:18:43] And so that's horizontal gene transfer, which is pretty cool, because for us, the second that sperm hits the egg, that's it. That's all your genes. You're not getting more. You're not losing more. Like you're, you're set. But bacteria are more fluid. [00:18:57] So there is this cool thing called the wine circle, and it's a cluster of five genes that are associated with making commercial wine. [00:19:05] And we do think because we see this wine circle and these particular five genes in so many wine strains, and because of their location and a whole bunch of other kind of genomic characteristics of them, Um, we think that they are horizontally transferred. And so we do see this wine circle of these five genes in the majority of this new clade of British Columbia strains. [00:19:33] Craig Macmillan: So just talking about moving things around the world, you said like people have things on their bodies and whatnot. I, I was fascinated by the Ecuadorian group. And is that literally like it was growing on plants in Ecuador, kind of native to that area that is found its way up the West coast of North America. [00:19:53] Aria Hahn: that's really what we thought happened. I know it is amazing, right? Like does the amount and transfer and you know how you go through the airport and they're like, you and It's like the end of the world. It's like I get it because we don't want to like do that on purpose, but also the ecuadorian yeast like it's coming up here [00:20:12] Craig Macmillan: right, right. Exactly. [00:20:14] So what I think is of interest to winemakers, and also has potential beyond that that I'll ask you about winemakers are looking for increased complexity in their wines, and they're also looking for a sense of place. And I'm really happy to hear more and more people talking about terroir, not just in terms of rocks, but in terms of the whole picture. [00:20:33] The soil microbiome, the practices that are done, as well as light and climate and all those kinds of things. What are some of the things about what you found that indicate or that suggest a uniqueness to that Okanagan area that may make it stand out as different than other locations? How does this translate into sense of place? [00:20:54] Aria Hahn: That's a fantastic question. I'm going to give two answers first on the east side. We see that many of that nucleate. don't have all five of those wine circle genes. And so we see a lot of British Columbian strains have that, but there's this whole clade of these natural yeast used in wine that don't have all five of those. [00:21:17] So then you just have different genes to work with. And since you have different genes to work with, it's not just those genes, but it's all of the genes, and it's the rate that those specific strains are able to break things down. [00:21:28] You do get this added complexity when you're not using a standard commercial yeast. You just have this bigger variety of genes to choose from, and That's going to make the flavors more specific, and different. [00:21:44] It also introduces a certain, the disadvantage of using these is that, you know, they are gonna vary year to year, month to month. Uh, Potentially, and, and so you might get really, really amazing results one year and not the next year, and understanding why, why that might be is a whole exercise in and of itself, probably doable, but it's really exciting to think that these yeasts that are there naturally , they just have that genetic diversity and they want to live in these diverse communities, and so you are going to get that difference and terroir. [00:22:16] The other piece that was really exciting and was a different piece of work, but very similar groups and very similar, , samples, was looking at the microbiome, so the bacteria on the grapes. And we kind of found two things, and so there is some literature that shows if you look at a single farm, a single vineyard, and you look at different red varietals of grapes, you see actually a fairly similar microbiome signature on all of the different varietals. [00:22:46] Okay, but if we look at three distinct vineyards that are all within , one kilometer radius of one another. So they're very close. They have the same rock, to your point. They have the same weather. They have the same climate chaos happening, [00:23:01] but they're managed differently. We actually see very, very distinct signatures on all three that persists year after year. So we looked at two years, , this was again, Jay Martinek's work, , and we see that each one of those, even though it's the same varietal of grape, it is more similar to itself, year over year, than among the three farms. and and that's very interesting because what that suggests is Exactly what you're saying. [00:23:29] It's not the rock. It's not the climate that's driving the microbiome there. It's actually the practices of that vineyard that are changing that. And to me, that's so powerful, because what that means is that there's so much of that craft and art in the management of the vineyard that's then going to go and affect the terroir. , I know that's not the yeast answer, but that's the bacteria answer, and it's like, the power's in your hands. [00:23:54] Craig Macmillan: I'm on the Central Coast of California, and we've had some very hot vintages in this last , 2024 season. We had, and it was 2022 as well, we had these really hot stretches of over 100 Fahrenheit. Not very friendly to yeast in general. [00:24:09] Probably friendly to some, but not to others. And I had conversations with winemakers along the lines of like, could you even do a natural fermentation this year, a native fermentation? Are they there anymore? Or have they been selected against due to the heat? And I now have a total reset of the microbiome, the microflora in my world. this is the kind of thing that bioinformatics would be able to determine. [00:24:34] Aria Hahn: yeah, for sure. So we love that. We love when we get the baseline. We're like, show us your year that you were like, this is my typical year. This is my regular year. We'll live for that because as soon as you have the baseline, then we can go and answer those questions. So we can say, okay, great. We know what your baseline is when you typical year. [00:24:52] Now you have this heat wave that comes in. , Let's go and look. Let's go see who's survived. And I know I anthropomorphize all of these things a ton, but it really is, like, who's there, right? , is it the same bug, but very decreased? Are we getting different E strains coming in? are we seeing less overall diversity? [00:25:13] Do we see the same diversity, but Their population is a quarter of the size, and how does that affect the dynamics? Like, what do we see? And bioinformatics can absolutely absolutely answer these questions. And that can be really powerful. [00:25:26] Craig Macmillan: In my research I didn't pick up on this Can bioinformatics put a quantity on things? Can you quantify the relative size of these different populations? [00:25:34] Aria Hahn: We can, yes. So, you have to use some kind of special techniques. There's a couple of main ways we do them. One is called qPCR, so quantitative PCR. And so we literally take the DNA and we can count the copies of it in a very quantitative way. That's straightforward, pretty inexpensive. [00:25:52] Another way we can do it is a little bit more sophisticated, , but you don't have to know what you're looking for. So with quantitative PCR, we have to know, like, we want to go count saccharomyces cerevisiae. But if we don't know all of the microbes that are there, all of these that are there, then we can't go and target it with qPCR. So then what we have to do is use a spiken. the concept is pretty simple. You put a known quantity of a piece of DNA that we would not expect to appear in nature. And then when we sequence it, we know how many we got back. So if we know we put in a hundred copies of it and we get 200 copies back, now we have a pretty good idea of like, everything there was, sequenced twice or if we get 50 copies back, we're like, okay, well, however many we have, we're going to double that and we have a good idea and we do do this in like a little bit more sophisticated way where we put in like a whole bunch at different quantities so we can double check our math and make sure that it's all good. [00:26:49] But that's the concept is with a spike in so you can do it quantitatively. [00:26:53] Craig Macmillan: Talking about all the things that are out there, there's a lot of interest right now in bioprotectants for fermentation, where you introduce non fermentative yeast, and they kind of take up the ecological niche against foliage organisms, and then you can add a Cerevisiae strain to do that, to do your fermentation. [00:27:10] Would you be able to pick up those other genus, of yeast in a bioinformatic way and gives us a sense of what else is out there. [00:27:18] Aria Hahn: Yeah, for sure. So we sequence the whole community and then we kind of in a. Like a puzzle. I'm going to put together the individual genomes of everyone who's there. And so we can look at not just the targets, but the unknowns as well. And so often, especially in soils, what we get is sometimes up to 80 percent of the genomes that we're able to recover from that sample are totally novel. [00:27:43] So they're new to science. It's really exciting. and we hate it. We love it and we hate it. So, we love it because it's really fun. You, you discover these new species of bacteria, of yeast, or these new strains, and, and you get to name them. You don't have to name them after yourself anymore, you have to name them about the place that they're there. Which is a totally logical thing. But, would have been fun. , [00:28:06] So we get to name these things, it's really exciting. [00:28:09] But it also means it's so much work. Because now you have this genome that's so new. And so now you're trying to figure out. What are all the genes? Do we know the genes it has, but just not quite the way that they're arranged? Do we not know what many of these genes do? And if we don't know what these genes do, like what kind of uncertainty and questions does that bring up? And so it can be really exciting, that discovery phase, and also quite overwhelming, honestly. [00:28:36] Craig Macmillan: what other applications might there be for bioinformatics in wineries or in vineyards? [00:28:41] Aria Hahn: Yeah, that's fantastic. So definitely monitoring. You know, regenerative farming is a really big thing right now. how can we introduce additional species, cover crops, , you know, planting additional or different plants in between. Like, what can we do to really increase the soil health, sequester carbon, the biodiversity of the soil, of the land, and how does that affect it? So we can monitor all those things with environmental DNA or eDNA. [00:29:09] One thing that we've been thinking about a lot is this concept of smoke taint, which I think has kind of affected the whole west coast of North America. [00:29:18] Are there microbial treatments that can kind of mitigate smoke taint, , can we feed bacteria, the bacteria that we know [00:29:29] can kind of break down those volatile phenols that cause the smoke taint. Get them to kind of break that down first before we make the wine. Like we're kind of looking at applications like that. [00:29:40] Obviously those are, I would say further out in terms of technological development biodiversity, which we can absolutely go and do today. , but there's interest in that smoke taint. Application, and we're really interested in that. [00:29:52] Then there's also kind of everything in between. So can we the harvest? Can we increase the quality of the grape? Can we help with years that are dry? Can we help with years that are wet or cold or hot? as we, kind of committed to a certain number of effects of climate change, we have to start thinking creatively. [00:30:14] I was on this call with an unrelated company. They wanted to do similar things but in the mining space, in the reclamation space. And I don't know how it happened, but I was on this call with this man. It was his last day before it was dark where he was. He's in Quebec. He's three hours ahead. [00:30:29] , You know, it was winter. So it's very, the mood was very, like, dark and somber, and this was his final call of his final day of work. And he was so hopeful about microbes, and he spent his career working with them. And just before he signed off the call, he says, I hope microbes save us all. [00:30:50] And then he kills the call. And, and, for, the next few years, I titled every single talk I did, Microbes may save us all because I just, the weight of that conversation was so big and I know that's not what we're talking about here in terms of [00:31:08] smoke taint, but I do think, you know, to bring us full circle to this like omnipresent godlike presence of microbes that there's something to that idea in that I think that they have this potential to save us from ourselves. If we can learn more, [00:31:25] Craig Macmillan: I think what we're talking about is bioremediation and the potential there. And bioremediation would work by identifying an organism that's going to play a certain role and then actually introducing it into the environment. For instance, like introducing it to wine that may have smoke taint, for instance. [00:31:40] Aria Hahn: , so there's a three main approaches to that. [00:31:42] So the first is exactly what we're talking about. You introduce a micro that we know and you, and you put it in there. The main challenge of that is this, this word we call engraftment. We actually steal that word from organ transplants. So, when you put in a new heart, not that I know anything about heart transplants, but when you put in a new heart, you have to engraft it. [00:32:01] And so people need to be on immunosuppressants, is my understanding, to make that heart transplant like stick in their body, have their body accept it. Kind of the same challenge when you introduce a microbe into an open, wild environment where you need that new species to engraft in that community. If you can't do that, you just have to keep adding it. [00:32:21] You have to keep adding it, keep adding it, it's time consuming, it's expensive, all of these things. So engraffing is still a challenge in that field. But that is one way. [00:32:29] The second way is to bioengineer. And so the concept here is that you take species or strains that are naturally occurring, so they do well in that environment, and you change something in their genetics and then reintroduce that. It does get around the concept of, [00:32:50] of engraftment in theory. The major issue with it is, there's not a lot of people or companies that feel ready, I think, to take a biologically engineered synthetic genome and introduce it into the environment en masse. We just don't understand the risks of it, or, or not, we don't know, but I think that's the point, is that we don't know, and so people are a little bit like, Maybe we're not quite there yet. [00:33:19] And then the third way is to say, I'm going to look at who's already there. And I'm going to understand what they like to eat and what their competitors like to eat and I'm going to try to starve their competitors [00:33:31] and really feed the ones who have the capacity to degrade those volatile phenols. I'm going to like try to get their population to do super well and thrive. and and try to kind of starve out and make the populations that can't do the job that I want lesser and less prevalent in the community. [00:33:51] And that approach I think is kind of one of my favorites where we understand and then we put some selective pressures. So this could be adding more nitrogen, adding different carbon sources. [00:34:01] It could be watering less to create a more aerobic environment. It could be you know, kind of drowning them to create an anaerobic environment. It's kind of those bigger controls that we have working with the microbes that are already there. [00:34:17] Craig Macmillan: Yeah, in the same way that we're not afraid to play with plant communities in agricultural systems, with cover cropping or intercropping or anything like that, same kind of idea, where maybe I plant something that I think will out compete a weed. [00:34:28] Same kind of idea. And we're pretty comfortable with that. [00:34:32] And also things will have a way of finding their stasis, finding their, their It's just getting it kind of pushed in the right direction. I think that he's super, super cool. [00:34:44] A lot of interest and work in the soil microbiome in terms of soil health. We mentioned regenerative agriculture. I have put my toe in that, in, in my professional world extremely difficult, extremely confusing, lots of holes you know, and, and trying to find markers or metrics has been. challenging for instance, I was trying to figure out how healthy some soils were. It, healthy in quotes, and I wanted to do analysis of respiration. And this very good soil ecologist said, well, that tells you how many folks are in the room, but it doesn't tell you what they're doing or who they are. [00:35:21] And I was like, that's a really good Point I could have a lot of respiration from organisms. I don't want and I wouldn't know what was who and who was what? What world can bioinformatics play in that [00:35:33] Aria Hahn: , that's a great question. So I would say it's the opposite in general, without the spike ins and kind of specific things, what? we can tell pretty inexpensively, 50 to 100 a sample, is basically who's in the room and in what relative abundance. So it is come down a lot in price. It doesn't tell us a lot about their genetic capability. [00:35:55] So if we know them because they've been previously studied, then we can say like, oh, yeah, these guys are known to do X, Y, and Z. [00:36:02] If we don't know them, for that kind of price point in those methods, we're kind of just like, yeah, we know their names. But that's it. [00:36:08] Then we can do kind of a deeper dive, , to a different type of sequencing called whole genome sequencing. And you get the whole genome. And so there we can actually say not only who they are, but what they're doing. Or what they have the ability to do. And so that's where the limit of DNA is, is that it can tell us the potential. They can potentially do this, but it doesn't actually tell us if they're choosing to do that, so to speak. [00:36:33] There are other techniques that are very related. Metatranscriptomics, it's looking at the RNA, and you could do metabolomics. So you can actually look at the metabolites that they're producing, and then it tells you what they actually did. But we often can start at that base layer of DNA. and build up. So those questions we can answer. [00:36:51] And I think you're right about there are a lot of holes and it's confusing and it's complex. And we say this to clients all the time, like, if you know way to solve a problem, do that. Biology is messy. [00:37:03] But if you don't, like let's look at biology and let's enjoy the mess , there's a lot of beauty in that mess. And that's one of the things we've actually loved about interacting with wineries they are incredibly scientifically minded folks. They're data driven, the amount of innovation and technology they're using. never fails to impress, but you also get that love of the art and the craft from them. We love that. We see art and science as like in a circular spectrum. And so we love when, our clients in the, in the wine start talking to us about kind of their secret sauce and the things that they've tried and how, and they always get a little bit nervous. [00:37:49] And they would, if they always kind of start, they were like, you know what else I do? And we're like, tell us. And then they tell us something and they're like, we just know from experience. Experience that this works that this changes the ferment, but we don't have any evidence for that And and I think they're worried we're gonna judge them but we're like no that is like their science is all way of knowing but [00:38:09] my friend says art is science and love and and I love that idea that is something that's been really really fun about working with wineries and vineyards is they kind of get that they're like, yeah, this is the love piece here [00:38:22] Craig Macmillan: That's cool I think there's beauty in the mess. I might adopt that if you don't mind I mean, I may use that for some of my own stuff. I think that's great What is one thing you would tell growers or wineries, , [00:38:35] Aria Hahn: their choices are directly impacting the microbiome, so that's the bacteria and the yeast And that that is going to affect the terroir, the complexity, the quality of the wine, and it is knowable. [00:38:50] Craig Macmillan: there we go. And we also know that some of the things that we do may affect that and that is part of what makes us special. Where can people find out more about you? [00:38:58] Aria Hahn: We have a website, it is koonke. com, K O O N K I E dot com. can also look me up, Aria Hahn, , and on Google Scholar, the internet, I feel like I'm very findable. [00:39:10] Craig Macmillan: Yeah, you are very findable and we will have a lot of links and other things on the show page. So please check that out. Really fascinating stuff going even beyond this. I want to thank you for being on the podcast. [00:39:21] This has been a great conversation. [00:39:22] Aria Hahn: Yeah, thanks for having me. Super fun. [00:39:25] Craig Macmillan: So our guest today was Aria Hahn. She is CEO and co founder of Koonkie, a bioinformatics company, and is doing some really fascinating stuff, not only around yeast, but lots of other topics. [00:39:35] And I just got lost down the rabbit hole when I took a look at that website, all the different things you folks have been involved in, and it was really fun. [00:39:48] Beth Vukmanic: Thank you for listening. [00:39:49] Today's podcast was brought to you by Sunridge. For over 45 years, Sunridge nurseries has supplied premium quality grapevines. to grape growers worldwide. A pioneer in the industry with a focus on clean quality vines and personalized dedication to their partnered growers has led them to be the largest, most well respected grapevine nursery in the United States. Sunridge Nurseries continues to lead the industry having undergone several expansions to their modern state of the art facilities and is the first and only grapevine nursery to have implemented the most advanced greenhouse Horticulture water treatment technology in North America. [00:40:26] Make sure you check out the show notes for links to Aria, an article titled, make better wines with bioinformatics plus sustainable wine growing podcast episodes, 201 balance hot climate, high sugar wine with green grape juice, 243 microbial communities in the grapevine. And 251 vine sap analysis to optimize nutrition. [00:40:50] If you liked the show, do us a big favor by sharing it with a friend, subscribing and leaving us a review. You can find all of the podcasts at vineyardteam.org/podcast, and you can reach us at podcast at vineyardteam. org until next time, this is sustainable wine growing with the vineyard team. Nearly perfect transcription by Descript
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