Horizontal Gene Transfer and Environmental Release of Engineered Microbes with Kiara Reyes Gamas

On this episode of The Climate Biotech Podcast, Paul Reginato is joined by Kiara Reyes Gamas, environmental synthetic biologist and non-resident postdoctoral scholar at Rice University's Baker Institute. Alongside her bench science, she has consistently engaged with the social and governance dimensions of synthetic biology, which shapes how she thinks about engineering microbes for environmental release.

Much of Kiara’s work has focused on horizontal gene transfer, the process by which microbes naturally swap DNA throughout the environment. It is how antibiotic resistance spreads, and it is one of the central reasons regulators worry about releasing engineered microbes. The problem is that we have very poor measurements of how often it actually happens in natural settings in complex communities, or which organisms participate. 

Kiara’s research also suggests that the field's default toward biocontainment may be missing the point for environmental applications. A microbe engineered to clean up an oil spill has to interact with the environment to do its job. The more useful questions are about which genes are safe to introduce, how engineered organisms behave under selective pressure in microbial communties, how to integrate human communities into the governance of these technologies, and whether the regulatory scrutiny applied to recombinant DNA should extend to any non-native microbe being released. 

Listen to learn how RNA-based barcoding extends the reach of horizontal gene transfer measurements across microbial species, what ecology has to teach synthetic biologists about environmental release, and why Kiara argues that community co-design is an engineering requirement rather than a regulatory checkbox. 

Transcript

Podcast: The Climate Biotech Podcast Hosts: Paul Reginato & Kiara Reyes Gamas

[00:00:03] Kiara Reyes Gamas: We’re living in a time with very public and wide distrust of science, and we need to do our best to actually earn that trust from people by showing that we’re working with people and not in opposition to people. And I think one of the worst attitudes I still see in science is that people who think that people are anti-GMO just need to be more educated and then they’ll be okay with it. And I think that totally misses the point.

[00:00:24] Paul Reginato: Welcome to the Climate Biotech Podcast, where we explore the most important problems in climate and environmental biotechnology and how we can solve them. I’m Paul Reginato, co-founder of Homeworld Collective. Together we have agency to build technologies that enable a brighter future for all life on earth.

[00:00:43] Paul Reginato: We are thrilled to welcome Kiara Reyes Gamas for a discussion today about climate biotech. Kiara is an environmental synthetic biologist, science illustrator, and non-resident postdoctoral scholar at Rice University’s Baker Institute. Her research focuses on developing RNA-based memory systems to study horizontal gene transfer dynamics in environmental microbial communities. She’s an advocate for the responsible use of synthetic biology tools to address the environmental crisis, while ensuring that their development and deployment are safe, effective, and socially responsible. Dr. Reyes Gamas is particularly interested in conversations around biotechnologies beyond conventional containment, or BCCs, and engineered microbes for environmental release, EMERs. She emphasizes the importance of interdisciplinary research, good science communication, and the integration of non-academic communities into the governance and decision-making of biotechnology. She holds a BS in bioengineering from Rice University, where she also earned her PhD in the Systems, Synthetic, and Physical Biology graduate program under the mentorship of professors Lauren Stadler and Joff Silberg. Kiara, thank you so much for joining us today.

[00:01:58] Kiara Reyes Gamas: Thank you for having me.

[00:02:00] Paul Reginato: Yeah, we’ve interacted a whole bunch through just through the climate biotech community historically, and got to meet a few times in person here in San Francisco. And it’s wonderful to be having this conversation in a way that many others can hear now. So why don’t we just start with getting to know you a little bit. Where did you grow up? How did you get here? Did you always know you’d work on environmental synthetic biology?

[00:02:27] Kiara Reyes Gamas: Yeah, so I was born and raised in Mexico City and then I studied abroad in the States starting sophomore year of high school. So I’ve been always really drawn to biology and animals and the environment, but I didn’t really consider what my career would be until my now husband showed me that researchers were growing artificial hearts in the lab, and I thought that was just the coolest thing. And so I ended up going to Rice University as an undergrad in bioengineering, and that’s where I found out about synthetic biology. So one of the things that drew me specifically to environmental synthetic biology though, was the possibility of using microbes for bioremediation. Plastic especially is a huge issue worldwide and we don’t really have great solutions to get rid of that contamination. And so I did a lot of work in undergrad to bring a composting program to my university. And so we tried to stay sustainable at home by minimizing plastic and animal products. So the idea of using microbes to eat microplastics, or clean up oil spills, was really appealing to me.

[00:03:20] Paul Reginato: So tell me a little bit about your journey at Rice University. You chose to do your undergrad, PhD, and postdoc all at Rice, so it seems like you’re having a good time there. But that’s also like an unusual degree of institutional continuity. So I’m curious what kept you there and how you and your research have evolved during your time there.

[00:03:41] Kiara Reyes Gamas: So there’s a couple of reasons why I stayed at Rice for so long. I think the first is that it’s really honestly such an amazing environment. There’s a fantastic group of researchers. They’re all doing cutting-edge work, and especially environmental synthetic biology work. So when I was thinking of next steps from undergrad, and especially when I decided that I wanted to study more environmental synthetic biology, it really didn’t make a lot of sense for me to go anywhere else when I was already at the best place to study exactly what I wanted to do. The second reason, though, is frankly, Rice has just been the place where I’ve gotten the best opportunities. I think part of that is knowing my way around the culture at Rice and knowing the people there. And that has meant that I can really rely on my community to have my back. So I think my research identity has stayed pretty consistent. I’ve really focused on working with really good advisors for grad school, and especially with people who would let me explore other dimensions of synthetic biology, of SynBio, outside of lab. I did a lot of work on science communication all throughout my career and on risk and responsibility. So one thing that Rice has been really great at is that the people — the students especially at the Systems, Synthetic, and Physical Biology program — they really encourage interdisciplinary work and they’re very involved in the social dimensions of SynBio. Yeah, I can’t recommend Rice highly enough. I love that place. I was in Houston for a decade. It’s been really a wonderful place to call home.

[00:04:55] Paul Reginato: Very cool. Very cool. So today we’re gonna talk about a lot of the research that you’ve done at Rice from your PhD into your postdoc and it has sort of evolved from specifically technical research into a much more holistic approach. Although from what you just said, it sounds like some of that more holistic stuff was there all along the way.

[00:05:18] Kiara Reyes Gamas: Yeah. Yeah, and I can talk a little bit more—

[00:05:19] Paul Reginato: Yeah, it’d be cool to hear about that. So let’s maybe start with your PhD work. And you can also share what you were doing in parallel to your PhD work as well. But you were in the lab focusing on building RNA-based memory systems, right? For tracking horizontal gene transfer. Maybe you can tell us a little bit about what horizontal gene transfer is to start with and why you and your collaborators wanted to build the tool to track it, and then we can talk about RNA-based memory systems and how that works.

[00:05:50] Kiara Reyes Gamas: Yeah, so horizontal gene transfer is any sort of gene exchange between two organisms that is not through sexual or asexual reproduction. And it’s a totally natural process that happens especially with microbes. They engage in gene exchange with each other to survive the selective pressures that come from living in very dynamic and very difficult environments. So this can happen in a number of ways, but there are three big ones. There’s transformation, where an organism will literally eat or uptake DNA from the environment. And then instead of using it for parts for its own DNA, it’ll end up keeping the genetic sequence around. Two is transduction, where a viral infection ends up not killing a cell and some of those viral genes end up being incorporated into that cell’s DNA. And then three is conjugation, which is physical contact between two cells, and they’ll actually send DNA through a protein bridge between them. It’s nuts. And that’s the one that I focused on a lot in my thesis work.

[00:06:43] Paul Reginato: So just to hover on that conjugation one — that’s pretty cool. You’re saying the organisms actually form a bridge made of protein between them and then through that bridge they pass DNA.

[00:06:57] Kiara Reyes Gamas: And sometimes they’ll pass proteins and RNA, but yeah. So a microbe will literally make a pilus and send it out, and that’ll attach to a recipient microbe’s cell wall. They’ll just come together and that’ll expand and form like a bridge between them, and through that space you can send over different things. There’s a bunch of protein complexes that’ll literally grab onto the DNA and shuttle it over to the other cell.

[00:07:26] Paul Reginato: Wow. So this is a very active process. The microbes really want to do this. And this is happening between microbes of different species. This isn’t just microbes in the same family.

[00:07:37] Kiara Reyes Gamas: Yeah, it mostly happens between microbes that are closely related to each other, but it also happens between very distantly related ones too. But I think the other thing is that it doesn’t just happen in microbes. It happens in macroorganisms — I guess that’s what we call species that aren’t microbial. We have quite a bit of viral DNA in our human genome that has just been acquired over evolutionary time just by surviving infections and keeping that DNA around.

[00:08:08] Paul Reginato: And in my understanding, a lot of the genes involved in human development and in our brains — some of the receptors, if I’m correct — I think are of viral origin.

[00:08:21] Kiara Reyes Gamas: Yeah.

[00:08:22] Paul Reginato: Anyway, that’s a little off topic for today. Today we’re mostly focused on microbes. And so I’m curious — microbes are out there exchanging genes, exchanging DNA, they’re building these pili to exchange DNA actively — what purpose are they doing it for? What effect does this actually have on the way that they live?

[00:08:46] Kiara Reyes Gamas: So if you imagine — I think a really easy example to understand is: imagine you’re a microbe in a wastewater treatment plant, and then your neighboring microbe finds an antibiotic resistance gene, and there are increasing levels of that antibiotic in the wastewater, right? Maybe you live close to the sewage of a hospital. So if you can acquire that gene and start producing the protein that is encoded by that gene, then that’s a really good survival advantage. So being able to incorporate DNA from the environment and from other organisms can be very helpful. And also there are ways that cells will weaponize this and will send bad bits of DNA into other cells to kill the other cells and reduce the competition around them, right? So it’s a whole arms race that happens. And I think a lot of it is also — if you’re lucky enough to just survive a viral infection, it might not even pose any advantage or disadvantage. It might just be like an extra bit of DNA you’re just carrying around. If it’s not bad for you, then there’s not really a selective pressure to get rid of it.

[00:09:51] Paul Reginato: Wow. So it reminds me a little bit of the way that—

[00:09:56] Kiara Reyes Gamas: Yeah.

[00:09:56] Paul Reginato: Humans — we can teach each other things. If I know how to do something useful, I can tell you how to do it. I could also lie to you and trick you—

[00:10:03] Kiara Reyes Gamas: Yeah. Yeah.

[00:10:04] Paul Reginato: —and I could also tell you something that you might not care about but lives rent-free in your brain for some reason.

[00:10:10] Kiara Reyes Gamas: Yeah. I think that’s a good analogy. We know a lot about it — we know a lot about the biochemistry — but the dynamics are really complicated, I think is the big thing.

[00:10:19] Paul Reginato: Okay. Yeah, so tell me more about the dynamics and the tool you built to measure these dynamics.

[00:10:25] Kiara Reyes Gamas: So for example, horizontal gene transfer frequencies are really hard to calculate, and they vary wildly depending on the method that you use to track. For example, for conjugation, you can literally put one population of bacteria with a specific plasmid that you’re trying to track next to another population of bacteria. You let them conjugate and maybe that plasmid has an antibiotic resistance gene. Then you’ll plate them later and see how many you get. That’s kind of the classical way of doing this, right? So that’s not very precise, and it also requires culturable microbes. So the estimated frequencies that we have of conjugation — or really any type of horizontal gene transfer — will vary a lot depending on both intracellular factors and also environmental factors. So it’s very difficult to determine whether a lab measurement will be representative or predictive whenever we’re looking at complex microbial communities in soil or wastewater. And this is a huge issue because horizontal gene transfer is of course something that people are very worried about whenever we’re introducing new organisms into the environment. And if we don’t really know what microbes are participating in it, or under what conditions it happens, or what makes it happen more or less, or what impedes it — then it’s very difficult to even assess the risk of adding new DNA into the environment.

[00:11:49] Paul Reginato: There’s a linkage here to any effort that we might make to use engineered microbes in the environment for whatever purpose, and we’re concerned about how the engineered portion of those microbes might actually spread to other—

[00:12:04] Kiara Reyes Gamas: Or the non-engineered ones, right? If we’re just adding a new microbe into a new community, how is that genetic information going to spread into the new environment? And then we’ll get into this later. But I can tell you a little bit about the technology that we developed.

[00:12:18] Paul Reginato: Let’s go into the technology and then we can zoom back up.

[00:12:21] Kiara Reyes Gamas: So this is a huge project between people in three different labs, and I wanna shout out my co-authors especially. So Prashant Kalvapalle, August Staubus, Matthew Dysart, Lauren Gambill, Li Chieh Lu, and Travis Seamons, and Lynn Fang, as well as the PIs that led this — so that’s Lauren Stadler, Joff Silberg, and James Chappell. So for our initial study, we developed a method called RNA-Addressable Modification, or RAM for short. And I like abstracting this a little bit and thinking of RAM as a stamp that can be used on a microbe’s passport. So if you think about what a passport is, it can record information about where its owner has been by being stamped whenever they travel, and then later on you can read the passport to see a record of where its owner has traveled. So similarly, we’re using the 16S rRNA as a passport because it’s a type of RNA that has variable regions that can help us identify which microbe has that particular sequence — kind of like the ID page. And it also has conserved regions that we can look for to actually find the passport inside all of the cellular machinery and stamp it. So RAM uses a plasmid that can be transferred through conjugation from a donor cell to a recipient cell, and that plasmid encodes for a catalytic RNA. This is a type of ribozyme — so that’s a piece of RNA that acts as an enzyme. So this catalytic RNA is transcribed. It’ll bind to a specific complementary sequence in the conserved regions of the recipient cell’s 16S rRNA, and then it’ll literally splice in a barcode. It’ll stamp the passport by cutting that RNA, and then adding a piece of RNA downstream of the sequence that it’s found. So what we did in our initial study is we took some wastewater back into our lab. We added a donor cell containing the plasmid that we wanted to track into the sample, let it conjugate into the microbial community overnight. And then we later sequenced the whole community RNA to look for all of the 16S rRNA. We look for the unspliced — so basically everybody’s passports, who’s in here — and then we looked at the spliced community. So who received the plasmid through conjugation? Who participated in this type of horizontal gene transfer? In our first study, we found that 50% of the wastewater microbial communities — so this is like 140 out of 279 members — had detectable spliced signal, which is huge. Being able to detect so many instances of this type of horizontal gene transfer just in one experiment was really great. I was the computational design lead on my team, so my job on the initial study was to make sure that this catalytic RNA actually found the passport in the microbes that it entered, and I took this further in my own thesis work by writing a computational program called RiboDesigner that can make custom catalytic RNAs to tag the 16S rRNA of specific microbial community members.

[00:15:04] Paul Reginato: Wow. Okay, so let me try and recap that. You have this catalytic RNA that carries a barcode that tells you that it came from some origin — like that’s your origin microbial species. And then when that species conjugates with another species, it passes DNA that expresses this RNA, and then it puts that into the new microbe’s rRNA. And then when you sequence the rRNA, part of that rRNA sequence tells you what the recipient microbe is, because that’s its passport. And then this other synthetic sequence may be there, which tells you that it has received conjugation from that original microbe. And so this lets you know which species of microbes received conjugation. Is that right?

[00:16:05] Kiara Reyes Gamas: Yeah, so which are compatible with this specific plasmid, this specific host cell. So yeah.

[00:16:12] Paul Reginato: And is it also able to tell you how efficient the conjugation was?

[00:16:17] Kiara Reyes Gamas: Yeah, somewhat. You can use it as a proxy, and I know we’re developing new methods to determine dynamics a bit more, but in our initial study we just used how much RNA we saw that was spliced over the baseline amount of RNA to get a proxy for frequency.

[00:16:35] Paul Reginato: Got it. And then the new iteration that you developed is designed to only stamp certain kinds of passports. Is that right?

[00:16:44] Kiara Reyes Gamas: Kind of — so it’s two things. Part of that program looks for shared motifs in a given dataset of 16S rRNA sequences and then designs catalytic RNAs that can tag the most organisms in that dataset. So what you can do is you can either make universal designs for a whole kingdom. So we made a universal bacterial design. We made an algal design — we would use 18S rRNA to do a design just for fun. But you can also use it if you give it a dataset of things you do wanna target and a dataset of things you don’t wanna target — you can make sure that you find designs that work really well for the first group and really badly for the second. And we were able to test that in vivo to make sure that it worked. Whenever we made a catalytic RNA that is specific to the Pseudomonadales order bacteria but not to the Enterobacterales order bacteria — so these are two really big orders in wastewater — we found that the ribozyme only really tags the Pseudomonadales and then completely avoids the Enterobacterales rRNA, even though they have similar levels of transcription.

[00:17:50] Paul Reginato: Got it. And why would you wanna tag only a subset of the microbes that are receiving conjugation?

[00:17:59] Kiara Reyes Gamas: Yeah. You can think of actually one thing that you can do as a kind of microbiome engineering. There’s a subset of this work where people have been looking at delivering kill genes like very selective antibiotics, right? So if you have a pathogenic species that’s very similar to a non-pathogenic species that’s really good to keep around — instead of having a broad-range antibiotic that kills everything, you can have a kill gene in your catalytic RNA that splices in only under the sequences it recognizes as pathogenic.

[00:18:39] Paul Reginato: I see. So instead of just a stamp in the passport, it’s actually delivering some kind of function.

[00:18:45] Kiara Reyes Gamas: Yeah. So instead of doing a random barcode sequence, you can just deliver a gene.

[00:18:50] Paul Reginato: And the reason you want it to be targeted is you might not wanna deliver that function to every microbial species — just specific ones.

[00:18:59] Kiara Reyes Gamas: Exactly. Exactly. And we’re playing to our strengths here because we’re using RNA. A lot of similar technologies will use DNA, which is great — it’s very permanent. But because we’re using RNA, we don’t have to use a lot of protein machinery, which is often used to modify the DNA in a recipient cell and can be very difficult. Those systems need a lot of accessory proteins and they need folding and it might just not work in every microbe. So I think the reason we got such a large proportion of signal in our initial study is because we’re using this RNA technology.

[00:19:32] Paul Reginato: It’s just a ribozyme — it’s one RNA. Very cool. And so now we’re starting to talk about microbiome engineering, and some of your more recent work is really focused on microbiome engineering and approaching it in a more holistic way. You’ve recently published a policy paper and you’ve organized a webinar series on engineered microbes for environmental release. So I’m curious to know what motivated this shift in focus for you, and also what preceded it in terms of other work you were doing alongside your technical PhD work that set you up to do this kind of very interdisciplinary — but also holistic — work spanning technical, community, communication, and policy dimensions.

[00:20:25] Kiara Reyes Gamas: So honestly, I don’t see it as a shift in focus. I see it as a way to bring my expertise in a space where I have something to contribute. I’ve been participating in conversations around “who decides” when talking about synthetic biology interventions all throughout grad school, where I brought my expertise on horizontal gene transfer to demystify it a little bit. And even during my undergrad I’ve advocated for international students and the environment. I think part of the work of being a scientist is to help your community, and I see a lot of possibility with environmental synthetic biology to solve pollution, or mine metals more sustainably, or increase biodiversity in endangered species. There’s just a lot of extremely exciting near-future applications for synthetic biology to deal with in human and environmental health that we really don’t have good solutions for otherwise. I think it’s really important to pursue these technologies because even if our human activities and mass industries stopped causing harm all of a sudden, we still have a truly inconceivable amount of pollution and waste and issues to deal with. But how can we make sure to do this while both reconciling with a deep history that we’ve inherited from genetic engineering and also with the use of biotechnology for the profit of companies at the expense of communities? Science has been used to hurt people over and over, and I think it’s at best ineffective and at worst extremely harmful to keep doing science as usual without considering the ecological and human context where our technologies could end up. We’re living in a time with very public and wide distrust of science, and we need to do our best to actually earn that trust from people by showing that we’re working with people and not in opposition to people. And I think one of the worst attitudes I still see in science is that people who think that people are anti-GMO just need to be more educated and then they’ll be okay with it. And I think that totally misses the point. I think a lot of people are understandably upset about how GMOs have been used to promote the interests of monocrop, big-ag companies while destroying the genetic diversity of heirloom crops. And also a lot of people are frustrated with how technologies like AI are being shoved down their throats for the benefit of a few billionaires without their consent. So to do effective science, we really need to be questioning a lot of the ways that science is done.

[00:22:31] Paul Reginato: The Climate Biotech Podcast is powered by Homeworld Collective, a 501(c)(3) nonprofit, unlocking biotech solutions for planetary health by fostering community, building knowledge, and directly supporting early-stage research. We are always looking to connect with scientists, innovators, and funders who want to accelerate progress in this space, whether in our current program areas of critical minerals and greenhouse gas removal, or in other application areas. If that’s you, reach out to us at hello@homeworld.bio.

[00:23:03] Paul Reginato: Maybe you could give some examples of where a technology that could be used in the environment — an engineered microbe in the environment — could be really beneficial but also could have some risks associated with it. There are directions that we don’t want it to go — so we can get a flavor for what this conversation looks like.

[00:23:25] Kiara Reyes Gamas: Yeah. Absolutely. I think a good example would be plastic-eating microbes, actually, because you think, “Oh yeah, just plastic-eating microbes, that’s great, that has no downside — we’re flooded with plastic.” But imagine if you release a microbe that can eat plastic into the environment and then it starts eating all of these PVC pipes, right? Or it starts eating ship parts. So it might not have a great interaction with human communities either. So there’s a balance, right? Where we have so much waste, but it’s very localized in these specific environments. And whenever you’re releasing something into the environment, you need to think about how much that would spread.

[00:24:03] Paul Reginato: Got it. And there are a couple of themes in some of your recent work — in your recent policy paper and webinar series — that I’d love to explore a little deeper. So one is this notion of using ecology and evolutionary biology to inform science and the risk assessment and regulation for engineered microbes in the environment. And the second is integrating non-technical communities into environmental synthetic biology research and governance to help with decision-making. So maybe we can talk about those — they seem like two sides of the approach. So why don’t we start with the first one. Where do ecology and evolutionary biology come in when we’re thinking about engineered microbes for environmental release?

[00:24:45] Kiara Reyes Gamas: I think both are really essential to the environmental introduction of species into a new environment. And I say species because I think this applies to all kinds of species, not just engineered ones. Whenever we’re making an organismal intervention into a new environment, we really should be considering the ecological context. So if we’re asking to add something into a new environment, we can learn from invasive species research — we have decades and decades of data on purposeful introductions of new organisms into new environments — where has that gone wrong, and where has it gone right? There are a lot of successful interventions of non-native species for conservation or environmental protection. So we have quite a large body of work in ecology to learn from as we plan to do the same with engineered microbes. Evolutionary biology is also essential because we’re not just dealing with a chemical introduction into the environment. So if I use a chemical to clean up a contaminant, any leftover chemical doesn’t disappear — it just stays there and continues its chemical reactions. But if I add a microbe, I’m adding a living organism, and that’s subjected to the same evolutionary pressures as any other living being. So that means it should only really keep around the genes that it finds useful for as long as they’re useful. So if we’re cleaning up a contaminant, that microbe should only have the pressure to keep the gene that helps it eat that contaminant while that contaminant is still around. And once it’s fully cleaned up, that gene is just dead weight and the microbes containing it have a strong selective pressure to not keep it around anymore. So we have a lot of studies about this on non-engineered microbes, and we have to look at ways where engineered ones are similar or different and under what conditions this happens. Ecology and evolutionary biology are both fundamental to making informed risk assessments, and understanding horizontal gene transfer is also essential for this.

[00:26:34] Paul Reginato: And when we make these decisions — what kind of experiments or new knowledge about the ecological and evolutionary biology of engineered organisms could we obtain that would help us make better decisions?

[00:26:56] Kiara Reyes Gamas: And you’ve hit on a difficult point here. We have a lot of engineered microbe data from labs — inside contained spaces — but we don’t have a lot of it from the environment, because there have actually only been very few engineered microbial interventions in the environment or even field-tested. And I think there have only been about eight commercialized engineered microbes, half of which are for agricultural use. So for example, there’s Pivot Bio’s nitrogen-fixation microbes that can replace some nitrogen fertilizer use. There’s a thing called NOGALL, which is crown gall prevention for stone fruit trees. And then three of those are for consumer use — so that’s a probiotic pre-cool and a sugar-to-fiber probiotic, and then Lumina’s cosmetic teeth-whitening toothpaste.

[00:27:40] Paul Reginato: Interesting.

[00:27:41] Kiara Reyes Gamas: Yeah, so there hasn’t actually been that many of these things. And part of it is because we face the situation where we want to show that it works and we want to show that it’s safe, but there aren’t spaces that are big enough or representative enough — while also not being connected to the environment — to show these things. So it’s a vicious cycle where we can’t generate the data to show that these are safe or not safe, because there aren’t any spaces in which to test this. So there’s no way to show that it actually does what it’s supposed to do in a representative environment. So I think one really important thing that I’d love to see is intermediate, large, enclosed spaces to field-test microbes before release. And again, not necessarily because they’re unsafe, but because we just need to get data to prove that, right? I’d love to see enclosed testing sites — kind of like the ones that some large corporations or militaries have — that biotechnologists could rent out to test their microbes.

[00:28:42] Paul Reginato: Very interesting. And so on the flip side, when we talk about making decisions in conversation with non-technical communities — what does that actually look like? Not just as a checkbox, but like meaningful community integration that actually shapes what happens.

[00:29:02] Kiara Reyes Gamas: Yeah. I think one of the things we need to do is include communities as partners in the research. Informed consent is basic, of course. In this context it’s the idea that a community must have a say on whether a technology is deployed in their backyard or not. And if they don’t want it — even if we as scientists are like, “Oh, you could be mining metals more sustainably or cleaning up a bunch of pollutants” — if they don’t want it, we need to respect that, even if we think it’s for the greater good of the environment. But ideally, if we’re making an engineered microbe to deal with a problem in a specific location, we need to include people from that location in the actual research and development of the microbe. So they need to be included not just after the fact, but as co-creators and researchers. And this is not just good for the sake of being good — of course it’s the right thing to do — but it’s also important to make products that actually succeed. So Dr. Emma Frow presented a report that she co-authored with Dr. Dalton George in our seminar series, where they look at case studies of engineered organisms through the lens of social containment. And if you think of biocontainment as how a GMO is kept separate from the environment, then social containment is how that GMO aligns — or doesn’t align — with the cultural and social practices of humans living in the place where it’s deployed. So it’s so expensive to bring a biotech product to market — it would be truly the lamest and most preventable thing for it to fail just because people didn’t like it or because it clashed with their cultural values. One example I like to talk about is Golden Rice. So this is the type of rice that was engineered to contain beta-carotene. It was developed by an organization in the States to solve malnutrition in countries where rice is a staple food. And this is a story that’s told a lot in science circles because this big corporation made it and said, “Look, we solved malnutrition with this engineered rice.” And people in the countries they went to were like, “We don’t really want this. We didn’t really ask for this.” And in science circles it’s framed as, “Oh wow, look at how these people could solve malnutrition if they weren’t so scared of GMOs and how we need to educate people or whatever.” But this was a crop that was developed by an American corporation to fix a problem with no local initiative, consent, or involvement. And it’s not as easy as saying that having someone from those communities in the research would have automatically made it widely accepted, but it certainly doesn’t help that this is a technology that was forced upon people who had no involvement in the research or the deployment of it.

[00:31:33] Paul Reginato: Got it. So when I asked the question, I was saying “integration of non-technical communities,” but that’s actually not what you mean. It could be integration of communities who do have a close and even technical relationship to the deployment environment — who are actually doing technical research, not just over in some other country as part of some other community — but actually doing the technical research in a way that genuinely brings engagement from individuals in the community where it will be deployed, who are researchers and scientists able to participate in the actual technology development.

[00:32:18] Kiara Reyes Gamas: Yeah, because even if they’re non-technical, I think everybody has expertise. Even if people don’t know the specific PCR or the specific assays that we do in lab, what they do have is deep knowledge of where they live and the place where we’re saying we want to put these things. So I don’t think in terms of “non-technical communities” — I think everybody has expertise. I think science should be better at accepting people who might not have the specific scientific training, bringing them to the table, bringing them up to speed, and understanding how valuable that experience is. If I’m making a microbe to clean up an oil spill — some sort of bioremediation — and I don’t understand the local seasonalities or anything, it’s just gonna get washed away. That’s a huge oversight on my part.

[00:33:04] Paul Reginato: Yeah. Yeah, very good. Very interesting — and fantastic and obvious point.

[00:33:12] Kiara Reyes Gamas: Yeah, I think that’s kind of the sad thing — as scientists we’re scared of touching any sort of social space because it’s, “Oh, it’s not my expertise. I don’t really feel comfortable with it. I don’t wanna mess it up.” But we really need to think about this as soon as we realize we’re going to make a technology that is going to be used by people. We need to start thinking about how it’s going to interface with the cultural values of those who will use it. We need to remember a core rule of engineering: meet with your client before building your product. If we’re saying that we’re an engineering discipline, then we should really be using engineering design.

[00:33:56] Paul Reginato: So a lot of this is forward-looking, right? In terms of how we should be doing things. I’m curious — you said there are only about eight engineered microbes that have actually been deployed as products. How does regulation work for those organisms? How does regulation work now, and do you think it will need to adapt?

[00:34:20] Kiara Reyes Gamas: Absolutely. I think a lot of these conversations end up being very theoretical, partly because scientists are moving with a lot of care and caution on these technologies, but also because regulation is very hard to navigate. So depending on your microbe’s use case — at least in the States — you’ll be regulated by either the FDA, the USDA, or the EPA. And there have been a lot of products that have gotten stuck in this regulatory landscape because they didn’t really think about how or through which agency their product would be regulated. There’s a lot of redundancy, and also a lot of focus on whether the engineered organism has recombinant DNA or not — meaning if an organism has DNA from multiple sources. Which is a somewhat silly distinction in this age, where you can use very precise gene editing to make all of your modifications within a cell without incorporating any outside DNA, right? So I think how scientists have responded to a lot of this historically is they’ve been working on biocontainment measures to make sure that any introduced genes that we add into the environment don’t get transferred into environmental microbial species. But honestly, I think these measures are not always the right conversation. I recently talked to Dr. Victor de Lorenzo and he said, “Why are we talking about making things that are so scary that they need to be contained?” And I totally agree. We’re talking about these technologies beyond conventional containment — we’re making something that can eat an oil spill in the ocean. This is something that is directly meant to interface with the environment, not be biocontained. We should really think about how we can design these organisms so that when they are released, and if there is horizontal gene transfer — and there will be, because life finds a way — the genes that we’re adding won’t cause harm to people or the environment. I think one specific, very easy thing is not adding organisms with antibiotic resistance genes into the environment. I think the other way regulation needs to catch up is that there needs to be the same scrutiny toward any microbe to be released in the environment — not just engineered ones. Because if the problem is adding extraneous DNA into the environment that can be incorporated, then whether it’s engineered or not doesn’t really matter biologically speaking. If I’m adding a natural microbe from somewhere else into a new environment, that’s actually quite a lot more genetic information than if I were to engineer a local microbe from that environment and only add one gene that we’re interested in adding in that context. So I hope regulation starts looking at how any type of introduced microbe follows best practices based on their genes, and also the environmental context of where they’re planned to be introduced. And hopefully also regulation that takes into account community consent.

[00:37:07] Paul Reginato: It’s a really interesting reductio ad absurdum that you showed there — with the difference between introducing a native microbe with one engineered gene versus a totally non-native microbe from somewhere else that has a whole genome—

[00:37:23] Kiara Reyes Gamas: Yeah, hold on — all of its little plasmids.

[00:37:26] Paul Reginato: —might not be engineered, but it isn’t native to that environment and could transfer into any of the organisms there. Okay, so for our listeners, we always like to try to get down to something actionable. So if someone is interested in the kinds of problems that you are working on and they’re just getting into the space now looking for ways to contribute — what are some immediate challenges that they could address across both the technical and social dimensions?

[00:38:00] Kiara Reyes Gamas: I’m gonna give a bit of a cop-out answer, honestly, just because I’m only talking about my specific expertise and what I have seen in this work. But there are a lot of different dimensions of synthetic biology and especially environmental synthetic biology. So me and a few other early-career folks — Dr. Alicia Johnson, Dr. Kelly Chappell, Dr. Dalton George, and Dr. Jordan Ez — who have been frustrated with the attitude of the field, have come up with the idea of an interdisciplinary seminar series that can bring people from all kinds of disciplines to weigh in on how and whether engineered microbes could be used in the environment. And we have voices not just in synthetic biology, but in microbial ecology, environmental justice, biotechnology governance, indigenous data sovereignty, and on alternate ways of doing science. All these talks are recorded and available on YouTube, so even if you can’t make the live session, if you’re an established researcher or a future researcher, you can have a crash course on these multiple dimensions of your work and contextualize it and come up with ideas. I think there’s not really a single actionable thing you can do right now — I think it’s partly about becoming informed on the language and on these other dimensions that we are not trained in as scientists.

[00:39:17] Paul Reginato: Okay, thank you. So we’ve now gone through most of our discussion. We’re gonna progress into some questions that we ask all of our guests. We call them our rapid-fire questions, and they’re intended to provide inspiration and a little more individual personality for the person we’re interviewing. So the first question is: what is a single book, paper, art piece, or idea that blew your mind and shaped your development as a scientist?

[00:39:48] Kiara Reyes Gamas: This is a deep cut, but the Glowing Plant Kickstarter project. I know it totally failed. I don’t know if you know about this, but there was a Kickstarter project — I wanna say around 2014 — where they discovered the idea of a gene gun and thought you could engineer plants really easily. And they were like, “Oh wow, we could insert luciferase into plants and then make trees that can act as street lamps.” And they made this huge Kickstarter project, and they were like, “Yeah, and if we hit this goal, we’ll give you a glowing rose and everything.” Turns out it’s not as easy to engineer biology as they thought. But I think that idea — that vision of using trees as street lamps — really shaped my idea of what synthetic biology could look like. Kind of a reimagining of our relationship to nature.

[00:40:28] Paul Reginato: Very cool. I remember being inspired by that too, actually when I was—

[00:40:32] Kiara Reyes Gamas: Yeah, it’s great. I wish it wasn’t as hard. I wish it was as easy as they thought it was.

[00:40:38] Paul Reginato: Okay. What is the best line of advice that a mentor has given you?

[00:40:42] Kiara Reyes Gamas: Yeah. This is mostly for those choosing a lab in grad school. Choose a great advisor over a perfect project.

[00:40:48] Paul Reginato: Very good. I would agree, definitely — because projects can easily change and you’re gonna get new ideas and you’re gonna be inspired by those around you.

[00:40:57] Kiara Reyes Gamas: Yeah. And you’re gonna love your project, and you’re gonna hate your project, no matter how good it is. Might as well make sure you have someone that you’re very compatible with when you’re working with them.

[00:41:07] Paul Reginato: Okay. If you had a magic wand to get more attention and resources into one part of biology — and it can’t be the specific research that you work on — what would it be?

[00:41:19] Kiara Reyes Gamas: I think it would be awesome to have more funding dollars into environmental synthetic biology in general. Honestly, I know there’s such a massive amount of waste, and I wanna see more money into these technologies that can help a lot, even if they’re harder to commercialize.

[00:41:32] Paul Reginato: Give us a hot take. What is one view that you hold related to climate and environmental biotechnology that you think some others in the field might disagree with?

[00:41:41] Kiara Reyes Gamas: I think we need to stop obsessing with scaling up, and we need to focus on scaling outward — or maybe even not scaling at all — because biology doesn’t make one silver bullet for every single problem. It makes thousands of potential solutions for very specific, small problems. So as synthetic biologists, we really should be playing to biology’s strengths.

[00:42:01] Paul Reginato: And so when you say scaling out or not scaling, you mean like very place-based?

[00:42:07] Kiara Reyes Gamas: Yeah. I think having one huge bioreactor is great if you want to 10x your money or whatever. But I think if we’re solving climate issues or sustainability issues, I’d rather have smaller local reactors that can bring profit and good things to the community — and not just make money.

[00:42:30] Paul Reginato: What is one aspect of personal development that you think biotechnologists need to spend more time on?

[00:42:36] Kiara Reyes Gamas: Yeah. I said this already, but I really want to move past being hammers looking for nails. Especially if we’re claiming to be an engineering field, we really need to start focusing on needs first and technology much later.

[00:42:51] Paul Reginato: Love the problem, find something that matters and figure it out.

[00:42:54] Kiara Reyes Gamas: Yeah. And instead of being like, “Oh, I have this thing that I spent so much time on” — and I know it’s tempting because I know how hard it is — if you get something that works, you’re like, “How can I apply this in every single direction?” But we really have to stop trying to force something that is just not gonna work in a particular context, or that people don’t want.

[00:43:13] Paul Reginato: I couldn’t agree more. And that is a big part of the philosophy we have at Homeworld — being problem-centric and trying to identify problems where we can contribute. Something that might be a very different big-picture problem than we’ve ever been able to contribute to — but when you break it down, sometimes you see something important that is actually within your means. And that is a very satisfying and important thing. Okay. We are at the end of our time, Kiara, but thank you so much for joining me today. It’s been fascinating to talk to you, and I love the spectrum of work that you engage in. It’s really cool to see someone who is deep in the weeds building RNA devices to make measurements in wild populations, and who is also leading the way in the conversation about how we can actually bring these things into the world in a way that is just and equitable and effective. So thank you for your work, and it’s been great to see you. I hope to see you again soon.

[00:44:18] Kiara Reyes Gamas: Thank you so much for having me.

[00:44:20] Paul Reginato: Thanks for tuning in. I hope this has been educational and inspirational for you as you navigate your own journey to bring the best of biology into planet-scale solutions. I’ll be back soon with another conversation. In the meantime, you can stay in touch with Homeworld on LinkedIn, X, or Bluesky. Huge thanks to our producer Dave Clark, along with Paul Himmelstein, Kayla Sims Austin, and Macario Sar Sozo for making these episodes possible. Until next time, I’m Paul Reginato, and this is The Climate Biotech Podcast.