Meet the Microbiologist

• Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia

  Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s.  Links for the Episode  New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper.  Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article.  Manuel Martinez Garcia’s Lab website.  How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute. Take the MTM listener survey! Watch this episode: https://youtu.be/CHCMO74_gIY Ashley’s Biggest Takeaways There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources.  Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago.  Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time. It can also provide key insights to changes in biodiversity. Featured Quotes:  Motivation for the Research Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet.   And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different.  [The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses.  The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less.  And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present.  We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically].  Sample Collection We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores.   And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany.   And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically, I said, ‘Hey, I think what you have in your research is a valuable material that that can provide interesting answers for climate change and microbiology.’ And they say, ‘Well, that's interesting. And we never thought about that.’ And then we started a collaboration to dig into these questions.  Shipping the Ice Cores We had a meeting after one of the first pandemic lockdowns, when they allow [me] to travel. I went to Bremerhaven to have a personal meeting with the team. And we decided to ship some samples to Spain.   They arrived frozen and very well packaged and preserved in an isolated container. But it was really surprising to see that that they were delivered in the same compartment with a dry ham. That was a that was a funny story!  Sample Preparation When we received the samples, the first thing was to basically decontaminate the surface of the [ice]. Because when you unpackage, you have an ice core, pieces like a half meter. And then, we have to think that this ice core has been manipulated by different groups, different people. And you have to decontaminate the surface of the ice core in order to just have the center of the ice core for the for the investigation.  And basically, we adapted a protocol in order to make sure that we didn’t have cross contamination from the rest of the from the surface.  So, what we did was we melted the center of the core—well, in fact, different parts of the core with different ages, from 1000 years old to 200 years old—and we melted in a very dedicated laminar flow hood that we have in a clean room. And then, we extracted the DNA from that piece. And in our case, the amount of DNA was so little that we had to amplify with some molecular techniques in order to have [enough] copies of this genetic material to do sequencing.  Sample Analysis I will say that we are in the middle of the project. We had, like, 2 years ongoing for the project.  The most surprising was 2 things. One, in the sea water, beneath the Antarctic, we discovered a very autoctonos (indigenous) viral community that was quite different from the rest of the world, I will say, from the rest of the ocean. So, I think this viral community is quite adapted to infect the microbes that are living in this peculiar environment beneath the Antarctica ice shelf.  And these viruses were carrying some genes that we think are very important for microbes. We call these genes auxiliary metabolic genes. And these genes are very important because somehow the viruses provide these pieces of information, of DNA material, to microbes that are driving important ecological roles, like, for example, carbon fixation.  It's very important, because carbon fixation is probably the primary step in all ecosystems—to provide food for the rest of the organisms. And if this is altering, or we are altering it with different factors—like temperature increase, like melting of the ice—its going to change these patterns and the rate of carbon fixation. This is going to produce a deep impact for the rest of organisms.  We are still investigating, but we think that it's interesting to think that microbes that live in our ocean now are responding to stressing factors like increasing temperature and also acidification by different ways. In fact, it is unclear—it is a very hot topic and a very hot question—because we don't know for sure what the fate of these microbes in our oceans is going to be. For example, people think that we are going to lose biodiversity. There are some hypotheses that say that heterotrophy is going to be more predominant in the sea water. But it's unclear, because we don't really have fossil records that can compare the past to the present, and this is what we can provide, or at least potentially provide. We can say, ‘Hey, we can go before the industrial revolution, before the CO2 increase, and try to compare series of different samples until the present in order to see if, for example, heterotrophy, or microbes that are heterotrophs, are more predominant in modern samples compared to unseen samples.   

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• Revenge of the Microbes With Brenda Wilson and Brian Ho

  Episode Summary Mother-Son duo, Brenda Wilson, Ph.D., professor of microbiology and the Associate Director of Undergraduate Education in the School of Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and Brian Ho, Ph.D., researcher and lecturer at the Institute of structural and molecular biology, a joint institute between the Department of structural and molecular biology at the University College of London and the Department of Biological Sciences at Birkbeck University of London discuss the inspiration and motivation for their recent book, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle, 2nd Edition, emphasizing the global nature of AMR and providing a unique perspective on what is needed to solve it. Ashley’s Biggest Takeaways: Dynamics surrounding the AMR crisis are complex and require an understanding of many different perspectives, including those of the farmers, health care professionals, pharmaceutical companies and individuals, in order to foster true and lasting global collaboration on the issue. Point-of-care diagnostics are critical to improving treatment decisions and reducing hospital costs. Better communication and education are needed in order to rebuild trust in scientists and institutions. Continuous research is necessary, as AMR will continue to evolve. Citizens are a key piece of the puzzle when it comes to pushing for change and supporting solutions to AMR. Featured Quotes: Wilson: “I'll start with actually my Ph.D., which is talking about bacterial antibiotic biosynthesis. And so, I did some work in that arena, but since then, I've actually been working on bacterial protein toxins. These are very potent eukaryotic modulators that when bacteria get into the host, they release these proteins that are very large, that are able to interact with very specific cells. They actually get inside the cells—into the cytosol—and then they affect various signaling pathways in the host that can go anywhere from killing the cell to modulating some of the processes that the cell undertakes, even differentiating them and causing cancer. So, one of my main focuses in my lab has always been to understand the structure and function of these toxins, to understand how they affect the eukaryotic cell system. And then now that we know a lot about them, we're actually moving more into the direction of trying to basically use them as biologics. We have some platforms that we call bacterial toxin inspired drug delivery, where we're using the mechanisms of how they work and their exquisite specificities to be able to actually use them for therapeutic applications.” Ho: “I got my start doing molecular genetics, actually, with John Mekalanos at Harvard, and I was kind of at the ground floor of the seminal work looking at the Type VI secretion system. And so, I got a front row seat to the kind of discovery and a lot of the initial understanding of the system. And I've kind of taken that work and expanded beyond it to look at kind of the ways different bacteria interact with each other within microbial communities. So my current work is looking at both DNA conjugation as well as the type six antagonism, and how the bacterial interactions kind of work together to build a larger population dynamics and interface with like the hosts that kind of house a your microbial communities.” Antimicrobial Resistance Wilson: “In 2005 [when the first edition of Revenge of the Microbes was written], there was very little activity or understanding about antibiotic resistance and how important it was. Outside of the field, doctors were encountering it. But oftentimes what was happening is they just said, ‘Oh, well, we'll just find another drug, you know.’ And pharmaceutical companies, they were recognizing that there was a problem, and they would go off trying to hunt for new ones. And then right around the late 90s, there was a big impetus, because they thought, ‘Oh, we, we have a miracle here, because we now do complete genomes. We can get out the comparative genomics and all the high throughput things, all the animations,’ and that this would lead to many more new discoveries. And I think the pharmaceutical companies were very disappointed, and they started backing out of what they deemed a huge commitment. Two decades later, people already were starting to get aware, at least in the field, and even the industry and the physicians. People were getting aware, but I think that they were stumbling, because of their silos, in trying to get interactions with each other. And I think part of it was that they felt that, ‘Oh, we can try to solve it ourselves.’ And in reality, this is a problem that that is concerning everyone, and everyone is contributing to it. Everyone has to find a solution to help, and we need to have more synergy. There have to be more interactions, and we have to do this at a much more global scale. And so that was sort of what, what we thought when we first started the [2nd edition of the book, Revenge of the Microbes].” Ho: “At that point, I was just starting my new faculty position, and so I started having to teach students directly. And a lot of students were coming in and giving their presentation on their research proposal or project that they have, and they very adamantly declared the reason why we have antibiotic resistance. ‘The problem is because doctors are over prescribing antibiotics.’ And I'm scratching my head—a little like, ‘Hmm, that's a really confident statement that you're making.’ Next student comes in and they're talking about, ‘Oh, it's all the farmers that are overusing antibiotics and causing the problem.’ And then the next student comes in like, “Oh, the greedy corporations or pharmaceutical industry is trying to milk us for everything, and antibiotics are not profitable enough.’ And, and I'm sitting here listening to the students who have a very narrow perspective. And clearly, they're getting it from whoever is teaching their classes. And so, it feels like every single perspective at every single stage, they only see things through their own eyes, and can't understand what the broader perspective is and why you have all these various different problems, and I guess we call them stakeholders in the thing. It is that that every different angle has its own personal motivations. Corporations do need to have money and persist to exist. Doctors, if you encounter a patient that is dying, well, you have a moral compulsion to actually treat them. And farmers having their livestock, well, their livelihood is at stake if they don't have their animals survive, right? And so, what I think was really important that we wanted to do is present the problem of antibiotic resistance and the way it works and why it's an issue, but also convey different perspectives on it, so that if people can kind of understand where everybody else is coming from, we can come together and have a more unified perspective, or understanding, at least, so that you're not thinking that everybody is this malicious actor, and you can actually work together to come with up with a complete solution.” Wilson: “The first book, was very important, because you needed to get people's attention right, right? But we got the attention. So, now let's come up with a plan! And we don't have a good plan. People are making progress. People are moving in the directions that need to be moved, coming up with alternatives, coming up with, you know, even financial solutions, to some extent. They're not enough, still, and it's going to take a global community to come forward and buy in to the problem. And I think we still have a large sector of our whole global community that are not really fully aware of what really this problem entails. They hear on the media and the news, ‘Oh, the crisis is here. We're in danger.’ And then a year later, they say, ‘Well, what happened? Nothing's happened.’ It hasn't impacted their lives yet, right? Or at least not in a way that they've noticed. And I think this is why we need more awareness. We need to get the word out there. We need to actually start having folks that make some of the big decisions, both financially, regulatory and other types of things, like education.” Ho: “One really big problem I think that COVID introduced us to, is that it's not just that we have to convince everybody it's important, but we have to also get people, in general, the population, to trust us. You know, that there is a problem. There's been a kind of an erosion in the trustworthiness, or trust in the institutions that we relied upon that are responsible for keeping everybody safe and healthy. And I think a big part of that is also communication education, that the populace needs to be better educated, but the communication level of people in charge, as well as researchers like us—we need to speak to the people in a way that people can understand.” Wilson: “We're not saying that we have a solution, but we do have some directions that, in many areas, have started, and we feel that they need more support. And we're hoping that folks that are reading the book actually appreciate that aspect of it, and then start realizing that, ‘Hey, I'm part of this solution too.’ It can be very little—being mindful of making sure that we have clean water, making sure that we have food security, making sure that we stay healthy and, therefore, we don't have as many infections, right? Just little things like that that we can actually do as individuals, that as a whole population, will actually contribute to improving the situation. Then, of course, we have to support our leaders in making some of the decisions. We have to let them know that we care about this. And I think at this stage, what we're hoping is that we can maybe encourage some folks to take a citizen stand on this, to ask questions, to start going and probing and saying, ‘Hey, congress person, what are you doing about this?’ And maybe just start the dialog. This is all we're doing, is starting a dialog.” Links for the Episode: The 2nd Edition of Revenge of the Microbes, details the intricacies of the antibiotic-microbe arms race. Beginning with a historical perspective on antibiotics and their profound impact on both modern medicine and present-day society. It also examines the practices and policies driving the discovery and development of new antibiotics, what happens to antibiotics once they are released into the environment, how antibiotic-resistant bacteria evolve and spread and the urgency for finding alternative approaches to combating infections. For anyone interested in antimicrobial resistance (AMR), this is a completely approachable 360-degree view of a very complex topic. Get your copy of Revenge of the Microbes today! Want to get involved and spread the word about AMR? Become an ASM Advocate Bacterial Pathogenesis: a Molecular Approach Take the MTM listener survey!

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  52:06
• Binning Singletons With Joseph James

  Joseph James, biologist at the U.S. Environmental Protection Agency, discusses his career trajectory and the creation of Binning Singletons, a unique mentorship program built on peer-to-peer networking at scientific meetings and conferences and was first implemented in 2019 at ASM Microbe. Links for the Episode Binning Singletons and Peer-to-Peer Networking Learn more about Binning Singletons. Contact Joe James: [email protected] Follow Binning Singletons on Bluesky. Binning Singletons: Mentoring through Networking at ASM Microbe 2019—mSphere article. Binning Singletons: Tackling Conference Networking When You Don’t Know Anyone—Guest post on Addgene Blog. Mastering a Mentoring Relationship as the Mentee—asm.org article that James says has really helped him explain Binning Singletons as a coaching form of mentorship. Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement—article on developing networks of mentors, another area Binning Singletons tries to address. #FEMSmicroBlog: Networking at Online Conferences (for Early Career Scientists). Take the MTM listener survey! James’ Research Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil. In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary. Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach. Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes. Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.

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  56:22
• Biorisk Assessment and Management With Saeed Khan

  Saeed Khan, Ph.D., Head of the Department of Molecular Pathology at Dow diagnostic research and reference laboratory and President of the Pakistan Biological Safety Association discusses the importance and challenges of biosafety/biosecurity practices on both a local and global scale. He highlights key steps for biorisk assessment and management and stresses the importance of training, timing and technology. Ashley's Biggest Takeaways Adequate biosafety and biosecurity protocols depend on a thorough understanding of modern challenges, and scientists must be willing and able to respond to new technological threats appropriately. In the microbiology lab, the threat goes beyond the physical pathogen. Implications of genomics and cyber security must be built into biorisk management techniques, including data storage and waste management practices. Risk assessments involve evaluation of both inherent and residual risk. Inherent risk is linked to the pathogen. Residual risk varies according to the lab, equipment, employee, environment, etc. As a result, biosafety and biosecurity risks are constantly changing, and assessments must be repeated strategically and often. Khan recommended repeating a risk assessment whenever a key variable in the equation changes, i.e., new equipment, new employee, new pathogen. He also recommended (at minimum) conducting routine risk assessments every 6 months, or twice a year. Featured Quotes:  “We need to have basic biosafety and biosecurity to stay away from these bugs and the modern challenges, like cyber biosecurity and genomics. These are the new areas, which are potential threats for the future, and where we need to train our researchers and students.” “Starting from simple hand washing or hand hygiene, the basic things we use are gloves, goggles and PPE to protect the workers, the staff and the patient from getting infected from the environment, laboratory or hospitals. These are the basic things, and it's very crucial, because if one is not using gloves in the lab or not wearing the lab coat, he or she may get infected from the sample, and the patient can get infected from the physician and doctors or nurse if they are not following the basic biosafety rules. These [things] are routinely important. Every day we should practice this.” “But there are [also] new challenges. Particularly in the microbiology lab, we [used to] think that once we killed the bacteria, then it's fine. But nowadays, it's not the way we should think about it. Though you kill the bacteria practically, it still has a sequence, [which] we call the genome, and if you have that information with you, you theoretically have the potential to recreate that pathogen… that can be used or maybe misused as well.” “[Working with] scripts of pathogens, like smallpox or the polioviruses, we call this synthetic biology. Different scientists are doing it for the right purposes, like for production of vaccines, to find new therapeutics, to understand the pathology of the diseases. But on [the other hand]—we call it dual use research of concern (DURC)—the same can be misused as well. That's why it's very important to be aware of the bugs that we are working with, and the potential of that pathogen or microbe, to the extent that can be useful or otherwise.” “So, we should be aware of the new concern of the technology, synthetic biology and DURC. These are new concepts—cyber, biosecurity and information security [are all] very much important these days. You cannot be relaxed being in the microbiology lab. Once we have identified a pathogen, declared a result to the patient and the physician, and it's been treated, we [still] need to be worried about waste management—that we discard that waste properly and we have proper inventory control of our culture. It should be safe in the locker or on in the freezers and properly locked, so we should not be losing any single tube of the culture, otherwise it may be misused.” Risk Assessment “The best word that you have used is risk assessment. So, it should gage the severity of the issue. We should not over exaggerate the risk, and we should not undermine the risk. Once the risk assessment been made, we can proceed.” “Right from the beginning of touching a patient or a sample of the patient until the end of discarding the sample, that is called biorisk management. It's a complete science that we need to be aware of—not in bits and pieces. Rather a comprehensive approach should be adopted, and each and every person in the organization should be involved. Otherwise, we may think [we are] doing something good, but someone else may spoil the whole thing, and it will be counterproductive at the end.” “We should involve each and every person working with us and the lab, and we should empower them. They should feel ownership that they are working with us, and they are [as] responsible as we are. So, this the whole process needs to be properly engaged. People must be engaged, and they should be empowered, and they should be responsible.” “Each and every lab has different weaknesses and strengths of their own, which play an important role in the risk assessment.” “There is inherent risk, which is linked with the pathogen, and there is another thing we call residual risk. So, residual risk everywhere and varies. Though the inherent risk may be the same, the residual risk is based on the training of the person, the lab facility that is available, the resources that labs have and the potential threats from the environment.” “It's not usually possible that you do a risk assessment every day. So, when you have different factors involving a new pathogen in your lab, you have new equipment in your in your lab, or some new employee in your lab—[a new] variable factor that is involved—you should [perform] the risk assessment. Otherwise, [a routine risk assessment] should [be done] twice a year, after 6 months.” “Training is important, and response time is very much crucial. And different technology plays a vital role, but the lack of technology should not be an excuse for not responding. There is always an alternative on the ground that you may do the risk assessment. And within the given resources and facility, we should mimic the technology and respond to any outbreaks or disease within our given resources.” Links for the Episode ASM Guidelines for Biosafety in Teaching Laboratories Pakistan Biological Safety Association Training to be a Biosafety Professional (video) Take the MTM listener survey!

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  49:59
• From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier

  Nicole Dubilier, Ph.D., Director and head of the Symbiosis Department at the Max Planck Institute for Marine Microbiology, has led numerous reserach cruises and expeditions around the world studying the symbiotic relationships of bacteria and marine invertebrates. She discusses how the use of various methods, including deep-sea in situ tools, molecular, 'omic' and imaging analyses, have illuminated remarkable geographic, species and habitat diversity amongst symbionts and emphasizes the importance of discovery-driven research over hypothesis-driven methods. Watch this episode: https://www.youtube.com/watch?v=OC9vqE1visc Ashley's Biggest Takeaways: In 1878, German surgeon, botanist and microbiologist, Heinrich Anton de Bary, first described symbiosis as the living together of two or more different organisms in close physical intimacy for a longer period of time.  These relationships can be beneficial, detrimental or commensal, depending on the organisms involved.  Microbial symbiosis research holds great potential to contribute to sustainable energy production and environmental health. Links for This Episode: Learn more about one of Dubilier's research vessels and see videos from the expidition. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Chemosynthetic symbioses: Primer. Take the MTM listener survey!

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  30:59

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