— Elizaveta Alexandrovna, microorganisms capable of surviving in extreme conditions are being actively studied throughout the world. Which of them interest scientists the most?
— Among the first such microbes to attract the attention of scientists were thermophilic ones  — microbes capable of surviving at high temperatures. But then the range of extreme habitats and their dwellers expanded considerably. These include, for example, halophiles — microorganisms that live in high salinity environments such as saltworks, salt lagoons, and deep salt lakes (brines); acidophiles, which grow in highly acidic environments such as where iron ore is mined or in acidic hot springs; and alkalophiles, which like alkaline conditions. The latter, for example, are studied by the remarkable microbiologist Dimitry Sorokin. In his research, he focuses on soda lakes, bodies of water with very high pH and high carbonate ion content. Despite the harsh conditions, such lakes are teeming with life. Another interesting group are the psychrophiles, microorganisms that "love the cold". Interestingly, companies today have demand for enzymes that work at low temperatures.

— At what temperatures can they survive?
— There is a difference between "living" and "surviving". There are psychrotolerant microorganisms that can grow in the cold but still do better at higher temperatures. Psychrophiles, on the other hand, don't just survive in the cold, they actually need it to grow. The lowest bacterial growth temperature I have encountered is -25°C.

— Where does that microbe live?
— In cryopegs, water lenses within the permafrost connected with the sea. The seawater freezes, leaving a so-called lens in which a non-freezing brine accumulates. That's where those microbes live. But in a broader sense, today's scientists are mostly looking not for extremophiles but simply for new microbes with novel properties. And there are still a lot of them.

— Not long ago, a new symbiosis between bacteria and archaea was discovered. How important is that discovery?
— Very. It was made by a true genius, the Mozart of microbiology, Japanese researcher Ken Takai. He makes grand discoveries with ease, and each of his works ushers in a new era. Not long ago, he cultivated a first-ever symbiotic pair of archaea and bacteria, thus confirming the crucial conclusion previously reached using molecular and genetic methods — eukaryotes (organisms whose cells contain a nucleus) evolved from archaea. The symbiosis is based on the bacterium absorbing the archaeon's waste products, thus facilitating its growth while also feeding. At some point those cells fused. Most importantly, the archaeon in this symbiosis belongs to the group closest to eukaryotes but so far known only from metagenomic data — DNA sequences obtained from natural specimens.

— Members of your lab have isolated new thermophilic microbes on expeditions around the world, from the hot springs of Kamchatka and Baikal to the deep-sea hydrothermal vents of the Pacific Ocean. How are such expensive expeditions organized?
— Usually we participated in international cruises to deep-sea hydrothermal vents. Someone gets a large grant to study hard-to-find but very intriguing microbes, which includes an expensive ocean voyage, and recruits an international team. This practice has allowed many members of our lab to access unique extremophile habitats.
There is also another format for major international projects. For example, the European Union's HotZyme, a "hot enzyme" project involving scientists from 13 countries, studied hydrolytic enzymes produced by thermophiles. Our group was lucky because we were able to discover thermophilic planctomycetes during that project. Planctomycetes themselves are very curious and complex bacteria that, along with microscopic fungi, are responsible for decomposing organic matter on Earth and returning inorganic carbon to the atmosphere. But thermophilic planctomycetes have never been seen before, even though their thermostable hydrolases may have applications in different areas of biotechnology. Another curious group of microbes isolated and described as part of the project includes hyperthermophilic archaea from the Kuril Islands, in which my colleagues discovered a completely new, unusual cellulase that remains active for several hours of incubation at 100 °C. The new microorganisms and their enzymes were profiled jointly with other project participants, and it was a big step forward for us and our research.

— Is there any interesting applied research?
— One of the most fascinating problems that not only we but also scientists all over the world are trying to solve has to do with the decomposition of plastic. The staff of the Department of Microbiology of Moscow State University and our laboratory at the Federal Research Center “Biotechnology" of the Russian Academy of Sciences are currently looking for plastic-degrading microorganisms among extremophiles. And we have already found thermophilic bacteria that degrade polyethylene and polyethylene terephthalate, although the process is currently taking longer than we would have liked.

— Sometimes it feels like publications about new microorganisms appear almost weekly, with most of them being discovered by bioinformaticians, who work on computers.
— Yes, that's the new reality. Molecular methods combined with bioinformatics have indeed led to a boom of discoveries concerning microbial diversity. And traditional microbiologists are outplayed here, because bioinformaticians can do almost anything without leaving the room: find a new genomic sequence, determine the properties of the microorganism to which it belongs, and even give a name to that virtual microbe. Essentially, you get a new group of microbes, sometimes of very high rank — an order, a class, or a phylum — although no one has ever seen those microbes. And it's all done in two months. Meanwhile, discovering, isolating, and describing a new microorganism by conventional wet methods takes two, three, or even five years, because it is very hard work.

— What takes up the most time?
— All microbiological work is quite laborious, including preparing the medium and optimizing it. Sometimes the microorganism just stops growing, i.e., dividing, for some unknown reason. Very often, the successful initial identification of a new microbe leads to no significant outcome. Moreover, it was discovered that the microbes with the most significant ecological roles tend to grow at a slow pace. In short, there are numerous technical hurdles and no one-size-fits-all solutions. Besides discovering, isolating, and studying a new microbe, it must be submitted to two international collections. Without this step, its name won't be included in the comprehensive list of officially recognized microorganisms. In these collections, the submitted microbe must be successfully reproduced and then preserved as a reference for a new name (this is called a "type strain"). Anyone can purchase a type strain for their research at a nominal cost and check if it indeed possesses the characteristics described in the initial report. By the way, in our country, we have an excellent All-Russian Collection of Microorganisms (VKM) located in Pushchino.

— Where do you send new microorganisms today, considering the sanctions?
— Typically, one collection should be national and the other international. We used to send new microorganisms primarily to the German DSMZ collection, but now it has become more complicated, so we frequently work with the Korean collection.

— If bioinformaticians discover a bacterium virtually and then other scientists isolate it in reality, who is considered the author of the discovery?
— This is a big issue today. The thing is that bioinformaticians assign new bacteria a "first and last name" — genus and species — and then append the term Candidatus. This leads to considerable confusion because this is also how microbes are named that microbiologists have already obtained in lab culture, studied their genome, but have not yet isolated in pure culture. But that's a different story, because at least you can examine those microbes and somehow describe their properties. Meanwhile, a microbe that no one has ever seen is a phantom. All this causes significant unrest and even conflict. Microbiologists have realized that the process is getting out of control. If you look at the charts, the count of these Candidatus is skyrocketing.

— So, how can this issue be resolved?
— A vote was held not long ago involving representatives from the global community on whether we accept these Candidatus and consider them equal to "regular" microbes. The vote was conducted through national microbiological societies, and it was ultimately decided not to consider Candidatus as full-fledged microbes. And it was mainly applied microbiologists — primarily medical doctors — who voted against it. For medicine, precise differentiation of microbes even at the intraspecies level is crucial, because genomic differences between, for instance, the anthrax agent and common closely related bacilli are minimal. Our Candidatus, especially some exotic new high-rank taxa, do not interest them and will only obscure the overall picture. But later, quite recently, it was decided that a new nomenclature code, SeqCode (Sequence Code), would be created for virtual and uncultured microbes, and DNA samples, genomic or assembled from metagenomes, would serve as material proof of their existence.

— Speaking of a scientist's calling, it seems you had no chance to choose another profession, given that both your parents were biologists.
— My father, Aleksandr Formozov, was indeed a rather famous zoologist and, I would say, a naturalist, because he was doing science mostly out of love for nature. He was much older than my mother, who was once his student. Needless to say, our family idolized my father. Dad created numerous incredibly beautiful scientific drawings. At home, our walls were adorned with pictures of animals and plants, and my brother and I grew up amidst that beauty. My brother, Kolya, also became a zoologist and has recently published two splendid books of our father's absolutely wonderful drawings. But despite all this, I didn't share my father's passions as a child and was not particularly fond of nature. I was always drawn elsewhere, wanting to become either an archaeologist or a historian. After high school, I felt lost because the humanities scared me with their ideologization, and I was afraid of STEM. The only remaining option was biology.

— So you just enrolled in a university? Was it difficult?
— No. I graduated from school with a gold medal, so I only had to pass one exam, in biology. I drew ticket number one about protein synthesis, answered it, and emerged as a student. I immediately fell in love with the student environment and the university life — a love that completely overshadowed my interest in science. You see, I graduated from a regular school located in the district I lived in, and the university was full of interesting kids from special schools who seemed more educated, freer, and more relaxed than me. This largely determined my scientific path because I joined the Department of Microbiology, which was not particularly popular at that time. Moreover, I got a "C" in math during the first exams and thought that I wouldn't be accepted anywhere else. After graduating from Moscow State University, having passed a rather challenging exam, I got into a postgraduate program at the Institute of Microbiology of the USSR Academy of Sciences, completely unaware of what and who was waiting for me there. I remember standing in front of room 509 and not yet knowing that my life was about to change dramatically. Like Alice in Wonderland, I opened the door and entered a completely different world.

— Who greeted you in that world?
— Georgy Zavarzin. A handsome tall man with red hair. Outwardly a complete Englishman, with very English, formal manners. He sat me down at a table in his office, showed me an aquarium filled with some black sludge with blades of grass sticking out of it, and asked, "Well, tell me, what is happening in there?" Being a straight-A student, I confidently answered "cellulose decomposition", and then there was a heavy silence because we were taught neither the ecology of microorganisms nor their diversity in our department. Georgy Aleksandrovich said, "I see," and accepted me into the postgraduate program.

— What was in that aquarium?
— Silt from the swamp next to his cottage. Because the aquarium was tall and upright (actually, it was a jar for developing chromatograms), there were oxygenated aerobic conditions at the top and no oxygen at the bottom. As a result, cellulose decomposition (of grass and leaves) was taking place under anaerobic conditions, causing bubbles to come from the aquarium, just like in a real swamp. You see, at that time, anaerobic processes were much less studied than aerobic ones, simply because they are more difficult to reproduce in a lab. In addition, many anaerobic microorganisms are very sensitive to oxygen, and all manipulations with them should be carried out under anaerobic conditions. Georgy Aleksandrovich became very interested in that topic just a few years before I came along. Like the captain of a ship, he was always moving forward, discovering new lands and often being ahead of the global science at the time. So we got a small head start before other researchers with more financial resources jumped at the new topic.

— What did you start with in your work?
— Georgy Aleksandrovich proposed two topics. One, quite understandably, was biochemical and was about cytochromes. The other was completely novel and involved the study of microbial communities that decompose organic matter into its end products — methane and carbon dioxide.

— Why exactly was it novel?
— It was a very unusual topic, because microbiology had always studied pure cultures. That is, they isolated a colony formed from a single cell and then propagated a population of perfectly identical microorganisms, obtaining and examining the so-called pure culture. But pure cultures don't exist in nature. Microbes thrive in complex environments, interacting and influencing each other, behaving quite differently than they would in a pure culture. I was given two weeks to decide, but I didn't need them as I promptly chose to pursue a more familiar biochemical subject. But that just wasn't meant to be. Georgy Aleksandrovich heard me out and said, "I've made a different decision." So I embarked on an entirely new venture, novel not just for me but for the entire lab as well. There were no established procedures to follow. Despite being preoccupied with his own work, Georgy Aleksandrovich spent a lot of time talking to me and showing me things. He was remarkable in a way that he crafted many of the equipment for experiments himself. The folks at the mechanical and glass-blowing workshops loved him and helped him bring all his ideas to life. As a result, our lab was constantly filled with various devices used for cultivating anaerobic bacteria and made from flasks and tubes welded together, along with many other homemade contraptions. Ultimately, my dissertation became the first of its kind in this field. Later, when it became clear that microbes should be studied in this manner, preferably in their natural habitat or at least in complex environments known as microbial communities, the microbiologists' perspective significantly shifted.

— During that time, the world was going crazy about thermophiles, extraordinary bacteria that thrive in hot springs. When did this hot topic catch the attention of Russian scientists?
— Interestingly, few people know that hyperthermophiles were discovered by the Russian scientist Sergey Kuznetsov back in the 1950s. In 1953, he published an article about microbes growing at 100 °C in Kamchatka. He discovered them quite literally with his naked eye, as these microorganisms are highly visible. In hot springs, you can often spot white-gray "ostrich feathers" quivering in the water flow. These are bacteria that oxidize dissolved hydrogen sulfide into sulfur, which then accumulates on long chains of cells. It all looks very beautiful, but cultivation attempts must have failed, and the discovery was forgotten, especially since it was published in a not-so-widely circulated collection of works from the Institute of Microbiology of the USSR Academy of Sciences. The research of thermophilic microorganisms gained popularity after renowned American microbiologist Thomas D. Brock began studying the microorganisms of Yellowstone Park in the late 1960s. It became evident that hot springs are inhabited by unique microbes that have much higher growth temperatures than the previously known "moderate" thermophiles. Naturally, everyone was curious about how these organisms' proteins maintain their structure and functionality under such conditions, given what we know happens to a chicken egg's protein when it's boiled. It turned out that the enzymes of these microbes are densely packed, contain additional "bridges" that maintain their structure, and have several other adaptations that prevent them from denaturing at high temperatures.

— The next wave of interest in thermophiles came about in the second half of the 1980s, when "black smokers" were discovered on the ocean floor.
— Indeed, it was a vibrant era in the history of science. It was discovered that underwater volcanoes are inhabited by microorganisms capable of reproducing at even higher temperatures. The current record holder is the archaeal methanogen Methanopyrus kandleri, which thrives at 122°C (incidentally, it was also discovered by Ken Takai). This organism was isolated from "black smokers", where due to pressure, water at great depths remains liquid even at temperatures far exceeding the boiling point. Microbes that live under such conditions started to be referred to as hyperthermophiles.

— The discovery of thermophiles led to the emergence of a plethora of new technologies. In your opinion, which ones are the most valuable?
— I believe the most significant application of thermostable enzymes is the use of DNA polymerase from Thermus aquaticus (Taq polymerase) in the polymerase chain reaction. This has greatly simplified and reduced the cost of the process, making it a routine method widely used in medical diagnostics, research of natural microbial communities, forensics, and many other areas. Thermostable hydrolases are also utilized. For instance, thermostable xylanase is used in the pulp and paper industry for paper bleaching, among other things.

— When did you start taking an interest in this topic? Biologists now travel worldwide for their research. What expeditions marked the beginning of these studies?
— When I joined the Institute in the early 1970s, there was already a department dedicated to thermophilic microorganisms, which primarily focused on applied problems. Georgy Zavarzin became fascinated with this topic in the early 1980s thanks to geologist and volcanologist Gennady Karpov from the Institute of Volcanology and Seismology of the Far Eastern Branch of the Russian Academy of Sciences (then the USSR Academy of Sciences). Gennady Aleksandrovich spent a lot of time working on various Kamchatka volcanoes, where he couldn't help but notice the communities of microorganisms developing in hot springs, leading him to collaborate with microbiologists. Members of our laboratory have participated in numerous expeditions to Kamchatka, isolating many new thermophilic microorganisms and studying the composition of their natural communities.

— What was the most important thing at that time? What kind of research were you conducting?
— We almost never focused on thermophilia itself, i.e., the resistance of bacteria to high temperatures. We were interested in the various ways of generating energy. And among bacteria, these ways are truly astonishing! The thing is, eukaryotes, or organisms whose cells contain a nucleus, are incredibly diverse in appearance, but their energy metabolism is identical. There are only two options — either photosynthesis or oxidation of organic matter by oxygen. But with microbes, it's the opposite. They look almost identical, simply because they are so tiny. After all, a typical microbial cell is ten or even 100 times smaller than a nuclear cell, with an average size of 1 micron, or 1/1000th of a millimeter. Their organelles consist only of ribosomes and sometimes intracellular membranes, with DNA freely floating in the cytoplasm. But we see an incredible variety of ways to obtain energy and the substrates from which they draw it — these are inorganic compounds such as hydrogen, hydrogen sulfide, ammonium, methane, various natural and non-natural biopolymers, etc. The list goes on and on. And the oxidizer can be not only oxygen but also various oxides, metals, and metalloids with variable valence. This is also a form of respiration, but it's anaerobic.
Microbes, specifically prokaryotes or nucleus-free organisms, are like real-life superheroes with a range of fantastic abilities. For instance, there are bacteria that can use sulfur as both an electron donor and acceptor, meaning they oxidize one sulfur atom and reduce another, and this process sustains their life. They live quite well, in fact, taking carbon from CO2 to build their cells. Others, for example, can grow in an atmosphere of 100% CO — carbon monoxide gas known to kill all living things. CO is oxidized to CO2, and hydrogen is formed from water. This amazing process, common to many thermophiles, was actually discovered in Georgy Zavarzin's lab. The variety of combinations of electron donors (energy substrates) and electron acceptors (oxidizing agents) in prokaryotes is so vast that we even have a graphic representation of these combinations, which is constantly being updated.

— Georgy Aleksandrovich even attempted to create a sort of "periodic table" for bacteria.
— Indeed, he published a book in the 1970s titled Bacterial Systematics: Space of Logical Possibilities. While it no longer functions as a systematics, the concept of a space of logical possibilities remains relevant. Georgy Aleksandrovich stated that all processes not prohibited by thermodynamics exist in the microbial world. In other words, if something isn't present yet, it simply means we haven't discovered it yet. We are now gradually filling in this matrix.

— Where have you personally discovered new microorganisms?
— My first expedition was in 1982, to the Uzon caldera. It is a remote area in Kamchatka, accessible only by helicopter. In my opinion, Uzon not only matches but in some respects surpasses Yellowstone Park. In Yellowstone, you need to drive from one spring to another, sometimes covering ten kilometers. In contrast, Uzon has a vast number of hot springs — dozens, even hundreds — all within a relatively small area, each with varying acidity and temperature. And accordingly, the life forms within them are also incredibly diverse. The sight is surreal. There is a constant bubbling and sighing around you, with remarkable "ostrich feathers" growing in one spring and colorful thermophilic phototrophs, known as cyanobacterial mats, growing elsewhere. Cyanobacterial mats are massive communities of thermophilic cyanobacteria, covering several square meters. These are prokaryotes capable of performing oxygenic photosynthesis like plants, and within these mats live organotrophic bacteria that feed on the byproducts of the phototrophs. During my first visit, I discovered a cyanobacterial mat that was literally layered with sulfur. It turned out that the decomposition of organic matter there occurred through sulfur and not oxygen respiration. That's where I first isolated a new bacterium, which Georgy Aleksandrovich beautifully named Desulfurella. It's my favorite bacterial genus.

— What do we know about it today?
— Desulfurella is a lithoautotroph, a microorganism that uses inorganic energy sources and CO2 as an inorganic carbon source. My Desulfurella feeds on hydrogen, with sulfur as its oxidizer, which it reduces to hydrogen sulfide. It can also consume acetate, as well as stearic and palmitic acids. It's always in the spotlight. It turned out to be a representative of a new order, named Desulfurellales in its honor, and now it has been found to have a unique method of assimilating inorganic carbon.d

— How are new microbes named today? What does the process of choosing and approving a new name look like?
— Firstly, you need to select a name with Latin or Greek roots that hasn't been used before. Secondly, the name should ideally reflect the characteristics of the new microorganism. Sometimes the name is composed of several roots to achieve this. For example, Thermoanaerobacter, where "thermo" means thermophilic, "anaero" means anaerobic, and "bacter" refers to a bacillus. Sometimes a species name is chosen in honor of certain people or geographical features. But generally, it's a real challenge every time. I have a childhood friend who graduated from a department of classical philology, and I sometimes ask him for help in coming up with something beautiful.

— How many new microbes have you discovered?
— Personally, I haven't discovered many, as most of them were isolated by my colleagues. I worked for many years with my dear friend Rita Miroshnichenko, who sadly passed away last winter. We went on expeditions together and described many new microbes. Rita was deeply loved and respected in the lab, and recently an archaeon representing a new order was named after her — Tardisphaera miroshnichenkoae.

— Are there any microbes named after you?
— Yes, and I found out about it quite unexpectedly. My colleagues went on an expedition to Chukotka, where hot springs bubble up right from the permafrost, and they isolated a bacterium that belongs to a new class in the underexplored Chloroflexota phylum. They didn't tell me anything, but during a conference at MSU they asked to speak and told everyone about their journey and the new bacterium that represents a new class Tepidiformia, where the type species is named after me — Tepidiforma bonchosmolovskayae. It was a pleasant surprise, although the name, frankly, is not very pretty, but what can you do... By the way, a flea with the species formozovi was named after my father, which he was extremely proud of. A portrait of that flea hung in his office.

— Why does it seem like microbiology is somewhat overshadowed by other branches of biology?
— I believe it's a great injustice. People know very little about general microbiology because it has been somewhat obscured by medical and sanitary microbiology. I recently told a woman that we are studying the microbes of the deep subsurface biosphere in oil mines 2,000 meters deep. She exclaimed, "Wow, they've even made it there!" In other words, people perceive microbes as the creatures crawling out of the toilet in cleaning product commercials. But the fact that our world is teeming with microbes and that without them nothing could exist is often overlooked. Indeed, microbial activity underlies all the natural element cycles. For instance, if you consider the nitrogen cycle, which is essential for all living beings to synthesize proteins and nucleic acids, it's important to know that only prokaryotes can consume free nitrogen from the atmosphere. Only then it is delivered in the form of accessible compounds to plants, and through them to animals, including us.
So I never miss a chance to talk about microbiology or even show how it works — we recently created a tabletop microbiology game at our department. In it, you can play as microbes with different properties and end up in different habitats, like a city dump, a hot spring, a swamp, or an ocean. If your traits give you an advantage in that habitat, your population grows. The game is quite competitive, because if you have the ability to, say, produce antibiotics, you can send your opponent back to the start. But if they have stocked up on the antibiotic resistance gene in time, they will be safe, and so on.