The microbiologist Michael Wagner explores the universe of microorganisms, those invisible beings he calls the original inhabitants of our planet that are of tremendous importance for life and health and whose diversity represents a rich treasure for humanity. The nature lover likes to relax in his kayak. © Private

The year is 1675, the place is the Netherlands. Antoni van Leeuwenhoek gazes into one of the microscopes of his own design. Although the optical microscope was known before his time, it still had shortcomings. The self-taught Dutch natural scientist studied the art of lens grinding and improved on it. In the course of his life, he built over 500 microscopes – consisting of tiny, biconvex lenses, which he fixed between two brass plates. This allowed him to observe objects attached to the tip of a needle. On one day in that year something revolutionary happened: for the first time he saw bacteria – he called them animalcules (tiny animals) – in pond water, rainwater and human saliva. The Royal Society initially responded to this discovery with derision, but his observations were confirmed five years later, and in 1683 van Leeuwenhoek was appointed a member of Britain’s venerable learned society.

Highest recognition

“Today, we consider the existence of microbes to be a matter of course, but the fact that at that time someone said to himself there just might be invisible life and built an enlarging device to search for it was a huge step and an example of the importance of purely curiosity-driven basic research not geared to any specific purpose,” says Michael Wagner. Wagner, a microbiologist, investigates the very universe of microorganisms that van Leeuwenhoek first discovered at the end of the 17th century. In spring 2019, the Director of the Centre for Microbiology and Environmental Systems Science at the University of Vienna was awarded the Wittgenstein Prize for his outstanding work. At 1.5 million euros, this award – also known as “Austrian Nobel Prize” – is endowed with a significantly higher sum than the Nobel Prize.

The original inhabitants of the Earth

Wagner, a native of Munich, is happy about the recognition and the money, but also about the increased attention paid to microbial research in Austria. “Microbes are the most important creatures on Earth. For billions of years, our planet was inhabited exclusively by them. They were the original inhabitants and have settled all over the planet – including in our own bodies, where they play an important role for our health,” enthuses the microbiologist and illustrates the unimaginable dimensions of this parallel universe with an example: “One gram of potting soil contains about 100,000 species of bacteria. In a few spoonfuls of soil you will find as many bacterial cells as there are people on Earth.”

“One gram of potting soil contains about 100,000 species of bacteria.” Michael Wagner

Microbial dark matter

For a long time, microbiology worked exclusively on microorganisms that were first cultivated and multiplied in the laboratory and then isolated in order to be examined. The problem was that most microorganisms were lost during this propagation process and thus eluded analysis, a phenomenon called “microbial dark matter” in analogy to astronomy, denoting the millions of bacterial species that populate the world but which nobody knows about. When he worked on his doctoral thesis, Michael Wagner already developed new methods of identifying the microorganisms in the “dark matter” in terms of molecular biology and of specifically staining them without multiplying them in the laboratory. He also discovered completely new development strains and species. He remembers that period in the 1990s as “a time of pure wonder”. “Even in the most trivial of samples, on a shoe sole, for instance, we found new species and, for the first time, were able to specifically mark them with a fluorescent dye and observe them under the microscope.”

Watching bacteria feed

The scientist was not content simply to map the diversity of these microbes: he also wanted to find out what functions were fulfilled by the bacteria he detected. His guiding principle: “You are what you eat,” meaning he derives what the bacterium does from what it feeds on. Wagner uses isotope-labelled feed, which the bacteria absorb into the biomass when feeding. But how do you watch a creature a thousandth of a millimetre in size eat? He uses processes from materials science or surface chemistry for this purpose. The Centre for Microbiology and Environmental Systems Science boasts the only so-called “NanoSIMS” in Austria, a device worth three million euros which shoots an ion beam at cells and then uses mass spectrometry to determine whether cells are isotope-labelled or not. However, such investigations are very time-consuming, which is why only relatively few samples can be examined.

Revolution in microbiology

Wagner's research group was the first in the world to watch bacteria feed in their natural ecosystem. “That was a revolution,” he notes, “we were the first not only to map, but also to begin to understand the functions of microbes.” Another revolutionary step was the sorting of the bacteria according to their functions. In cooperation with Roman Stocker from ETH Zurich, the Vienna researchers have developed a finger-sized cell sorting machine that uses laser beam and Raman microscopy to remove isotope-labelled cells from a sample as though with tweezers, in order subsequently to cultivate them or to examine their genome sequence.

Intestinal bacteria and diseases

In recent years, microbial communities have also taken on increasing importance in human medicine. Today it is known that the composition and activity of intestinal bacteria plays an important role in the development of many diseases and that there is even strong evidence for the involvement of the intestinal microbiome in the development of certain types of cancer and mental disorders such as depression. Medical experts are therefore looking for ways of specifically modifying the intestinal microbiome, which is a more complex undertaking than one might think. Every human being has a specific composition of intestinal bacteria, which is not only influenced by factors such as genetics, nutrition, exercise or medication.

“The type of birth is already decisive - whether through the birth canal or by Caesarean – and whether a baby is breastfed or not,” says the biologist and adds: “This is why certain drugs have an effect on one patient but not on another, because bacteria convert and degrade active substances. If you host a bacterium that degrades the active ingredient of the drug, it cannot work or only to a lesser extent.” Targeted changes in the intestinal microbiome are not a trivial affair because each patient represents an ecosystem in its own right. Probiotics contain the same types of bacteria for all patients. “For many patients, taking these probiotics is like putting a cow and a bull in the rainforest, where they will not develop a population because they have too many enemies there,” is how Wagner, a great lover of nature, illustrates the complexity. He sees the future in personalized probiotics that are tailored to the intestinal microbiome of the particular patient.

“10 years from now, it will be standard procedure to take a stool sample for microbial analysis.” Michael Wagner

Expertise for the Vienna General Hospital

Wagner sees human microbiome research as one of the most important research areas of this century. In the centre he heads, several working groups are focusing on this topic. In close cooperation with the Medical University of Vienna they are making their expertise available to the Vienna General Hospital as part of the “Joint Microbiome Facility” founded in 2018. “Human microbiome research uses concepts and methods of environmental microbiology, which has been investigating complex microbiomes intensively for decades. The greatest breakthroughs can be expected at the interface between environmental and medical microbiome research. We would like to make a contribution to ensuring that Austria does not miss the boat when it comes to developments in this area which is so important for public health, and we are grateful for the opportunity to set up such a facility here in one of the largest hospitals in Europe,” says the expert. Wagner is convinced that ten years from now, the hospital will not only a take a blood sample but also a stool sample for microbial analysis as a standard procedure.

Nitrogen cycle

One of Wagner's main research areas deals with microorganisms that play a central role in the global nitrogen cycle. The Earth's natural nitrogen cycle is massively influenced by human activity, above all by fertilizers used in agriculture. In the ground, the ammonium used for fertilization is first converted to toxic nitrite by microorganisms and then into the slightly less harmful nitrate.

Bacteria, so-called nitrifiers, play an important role in the nitrogen cycle. They convert ammonium into nitrate, thereby producing laughing gas (nitrous oxide). The "Comammox" bacteria discovered by Michael Wagner's research group in 2015 produce considerably less nitrous oxide than the previously known species. © Holger Daims

Dead zones in the water

This two-stage process of “nitrification” is of tremendous ecological significance. As nitrate washes out of the soil with particular ease, more than half of the fertilizer is lost and leads to nitrogen pollution of groundwater, rivers, lakes and oceans. The eutrophication of bodies of water turns them into “dead zones”. “In the Gulf of Mexico, where large areas of the USA are drained by the Mississippi and the Atchafalaya, there are huge so-called dead zones where algae grow explosively as a result of over-fertilization. The algae are broken down by bacteria that deplete the oxygen in the process, which is why no higher life can survive there any longer,” notes Wagner in giving an example of these dynamics.

The problem of nitrous oxide

Nitrogen fertilization causes yet another problem: during nitrification, the microbes release “laughing gas” (nitrous oxide), a greenhouse gas that is 300 times more powerful than carbon dioxide and destroys the ozone layer. While these nitrifying microbes are very problematic in agriculture, they play an important role in water treatment plants by converting the ammonium from the wastewater into atmospheric nitrogen. For this process they join forces with so-called denitrifying bacteria. However, it is precisely under oxygen-poor conditions as they are found in sewage treatment plants and also in fertilized soils after rainfall, that a particularly large amount of nitrous oxide is released. For this reason, microbiologists have been looking for a long time for nitrifiers that release less nitrous oxide and have wondered whether it was possible to specifically promote their growth in such systems.

“Comammox” – a scientific breakthrough

In 2015, Wagner’s research group was exploring new nitrifiers when they achieved another scientific breakthrough in cooperation with Holger Daims from the University of Vienna: they discovered “Comammox” bacteria (complete ammonia oxidizers). These bacteria are particularly efficient nitrifying agents that convert ammonium into nitrate on their own without the need for microbial partners. And, as a great boon, only small amounts of nitrous oxide are released in the process. “A green nitrifier, if you like,” laughs Wagner. For the time being, the Viennese researchers are the only ones worldwide who are able to breed Comammox in the laboratory. They are now investigating the growth conditions of this bacterial species. Their vision for the future is to use these findings to promote the growth of Comammox in the environment in order to develop new, more environmentally friendly approaches in agriculture, wastewater treatment plants and drinking water treatment.

A formative childhood experience

For the 54-year-old Wagner, the decision to studying biology was a gut decision, as he had always been interested in the diversity of life. He had not planned ending up in microbiology, but perhaps this trajectory was fostered at the unconscious level by childhood experiences that had a great impact on him. When he was seven years old, his mother suddenly and unexpectedly fell ill with a brain infection caused by an unknown pathogen. Family life thus changed radically from one day to the next. “The question as to what illness my mother suffered from and how she could best be treated has been with us for many years,” recalls the father of four. “It is, perhaps, not entirely by chance if today I find myself developing methods for the identification and functional investigation of unknown microbes,” he speculates.

From a “village of indomitable Gauls” to world renown

After studying biology at Munich Technical University, the young postdoc spent a year of research at the US Northwestern University in Evanston and then returned to the Technical University of Munich and qualified as an associate professor. In 2003, he was called to Vienna and took on the position of Professor of Microbial Ecology at the University of Vienna. He was accompanied by Holger Daims, Matthias Horn and, a little later, Alexander Loy, formerly doctoral students in his team and, today, highly distinguished scientists. “We sat together in an office and planned the new department,” he remembers these early days. “We felt like the small village of indomitable Gauls: that forges a great sense of community.” One can still see this community spirit in the photo taken at the award ceremony for the Wittgenstein Prize 2019, where he is visibly buoyed by his colleagues’ cheers. “The others are well and truly delighted for me. That's the most beautiful thing.” Today, the “small Gallic village” boasts about 150 people from 29 countries. Fifteen of them are principal investigators and six of them have received one of the highly coveted ERC grants from the European Research Council.

FWF Wittgenstein-Gala 2019 © Michèle Pauty

“The diversity of microbes is a huge treasure for mankind.” Michael Wagner

Developing the technology further

For the next few years, Wagner anticipates that he will focus on further methodological improvements. Physicists at Boston University have developed a new Raman technology. This is a particularly fast type of chemical microscopy that reveals not the shape but the chemical composition of the cells. Wagner now wants to adapt this technology for microbial research in collaboration with the American teams. “This is high-risk research,” notes Wagner, because nobody has yet tried out whether this sophisticated technique can be combined with fluorescence microscopy and therefore be applied in the analysis of microbial communities. “If it works, we can watch the bacteria feeding almost in real time and see, for example, how different diets affect the activities of intestinal microbes.” That would represent yet another scientific breakthrough. Another thing becomes very clear: microbial research is strongly technology-driven. It is an area where technological progress often triggers the decisive next step.

More risk commitment

Wagner would like to see more commitment to risk from research funding institutions in general. He is very positive that the Austrian Science Fund FWF is moving in this direction with its newly conceived 1,000 Ideas Programme: “With this programme there is no need for any prior work before you apply for funding, which is very good, because there is currently a large funding gap in the area of high-risk research."

“The FWF should sometimes draw lots”

Wagner would, however, go one step further in supporting research: “In some cases, the FWF should consider drawing lots! From my time as a member of an ERC selection panel, I know that when looking at applications you recognize the outstanding and the rather weak with relatively high reliability. But often, when it comes to funding decisions, you have to make choices in an area where the decision is not easy, because you have to decide between applications from different disciplines that are all very good. In my opinion, it would be fairer to let chance decide in such contexts. This would also open the mind for ideas that are outside the mainstream.” Wagner admits that this approach is difficult to “sell”, but points out that some funding bodies, such as the Swiss National Science Foundation, have already begun to experiment with such a system.

Huge treasure for mankind

Wagner, a passionate kayaker, has not lost any of his enthusiasm for the universe of microorganisms and sees it as a great privilege to do research every day on something that fascinates him. “If you look at the family tree of life, there are bacteria, archaea and only a surprisingly small part is made up of plants, animals and humans. I’m exploring the miracle of life,” he says with a radiant smile. And there still is a lot to discover – including things of relevance for actual application. “These few grams of earth,” says Wagner, pointing to the flowerpot in his office, “may well contain new antibiotics and new enzymes for biotechnology. This diversity is a huge treasure, and one of which large parts have yet to be unearthed.”

Basic research is extremely important

Beyond the realm of applied science, Wagner considers non-purpose-oriented basic research to be “extremely important and worthy of protection”. He cites the example of penicillin, discovered by chance in 1928 by the bacteriologist Alexander Fleming because he had failed to clean up his laboratory before the summer holidays and fungi grew on leftover bacterial culture plates. Fleming had excellent powers of observation and noticed that these moulds destroyed the bacteria, which led to his ground-breaking discovery that he could never have planned. Just as van Leeuwenhoek could not have guessed what an important discovery he would make driven by curiosity, the development of new methods and his powers of observation.

Personal details

The microbiologist Michael Wagner is the Director of the Centre for Microbiology and Environmental Science at the University of Vienna. He studied biology at the Technical University of Munich, was a postdoctoral fellow at Northwestern University in Evanston, USA, and qualified as a professor in 2000 at the Technical University of Munich, where he held the position of Associate Professor until 2002. In 2003, Wagner was given a chair for Microbial Ecology at the University of Vienna. In addition to numerous awards, he received an ERC Advanced Grant from the European Research Council in 2011, an Einstein Professorship from the Chinese Academy of Sciences in 2014, the Schrödinger Prize from the Austrian Academy of Sciences in 2015, the Jim Tiedje Award from the International Society for Microbial Ecology (ISME) for his life's work in 2018, and the FWF Wittgenstein Award in 2019.