Invisible diversity: The biodiversity of microbes

“When most people hear the term biodiversity, they’re probably more likely to think about exotic plants and tropical butterflies, not so much about less spectacular insects and least of all microorganisms,” says Professor Jörg Overmann. “But microorganisms account for a huge amount of biodiversity.”

Since August 2025, Overmann has held the Chair of Biodiversity Research at LMU’s Faculty of Biology. At the same time, he is the new, and first full-time, Director General of the Bavarian State Collections of Natural History (SNSB). This dual role will enable him to combine two perspectives in the future: molecular research into the invisible diversity of life, and the further development of large natural history collections.

A thimbleful of soil

Up until now, we have only been able to estimate how great the diversity of life really is. It is currently assumed that there are about eight million species of animals and around 200,000 species of plants. But in the case of bacteria and archaea, which are microorganisms without a cell nucleus, estimates range from ten million to well over a billion species. Every insect, every tree and every mammal alone boasts its own microbiome – an individual cocktail of microbial species that colonize them. So as each new species of animal or plant is described, on average there will also be a number of previously unknown species of microorganisms. At the moment, the current databases record and describe 22,500 species of bacteria. This means that the vast majority of bacteria are still not scientifically known.

“The smaller and more inconspicuous organisms are, the more they become imperceptible to us,” says Overmann. This is particularly true of soils, in which microbial diversity is largely invisible and yet huge at the same time. “In a thimbleful of soil, you’ll find traces of up to 50,000 different species of bacteria.” If you were to take another thimbleful of soil from a location right next to the previous one, you might well find thousands of different species in this sample. “This shows how little we actually know.”

Single-cell antiheroes

Overmann also wants to correct the image that people have of microbes: “Most people’s predominant image of bacteria is in fact completely distorted. In the public perception, they’re often considered to be equivalent to pathogens.” But in reality, only a very small proportion of the bacteria we’re aware of are dangerous to humans. The vast majority of these “evil” pathogens – roughly 1,000 species – have been known for long and are well studied since the days of Robert Koch because they can be cultivated in the laboratory and have important implications for medicine.

However, the overwhelming majority of bacteria live in the soil, in water, on plants, in animals or other ordinary and extraordinary habitats, where they perform key roles. Most of them are not dangerous pathogens, but “do things that in most cases are absolutely vital, for example maintaining the fertility of the soil”.

What is more, microorganisms are not just genetically diverse, but they are also surprisingly different from a biochemical perspective, says Overmann. Some of them live without oxygen, others can survive in temperatures of more than 100 degrees Celsius, and others can even metabolize substances that higher organisms are unable to access. “Although they might all look quite similar, in biochemical terms they boast much greater diversity than plants and animals.”

Huge amounts of data

The fact that researchers are now able to capture all this hidden diversity is due to the advances made in molecular biodiversity research. Modern high-throughput sequencing makes it possible to read and compare traces of DNA from samples taken from the environment. The data will then reveal molecular signatures that can’t be assigned to any described species – and yet still provide an indication of how great this unknown diversity is.

Overmann completed his doctorate at a time when comprehensive sequencing was not yet available in microbial ecology. The first PCR devices then began to appear in laboratories at the start of the 1990s during his postdoctoral period. At the same time, there was a growing awareness that many of the key processes in ecosystems are driven by organisms that scientists had previously been unaware of.

While studying for his habilitation at Carl von Ossietzky University in Oldenburg, Overmann set up a molecular biology laboratory in his research group at the time to carry out studies in this area. Looking back now, these initial molecular methods heralded the beginning of a field of research that has evolved at rapid pace ever since.

However, the new methods also saw an explosion in the amount of data. Overmann recalls his early days at the Leibniz Institute DSMZ, the German Collection of Microorganisms and Cell Cultures in Braunschweig: “At my previous place of work, this led to a situation where for the first time we actually overloaded the servers.” When millions of sequences are generated and compared with each other at hundreds of sampling points, this places huge demands on computing power, databases and bioinformatics.

 From LMU to Braunschweig – and back

Overmann is well acquainted with LMU. It is where he worked as a professor in the field of microbial and molecular ecology from 2000 to 2010. During this time, his working group made significant progress that he was then able to continue to build on when he moved to Braunschweig. Overmann served almost three terms of office as Director of Department I in the Faculty of Biology. Looking back, he says it was also good training for roles he would go on to assume in science management: “Developing, persuading, managing people.”

In 2010, he moved to Braunschweig to take up the directorship at DSMZ, the German Collection of Microorganisms and Cell Cultures. This facility is one of the most important microbiological collections anywhere in the world, with around 80 percent of all scientifically described species of bacteria being stored and provided to the research community.

Overmann has continued to expand the collection greatly in recent years. He set up a sequencing department, introduced long-read technologies at an early stage, and established a bioinformatics, IT and database department. During his tenure, the number of people working at DSMZ doubled from less than 120 to almost 240 employees.

He focused in particular on digitizing the collections. New, curated databases have made it possible to make information about bacterial strains accessible and capable of being evaluated not just in analog form via material samples, but also digitally. “Our databases have been made AI-ready,” says Overmann.

Natural history collections of the future

Overmann is now bringing all this experience to his new role in Munich. As Director General of the SNSB, his perspective has become much broader. The collections include not microorganisms but the whole of animate and inanimate nature.

But the microbiologist sees clear lines connecting macro- and microorganisms. Microbiome research plays a role in almost all areas of nature: in the root zone of plants, in digestive symbioses of animals, and in insects, whose microbiomes are often still almost an unknown quantity. This is where he wants to keep contributing his technical expertise. Above all though, he is keen to keep strengthening SNSB when it comes to research and in particular to bioinformatics, databases, IT and sequencing – his long-term vision is to join the Leibniz Association.

Hotspot for biodiversity research

As Director General, you’re not just an expert academic, says Overmann, but “to a large extent you’re a manager”. The role involves integrating all components of science-focused institution “into a greater entity” and developing it into a powerful organization that has an international presence and a shared mission.

The link to LMU is really crucial for him. He hopes that his work at LMU and directorship of SNSB will bring together shared goals and topics at the two institutions. At the Faculty of Biology, evolutionary ecology, adaptation and biodiversity all play an important role – there are clear areas of overlap with the research conducted at SNSB. The SNSB will bring additional perspectives – from paleontology and anthropology to paleoanatomy.

Overmann believes this presents a special opportunity for Munich. “I’m convinced that the work of LMU and SNSB is highly complementary and fits together very well in terms of its strategic focus.” Closer cooperation could produce shared priorities and enhance the visibility and prominence of both institutions throughout Germany.