Even in their own environment, specialist microbes are dominated by generalists

Large, global dataset leads to new insights about microorganisms

Specialized microorganisms that are found in only one type of environment turn out to occur there in relatively low but stable numbers. Microorganisms that live in many different types of environments, on the other hand, are able to rapidly increase in numbers when conditions are favourable. Researchers from Utrecht University and the Friedrich-Schiller-Universit├Ąt Jena conclude this based on a new method to distinguish generalist and specialist microbes, which they applied to a large, global dataset. The results of the study were published yesterday in the journal Nature Ecology & Evolution.

Bastiaan von Meijenfeldt, first author of the paper and former PhD candidate at Utrecht University, explains what made this study possible. Von Meijenfeldt: "It has actually only recently become possible to take a sample from the environment, for example from the sea, the soil or the intestines of a human being, and then use the DNA in that sample to determine which microorganisms such as bacteria and archaea are present in it. In recent years, a lot of researchers around the world have done so, and their datasets have often ended up online. We decided to collect this online data. Doing so, we were able to combine data from more than 22 thousand samples taken from all kinds of different environments, such as coastal zones, plants and human faeces. Then we used that data to investigate, for the first time on such large scale, which microbes are generalists and specialists."

Microbiomes

Een gemeenschap micro-organismen
A community of microbes

Within ecology, organisms are called generalists when they occur in many different types of environment. But how do you define these environments? Von Meijenfeldt: "For a bacterium, a human gut may be virtually the same environment as a monkey's gut. On the other hand, a certain pond may be a completely different environment for a microbe than another pond."

The researchers chose to develop a new method to overcome this problem. Von Meijenfeldt: "We decided to look at microbiomes, communities of microorganisms. If two different samples contained the same combinations of microorganisms in the same proportions, we considered the two samples to belong to the same microbiome. We then determined the total number of microbiomes that were present in our data set. We referred to microorganisms that occurred in several of those microbiomes as generalists, and we classified microorganisms that were found in only one microbiome as specialists."

Generalists turn out to be opportunistic: if conditions are right, they overgrow everything.

Bastiaan von Meijenfeldt

Generalists dominate

Remarkably, the researchers found that generalists dominated in most samples, meaning that they occurred in greater numbers than specialists. This goes against the prevailing idea that generalists are usually unable to compete with local specialists. Von Meijenfeldt: "The idea is that generalists can do everything, but only just a little bit of everything. And that specialists are highly adapted to their own environment. Therefore, the expectation was that specialists would dominate locally. But what we see is exactly the opposite. Generalists turn out to be opportunistic: if conditions are right, they overgrow everything. Specialists occurred in lower, but more stable, numbers."

Attuned to adapt quickly

By analysing the DNA of generalists and specialists, the researchers came to even more surprising discoveries. It is often suggested that generalists need a lot of DNA, as a diverse gene pool would allow them to live off a variety of different food sources. But Von Meijenfeldt and colleagues did not observe that generalists had more DNA than specialists.

Generalists who are related to each other were however found to be genetically less similar than specialists who are related. This is partly because generalists appear to be more attuned to absorbing new DNA from their environment or via other bacteria or viruses, which helps them to adapt quickly to new environments. The DNA of specialists, on the other hand, appears to be stable and not as likely to change. Von Meijenfeldt: "Specialists often live in similar environments, so they simply do not need to change that quickly."

We actually still know little about how microbial communities form and why one microbe lives in a certain place and another microbe lives somewhere else.

Bastiaan von Meijenfeldt

Better understanding

Von Meijenfeldt says that the research provides a better understanding of how communities of microorganisms work. Von Meijenfeldt: "We actually still know little about how microbial communities form and why one microbe lives in a certain place and another microbe lives somewhere else. This is striking, since it is clear that microbes are very important. Just think of the bacteria that live in our gut and the role microbes play in chemical cycles. Our research provides insight into how microbial communities function ecologically and evolutionary."

Publication

A social niche breadth score reveals niche range strategies of generalists and specialists

Nature Ecology & Evolution, 3 April 2023. DOI: 10.1038/s41559-023-02027-7

F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, Bas E. Dutilh