Video: A time-lapse recording shows how a bacterial colony spreads and structures itself on a culture medium in the laboratory. © Biozentrum, University of Basel
Microbes are not simple: bacterial communities can be structured in a sophisticated way and the single-celled organisms benefit from each other over generations, a study shows. Pioneers in a colony leave behind certain metabolic products as a source of food for their offspring. The researchers were able to demonstrate this using a newly developed investigation method using a model bacterium. They combined microscopic and genetic techniques so that the activation of certain programs in the microbes can be linked to the different development stages.
They are so tiny that we cannot see them with the naked eye, and yet they are giants in our planet’s living environment: Bacteria are teeming everywhere, some of which play fundamental roles in natural processes. Some species decompose biomass in the soil, others help with digestion in the intestines and, as we know, some can also make us sick. As a rule, these unicellular organisms do not live alone, but form communities. Living together can offer them many advantages: As a collective, they develop certain characteristics that serve their nutrition and help them withstand difficult conditions and attacks. For example, some species form so-called biofilms – slimy layers that allow them to adhere better.
Methodological progress
Because of their importance for microbial life, insights into the formation processes of such bacterial structures are important. An international research team led by Hannah Jeckel from the University of Basel has now made an important contribution to this. Their new examination method is based on the combination of modern microscopy, genetic analyzes and automated sampling. In the system, a bacterial colony growing on a culture medium is targeted by a microscope that can flexibly focus on specific areas. It is coupled with a robot arm that, thanks to its extremely fine mobility, enables precise sampling of the microbes at specific locations and at different times.
The material can then be submitted to genetic analysis procedures that reveal which genetic makeup is active in the microbes. In this way, the scientists can record this so-called spatiotemporal transcriptome of the bacteria and link it to certain features that show up in the microscopic images.
The researchers applied their method to the model bacterium Bacillus subtilis, which is also found in the human intestinal flora. As they report, their results made it clear how complex and dynamic things are in the colonies of these microbes. This showed how cooperatively the bacteria behaved for the benefit of the entire community, which the team describes as a swarm. The division into different subpopulations apparently also serves this purpose. As the researchers report, the gene activity profiles of these units reflect the fact that they produce and use different metabolic products.
Prevention and structuring benefit the community
A particularly interesting finding was that the unicellular organisms apparently provide for the nutrition of their successors: During their migration, earlier generations of bacteria deposit metabolic products that can be used by later ones growing in the same place. “Our observations showed that these collectively living bacteria cooperate with each other over several generations,” says senior author Knut Drescher from the University of Basel.
The type of substances available in turn influences the spread and behavior in the bacterial community. According to the researchers, it can be divided into three units: the swarm front, the intermediate region and the center. However, the transitions are fluid. “Depending on the region, the bacteria differ from each other in appearance, properties and behavior,” says Jeckel. “While they are mostly mobile at the edges, the bacteria in the center form long, immobile threads and assemble into a 3D biofilm,” says the researcher. This spatial and temporal distribution of bacteria with different properties allows the community to expand and at the same time entrench itself in a protective biofilm, the scientists explain.
According to them, the new procedure could now be a methodological breakthrough in microbial research: They hope that their system and the results already achieved can now benefit further research into the complexity and dynamics in the mysterious world of microbes.
Source: University of Basel, specialist article: Nature Microbiology, doi: 10.1038/s41564-023-01518-4