Positive news on the social life of bacteria


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Positive news on the social life of bacteria

Bacteria are social organisms and interact with other organisms in their vicinity. They can have a positive effect, by producing compounds that other bacteria can use, or even serve as protection against intruders or a harsh environment. But bacteria can also be at war with each other, for instance when they compete for food, or when they produce compounds that are harmful. In any case, the type of interaction is not determined by just one party, because both species determine the outcome. In other words: the two one-way interactions determine the outcome of the bidirectional interaction.

This means that many kinds of interactions exist since one species can either have 1) no effect, 2) a positive effect, or 3) a negative effect on the other species. An overview of the possibilities is given in the figure below.

Different kinds of interactions. Created with Biorender.com

Previous studies find that cooperation is not very common, as we already reported in this article. Here, the authors claim that competition is the rule in microbes as they found positive interactions in less than 10% of all interactions. But this study could be biased – they tested only one environmental condition. However, metabolic modeling and preliminary studies show that positive interactions can happen depending on the environmental conditions (the kind and amount of nutrients available).

But why do we want to dig so deep into the social life of bacteria? And why are we specifically interested in the positive interactions? By gathering all this information, we get a better idea of which factors are necessary to change a microbial community. Ultimately, we want to be able to design communities that can boost or restore unbalanced ecosystems, which will help with environmental conservation, crop health and human health.

So what is the prevalence of positive interactions, and why do they occur? In this article published in Science Advances, Jared Kehe and colleagues used a high throughput screening platform called kChip, and looked at the interactions for more than 150.000 bidirectional cocultures. They used 20 different bacterial strains originating from the soil and tested 40 different environments (different carbon sources in different concentrations). A more detailed description of this method is given in the figure below.

Two bacterial strains – one of the two is fluorescently labeled with GFP – are mixed together with a certain ‘environment’ (different carbon sources). Then these cocultures are grown in the kChip device. The effect of the unlabeled bacteria on the labeled one can be monitored by looking at the intensity of GFP over time. This not only shows what kind of interaction it is but also how strong it is when the outcome is compared to each of the bacteria growing alone. 

Interestingly, they found that positive effects occurred in more than 40% of the cases, with parasitism as most reported ‘positive’ interaction (22%). How can parasitism be positive? Positive here means that one bacteria has an increased growth rate when growing together with another bacteria. Only 5% of the interactions were mutualistic, where both strains seemed to benefit from the presence of the other. There was also a big proportion of interactions that showed no positive or neutral effect (53%). See the figure below for a detailed overview. 

Types of interactions measured in >150.000 cocultures

The researchers noticed that the same two species behaved differently in different environments. So in one environment, they could have a mutualistic relationship, whereas in the other you might find parasitism. This makes it quite difficult to predict what type of interaction two bacteria can have in any given environment. 

So could they find any predictive element that would help to predict what kind of interaction could take place? Yes! Apparently, more positive interactions were found in strains that were taxonomically dissimilar (further away from each other in the ancestry tree). Also, strains that liked to grow on different carbon sources were more likely to show positive interactions. Interestingly, the interactions also depend on how well the bacteria were growing in a certain carbon source: there were more negative interactions (competition) if one of the bacteria was a fast grower on a certain carbon source. This explains how the interaction variability between the same pairs on different carbon sources can change.

Another interesting observation of the researchers was that some bacteria could not grow by themselves on a certain carbon source, but when another bacteria was introduced (that could grow on that carbon source), it facilitated the growth of the non-grower up to 85% of the time. At least one coculture partner could usually be found to support the growth of the otherwise non-growing strains on almost any carbon source, which could potentially explain how biodiversity can be supported when few carbon sources are available. 

The authors formulated a few mechanisms that can explain the prevalence of positive interactions:

  • Helped strains might grow on components of accumulating dead cells (See our article about bacterial cannibalism). This is however not very likely in the timescale of the experiments done in the paper (24-72 hours)
  • Bacterial strains with a positive influence on other strains might secrete carbon source-degrading enzymes, increasing overall carbon availability
  • Strains can secrete metabolites used by other strains, improving their growth

Keep in mind: this is a laboratory experiment, which does not depict bacterial diversity or environmental complexity we find in the real world. But it does give a small glimpse into an otherwise invisible world, and could eventually lead to efficiently designing and controlling beneficial microbial communities.

Link to the original post: Jared Kehe, Anthony Oritz, Anthony Kulesa, Jeff Gore, Paul C. Blainey, Jonathan Friedman, Positive interactions are common along culturable bacteria, Science Advances, November 2021

Featured image: Made with Biorender