April 29, 2021

In search of the soil microbial interactome: high-throughput exploration of bacterial interactions in microbeads

Soil microbiomes are rich of thousands of microbial species that live next to each other in a physically and chemically complex habitat. These microscopic inhabitants of soil are not mere bystanders: their metabolic activity is key to a dynamic soil, from global carbon turnover to the release of rare minerals. 

Microbial ecologists still strive to understand what controls the activity of this complex soil microbiome. One important piece of that puzzle are the countless metabolic interactions that take place between microbial species – which cover the whole spectrum from helping to killing each other – and the environmental factors that modulate them. Yet, experimental methodologies that can probe microbial interactions in the laboratory are usually not well suited to the diversity and (often) intractability of soil microbes.

Now, a new study from the group of Jan van der Meer (University of Lausanne/NCCR Microbiomes) proposes an approach that circumvents both the reliance on culturable isolates and the relatively low-throughput nature of classic interaction experiments on agar plates. The lead author, Manupriyam Dubey, used thousands of agarose minibeads (approx. 50 microns in diameter) that embedded single cells or pairs of bacterial cells isolated from a natural sandy soil near the University. Using quantitative imaging developed by Serge Pelet and Noushin Hadadi, the study measured microbial growth in the microbeads, revealing a counterintuitive result: mixed pairs of cells grew more productively than single cells, highlighting positive interactions among soil microbes.

However, while certain pairs led to synergistic growth, the authors also observed many negative outcomes, with only one partner emerging victorious. The forced confinement in beads had thus an inadvertent but important consequence: it appeared to intensify interactions. It followed that, compared with cultures in liquid media, the global community diversity in beads was low. Mathematical models of community growth suggested that this was the result of negative interactions becoming more dominant in the confined and less connected environment of the beads. Such findings on interactions within soil microbial communities will inform future efforts to influence or engineer microbial functions, a long-term goal of the NCCR Microbiomes.

You can read Jan van der Meer’s ‘behind the scene’ take on the paper here.

Image of microbeads courtesy of J. R. van der Meer.