Mohrlok, M. | bioRxiv Science

bioRxiv2026

An experimental model system to investigate microscale mechanisms behind the soil priming effect

The soil priming effect plays an important role in the global carbon cycle. Although well-studied, the mechanisms behind it remain elusive. So far, studies measured the phenomenon at the bulk soil scale, neglecting that it arises from spatially explicit processes that take place at the microscale. Here, we present a novel approach using a microfluidic device to directly assess the response of soil microbes living on a patch of complex substrate to a pulse of easily available substrate. Using time-resolved fluorescence microscopy, we tracked motility, position, shape characteristics and attached biomass of green fluorescent protein expressing Bacillus subtilis cells living on a transparent carboxymethylcellulose substrate patch exposed to a pulse of growth medium with differing concentrations. Assessing CMC decomposition via Congo-Red staining after 42 days of incubations with constant observation, we observed increased decomposition upon addition of enough labile substrate, resembling a priming effect. The pulse triggered a transient increase in bacterial motility, indicating the formation of exploring and growing subpopulations respectively. We observed a concentration-dependent growth response, resulting in different behaviors. High concentrations led to high biomass and decomposition of CMC, however growth was quickly limited, possibly by depletion of necessary nutrients and waste accumulation. Intermediate concentration, however, resulted in a more sustained attached biomass, that showed evidence of spatial self-organization, leading to similar decomposition. We present a novel experimental model system to study the behavior of soil microbes decomposing complex substrate and provide a unique view into the response of such a population to a labile substrate pulse.

microbiology↗

bioRxiv2023

Bacteria face trade-offs in the decomposition of complex biopolymers

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of systems complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes. Author summaryThe decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate. Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities.

microbiology↗