Microscale mechanisms behind the priming effect - Insights from a novel experimental model system

Pulses of labile substrate, as for example exuded by plant roots, have been shown to accelerate decomposition of complex Soil Organic Matter (SOM), with strong implications for soil carbon balance and the global carbon cycle. Despite its importance, the mechanisms behind this so-called priming effect’ are still not fully clear. Most studies to date focus on investigating priming effects at the bulk soil scale. However, as this effect is caused by the action of soil microbes, it can be assumed that it fundamentally emerges from microscale processes. Observing the activities of microbial decomposers at the microscale could thus be the key for a better mechanistic understanding of the priming effect, but this has been hampered by technical challenges of microscale in-situ observations in soil so far. 

Here, we present a novel approach to study the priming effect on scales relevant to its main actors. We developed a microfluidic model system and image analysis pipeline that allows us to track microbes living on transparent agarose patches containing carboxymethylcellulose (CMC) with time-resolved fluorescence microscopy. Using this system, we exposed fluorescently tagged cellulose-degrading soil bacteria (Bacillus subtilis) to pulses of labile substrate at different concentrations. Total CMC decomposition was finally assessed by Congo Red staining of the substrate patches.

After 42 days of incubation with periodic observations, we observed a positive priming effect in our system: Increased decomposition of CMC upon addition of enough labile substrate. Our image analysis suggests that different mechanisms caused decomposition at different substrate concentrations: In chips supplied with the highest concentration of labile substrate, decomposition was associated with microbial biomass, which peaked shortly after the substrate pulse but then quickly declined, possibly due to depletion of essential nutrients or waste accumulation. On the contrary, a lower but more sustained and spatially organized biomass at intermediate concentration led to the same amount of decomposition. Additionally, we found that motility was transiently increased in the bacterial population after the pulse, suggesting that substrate pulses can facilitate the colonization of soil microhabitats. 

Our approach, albeit strongly simplifying the microbial environment in soils, allows novel insights into fundamental microbial mechanisms at the microscale that could play a role during rhizosphere priming.