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Empirical soil models reproducing soil characteristics can help to reduce the inherent complexity of soils in experiments. Microengineered or microfluidic soil chips can simulate the soil pore space at microscale in a transparent material that enables direct visual investigation of soil- and soil microbial processes including monitoring of single cells and their interactions in communities. Through the chips it is possible to control and closely monitor microhabitat conditions including oxygen levels and pH, and to single out factors such as spatial relations, pore space structure or resource patch size. They can be designed either close to realistic conditions such as based on µCT measurements, or using simple geometrical patterns that can be frequently replicated and modified within the chip design. They can thus be tailored to fit scenarios of spatially explicit soil computer models and used for iterative in-silico – in-situ experiments. We found amongst others that the geometric shape of a pore space and its connectivity influences bacterial and fungal growth, their interactions and enzymatic activity. We can measure those factors spatially resolved at cellular scale. We want to initiate a discussion for future collaborations between soil chip experimentalists and computer modelers.

Microfluidics is a multidisciplinary platform that integrates microfabrication, physical chemistry analysis, automation, and microscopy. It has the advantages of precise liquid manipulation, rapid measurements, and real-time visualization at the microscale, which is especially of interest and benefit to microbial studies. Soil Chips are microfabricated microfluidic devices typically made of glass and polydimethylsiloxane (PDMS), designed to mimic the real soil network and allow real-time visualization and characterization of microbial activity at the micro-scale. They have so far been used to investigate microbial activities, interactions, community composition, and distribution under different conditions in soil analog systems. Challenge comes when working with natural soil samples. Due to mineral aggregates and debris, valuable information such as the abundance of individuals, cell morphology, and the relationship between bacteria and their geochemical and physical environment are difficult to extract via a simple thresholding method. Since microorganisms and microfluidic structures have distinct features from the noisy background that can be easily picked up by our eyes, a biologically inspired convolutional neural network model for object detection is the most suitable tool for this task.We used a small part of data from three different experiments to train a well-developed object detection and segmentation algorithm Mask RCNN and implemented further analysis of bacteria abundance, spatial distribution, and morphological characterization. We are able to plot the distribution of all the detected bacteria including clusters in terms of abundance, size, shape, and index of aggregation. A distinct difference in bacteria characteristics can be observed in the samples acquired from three locations (Greenland, Sweden, and Kenya). We are now planning to extend the classification library to include other microbial groups including fungi, protists, invertebrates, and micro arthropods.

Micro- and Nanoplastics have become a very common pollutant of soil ecosystems, but their effect on soil microorganisms is not well understood. We exposed a model soil bacterium (Pseudomonas) and a model soil fungus (Coprinopsis) to different concentrations of nanosized polystyrene beads in microfluidic soil chips. The transparent chips allowed us to perform direct investigation of the effect of beads on abundance of the microbes and on interactions of individual cells with the nanobeads. Growth of both the bacteria and the fungi was reduced by the exposure to nanoplastics, along with a reduction in bacterial enzymatic activity. Nanobeads were strongly attracted to fungal hyphae, causing a high concentration of beads along the first hyphae to enter a pore space, and thus freeing the surrounding from a large proportion of the beads. This study contributes to our understanding of direct toxicity effects and interactions of nanoplastics to soil microbes.

Soil organisms live and interact in the intricate soil pore space labyrinth, but their natural habitat and natural interactions are difficult to study because of the opaqueness of the soil. We recently developed microfluidic model systems that simulate the spatial microstructure of soil microbial habitats in a transparent material, which we call Soil Chips. They allow us to study the impact of soil physical microstructures on microbes, microbial behavior and realistic microbial interactions, live and at the scale of their cells.Using soil inocula, we get a large proportion of the natural microbial community into our chips and can study soil bacteria, fungi and smaller protists and nematodes in their food webs and in different spatial habitats. We were especially interested in soil protists that are generally understudied in their diversity and ecosystem functions. We were able to observe a large variety of flagellated, ciliated and amoeboid protists in the chips, predating on the bacterial populations and even on fungal hyphae. Some larger amoebae only entered the chips with their pseudopodia for predation. The colonization succession pattern of the chips showed predator-prey oscillations, with periodically high levels of different protists, followed by retreat or encystation. In chips that were containing initially dry pore spaces, colonization success of protists was strongly increased by the presence of fungal hyphae, which paved the way for protists by wetting pore spaces.The soil chips enable us to study the influence of trophic interactions such as the presence of predators on bacterial and fungal nutrient cycling. Disturbances that stronger influence protists than bacteria may have a pronounced effect on bacterial population sizes and their organic matter degradation activities. Beyond the scientific potential, the chips can also bring soils closer to people and hopefully increase engagement in soil health conservation.

A better understanding of soil carbon sequestration is important as the rapid elevation of carbon emission has significantly impacted our climate. The soil carbon dynamic process is strongly associated with trophic interactions in the soil communities. However, direct investigation of microbes and trophic interactions at microscale has been a major challenge due to the opacity of soil and the exceedingly complex pore spaces that limit direct in situ observation of trophic interactions and their variations with soil structure. As such, we decide to use microfluidic technique to create a two dimensional heterogeneous porous microenvironment containing nutrient patches of different quantity and quality to mimic the complex soil pore network and its heterogenous distribution of resources. This allows us to directly visualize and investigate the ability of organisms to access spaces starting from an initial ecophysiological precondition to changes of spatial accessibility mediated by interactions with the microbial community.Microfluidics is a multidisciplinary platform that integrates micro fabrication, physical chemistry analysis, automation and microscopy. It has been widely used in life science and chemistry as it allows precise liquid manipulation, rapid measurements, real-time visualization at microscale, which is especially of interest and benefit to microbial studies. We created a complex pore network mimicking different soil environments – earlier considered impossible to achieve experimentally. The microfluidic channel contains a random distribution of cylindrical pillars of different sizes so as to mimic the pore space variations found in real soil. The randomness in the design creates various spatial availability for microbes. The nutrient patches within the pore space are achieved via capillary force trapping or UV curing hydrogel. In the former method, the patches are created by trapping nutrients in the predesign pore space due to interfacial tension between air and nutrient liquid. However, displacement instability during air injection makes it hard to control the formation of the patches. The latter enables better and more precise patches size and location manipulation but hydrogel biocompatibility with various fungal species remains a major challenge and hydrogel curing requires special facilities. The microfluidic nutrient patches provide spatial heterogeneities of resource distribution, which allows us to have a better understanding of the influence of spatial accessibility on the microbial community. The chip has five different nutrient distribution levels, ranging from centralized – a single large nutrient patch- to increasingly dispersed nutrient distributions - sets of up to 49 loosely distributed nutrient patches of equal total volume. The experiments will be carried out using sterile cultures of fluorescent bacteria and fungi, synthetic communities of combinations of these, or a whole soil community inoculum. We will quantify the consumption of organic matter from the different areas via fluorescent substrates, and measure the bio- and necromass produced. We hypothesise that denser distribution will increase the net decomposition of organic matter as a centralized nutrient location increases the interactions within the microbial communities and individuals present in that area, which induces higher competition stress in the different communities.