The influence of soil structure on microbial processes in microfluidic models

Abstract: The way microbes behave in nature can vary widely depending on the spatial characteristics of the habitats they are located in. The spatial structure of the microbial environment can determine whether and to which extent processes such as organic matter degradation, and synergistic or antagonistic microbial processes occur. Investigating how the different spatial characteristics of microhabitats influence microbes has been challenging due to methodological limitations. In the case of soil sciences, attempts to describe the inner structure of the soil pore space, and to connect it to microbial processes, such as to determine the access of nutrient limited soil microorganisms to soil organic matter pools, has been one of the main goals of the field in the last years. The present work aimed at answering the question of how spatial complexity affects microbial dispersal, growth, and the degradation of a dissolved organic substrate. Using microfluidic devices, designed to mimic the inner soil pore physical structures, we first followed the dispersal and growth of soil microbes in the devices, using soil inocula or burying the microfluidic devices in the top layer of a soil (Paper I). We found that inter-kingdom interactions can play an important role for the dispersal of water-dwelling organisms and that these physically modified their environment. To reveal the effect of the different structures on microbes in more detail we tested the influence of increasing spatial complexity in a porespace on the growth and substrate degradation of bacterial and fungal laboratory strains. The parameters we used to manipulate the pore space’s complexity were two: via the turning angle and turning order of pore channels (Paper II), and via the fractal order of a pore maze (Paper III). When we tested the effect of an increase in turning angle sharpness on microbial growth, we found that as angles became sharper, bacterial and fungal growth decreased, but fungi were more affected than bacteria. We also found that their substrate degradation was only affected when bacteria and fungi grew together, being lower as the angles were sharper. Our next series of experiments, testing the effect of maze fractal complexity, however, showed a different picture. The increase in maze complexity reduced fungal growh, similar to the previous experiments, but increased bacterial growth and substrate consumption, at least until a certain depth into the mazes, contrary to our initial hypothesis. To increase the relevance of our studies, we performed experiments in both microfluidic device designs inoculated with a soil microbial extract and followed the substrate degradation patterns over time (Paper IV). We found that as complexity increased, both in terms of angle sharpness and fractal order, substrate consumption also increased. Our results, specially in mazes, might be caused by a reduced competition among bacterial communities and individuals in complex habitats, allowing co-existence of different metabolic strategies and the onset of bacterial biofilm formation leading to a higher degradation efficiency, but further studies are required to confirm this. Our results show that the spatial characteristic of microhabitats is an important factor providing microbes with conditions for a wide variety of ecological interactions that determine their growth and their organic matter turnover.