Investigating How Spatial Confinement May Drive Microbial Interactions in Soils and Sediments.

Spatial confinement affects the behavior of microbial communities that occupy critical niches in the environment. Microsites in soils and sediments are thought to comprise unique microbial populations and activity that may be substantially different than what is represented in the bulk environmental matrix. However, the influence of spatial confinement on microbial growth is poorly understood. To better understand the effects of spatial confinement on microbial interactions, and to mimic the fine-scale heterogeneity of soils and sediments, we have developed transparent microwell arrays on a glass microscope coverslip using photolithography. The transparent microwells (5-100 µm diameter; 5 µm depth size range) allow for both high replication and high resolution imaging during microbial growth under environmentally relevant conditions in the laboratory. Important soil and sedimentary bacteria have recently been studied, including anaerobic organohalide/Fe(III)-reducer Geobacter lovleyi SZ, and aerobes Pseudomonas sp. GM16 and Rahnella sp. OV588 from the ORNL Plant Microbe Interfaces (PMI), Populus rhizosphere collection, which are important for C and N cycling. Current experiments are aimed at directed cobamide production by Geobacter to stimulate the growth of corrinoid auxotrophs in mixed culture. Biofilm formation, motility and salicin/salicyl-alcohol cycling in Pseudomonas and Rahnella cultures are being studied to better understand their functional role in the rhizosphere of Populus. Analytical techniques such as MALDI-MS, whole genome amplification, qPCR and next generation sequencing (NGS) are being adapted to collect information from individual microwells. We are concurrently developing an agent-based model to examine both observed and hypothetical microbial interactions under different conditions of interest. By investigating microbial behavior in microwells that spatially mimic fine-scale features in soils and sediments, we aim to link microscopic biological and physical parameters to large-scale dynamics, and explore how spatial confinement may drive microbial interactions in the environment.