Mapping microbial growth, turnover and necromass formation in soil microhabitats using photothermal infrared spectromicroscopy

Current efforts to enhance carbon storage and minimize losses in natural and managed soil systems increasingly recognize microbial necromass (i.e., the sum of extracellular microbial products as well as dead cells) as a major contributor to persistent carbon. To date, however, the abiotic and biotic factors controlling necromass formation and persistence in complex and diverse soil microhabitats are poorly understood. Here we combine microfluidics experiments with optical photothermal infrared (OPTIR) spectromicroscopy and fluorescence microscopy to track microbial growth, turnover and necromass production within different microhabitats. The microfluidics approach allows us to create different microenvironments that vary in pore connectivity and, thus, show gradients in substrate, oxygen, and nutrient availability. We inoculated microfluidic plates with bacterial species isolated from a topsoil in Switzerland (21 species; see Čaušević et al., 2022), representing four major phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Using diagnostic infrared spectra along with fluorescence labelling, we can follow the growth dynamics of different bacterial species within synthetic communities as well as their turnover and associated necromass formation. Spectra were obtained for soil bacteria known to differ in essential ecophysiological characteristics, such as EPS production, Gram classification (Gram-positive vs. Gram-negative), and predatory versus non-predatory behaviour. We will report on a first proof-of-concept experiment that highlights the potential for this approach to reveal critical interactions between bacterial traits, microhabitats characteristics, growth dynamics, and necromass formation. 

 

Literature cited:

Čaušević, S., Tackmann, J., Sentchilo, V., von Mering, C., & van der Meer, J. R. (2022). Reproducible propagation of species-rich soil bacterial communities suggests robust underlying deterministic principles of community formation. Msystems, 7(2), e00160-22.