Abstract
Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
Highlights
After bacterial cell division on surfaces, daughter cells often remain in close proximity to their mother cells
For all measurements performed on colonies, including microscopy-based measurements, the colonies were grown on top of filter membranes that were placed on M9 agar (Figure 1—figure supplement 1A)
We observed that under anoxic conditions, E. coli cannot utilize alanine as a carbon or nitrogen source (Figure 3D). These results suggest that the alanine secreted in the glucose- and ammonium-rich anaerobic region of the colony can be consumed in the aerobic region of the colony as a cross-fed metabolite
Summary
After bacterial cell division on surfaces, daughter cells often remain in close proximity to their mother cells. This process can yield closely packed populations with spatial structure, which are often held together by an extracellular matrix. Bacterial growth into densely-packed spatially structured communities, and metabolic activity of the constituent cells, naturally lead to physiological differentiation (Evans et al, 2020; Røder et al, 2020; Serra, Richter, Klauck, et al, 2013; Stewart & Franklin, 2008)
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