Bacterial metapopulations in nanofabricated landscapes

Abstract

We have constructed a linear array of coupled, microscale patches of habitat. When bacteria are inoculated into this habitat landscape, a metapopulation emerges. Local bacterial populations in each patch coexist and weakly couple with neighbor populations in nearby patches. These spatially distributed bacterial populations interact through local extinction and colonization processes. We have further built heterogeneous habitat landscapes to study the adaptive dynamics of the bacterial metapopulations. By patterning habitat differences across the landscape, our device physically implements an adaptive landscape. In landscapes with higher niche diversity, we observe rapid adaptation to large-scale, low-quality (high-stress) areas. Our results illustrate the potential lying at the interface between nanoscale biophysics and landscape evolutionary ecology.biophysics ͉ microbiology ͉ landscape ecology ͉ metapopulation biology

Bacterial predator–prey dynamics in microscale patchy landscapes

“…We used strain JEK 1036 previously described in [18], which is wildtype E. coli W3110 labelled with a green fluorescent protein (lacZY::GFPmut2). JEK 1036 was grown overnight (O/N) from glycerol in Luria-Bertani (LB) broth at 308C whilst shaken at 200 r.p.m., diluted 1 000-fold the next morning in Diluted Nutrient Broth (DNB, 0.8 g l 21 NB, 2 mM CaCl 2 .…”

“…To emulate the patchy geometry of natural bacterial habitats with relevant spatial dimensions (figure 1a), and to allow for the quantitative study of predator-prey interactions as a function of space and time, we created a well-defined linear array of habitat patches on a silicon chip, that are connected to each other by narrow corridors (figure 1b,d, top) [18,35]. As a control for the patchiness of the patchy geometry, we also designed a continuous landscape of identical volume that consisted of one large habitat without internal constrictions (figure 1e).…”

“…As a control for the patchiness of the patchy geometry, we also designed a continuous landscape of identical volume that consisted of one large habitat without internal constrictions (figure 1e). Microhabitats were fabricated in silicon using a two-step procedure of photolithography and reactive ion etching following a previously published protocol [18,35]. The patchy microhabitats consisted of 85 patches (each 100 mm in length, 100 mm in width, and 15 mm in depth) connected by corridors (50 Â 5 Â 15 mm), the continuous microhabitats consisted of a single patch (8 500 Â 100 Â 15 mm) with a total volume identical to the volume of the patchy habitat.…”

“…Over the past few years, microfabrication techniques have allowed for the creation of microscale synthetic ecosystems that are structured at the spatial scales relevant to bacterial populations [17][18][19][20][21]. It thus has become technically feasible to quantify bacterial predator-prey interactions in each of the individual micrometre-scale patches of a landscape under controlled conditions over many generations.…”

Physics of cancer propagation: A game theory perspective

“…11 The GASP mutant has an interesting gene rearrangement which leads to the GASP phenotype. The main difference between the wild-type alleles is a duplication in the GASP mutant of the rpoS 819 sequence (gcaggggctgaatatcgaa).…”