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The results illustrate the potential lying at the interface between nanoscale biophysics …


Biology Articles » Biophysics » Molecular Biophysics » Bacterial metapopulations in nanofabricated landscapes » Methods

Methods
- Bacterial metapopulations in nanofabricated landscapes

The basic idea in our device is the creation (by etching in a Si wafer) of a row of microfabricated 100 μm × 100 μm × 30 μm MHPs that are weakly linked to each other and to a source of food (Fig. 2A). The MHPs are weakly linked together by 50-μm-long, 5-μm-wide, and 30-μm-deep corridors connecting adjacent MHPs (Fig. 2B). The final (1D) device consists of a chain of 85 MHPs (Fig. 2A). It is seeded from one end by bacteria from a larger “interface chamber” (see Supporting Appendix).

To make an ecosystem with a rate-limited supply of resources, we weakly link patches to two feeder channels for the supply of food (Fig. 2B). In this rate-limited scenario, organisms must adapt their demands on their environment. Each of the two feeder channels are connected to the MHPs via five nanoslits that are only 200 nm deep but 15 μm wide and 20 μm long. Thus, they act as weak links between the MHP and the feeder channels. These nanoslits allow nutrients (and waste) to diffuse into and out of the MHPs but are too thin for E. coli to pass through. They provide a critical role beyond the supply of food and removal of waste. By building a different number (m) of nanoslits feeding different MHPs, we introduce relative niche differences among collections of MHPs (Fig. 2C). We can build MHPs with no exchange, λmin = 0; intermediate exchanges, m × λ* for m ∈ {1, …, 9}; and maximum exchange, λmax = 10 × λ*. The value λ* here represents the contribution to the exchange rate by a single nanoslit. In this way, adaptive (fitness) landscapes (∇λ) can be created by patterning ecotopes (spatially connected collections of MHPs sharing the same λi) onto the habitat spatial distribution. The 1D experiments we describe in this article were conducted in three types of adaptive landscapes: (i) a flat one, consisting of a single ecotope of MHPs where all 10 nanoslits are open; (ii) a B&W landscape, consisting of two ecotopes (at the right of the array we place MHPs with all 10 nanoslits open, and on the left we put MHPs with all nanoslits closed); and (iii) a more complex “rugged” landscape, consisting of three zones [to the left a nutrient-limited “stress” domain made of MHPs with all nanoslits closed (no supply), at the center a high nutrient-supply zone, separating the stress zone from a rugged zone (to the right), made of clusters of all-open and partially open MHPs embedded on a desert of stressed MHPs].

Because metapopulations are expected to have a complex behavior, a simple 0D MHP was constructed (Fig. 2D) to allow simple studies of a single MHP.


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