The adaptation chip: repurposing the principles of the ichip for guiding in situ experimental evolution

Soil microbial ecosystems are complex and difficult to replicate in laboratory settings. It is often unclear which pressures most strongly shape microbial survival and evolution in situ, and new methods are needed to intersect the manipulative power of the lab with the reality of field environments. One recent innovation was the "isolation chip," in which many new microbial isolates could be cultured on agar within a buried diffusion chamber while exposed to environmental inputs through fine-pored membranes. Here, we created a modified version of this device containing biologically-cleared soil instead of agar, to trial an in situ reverse ecology experimental evolution approach. Using these "adaptation chips (aChips)" we exposed populations of two different soil-dwelling bacteria (Priestia megaterium and Streptomyces lydicus) to several farm soils in the Northeast US for up to two years, documenting mutations arising in the evolving populations. While evolution was remarkably slow in the field, P. megaterium populations accumulated many mutations pre-burial during aChip construction which seemingly reflected zinc limitation in the aChip carrier soil. Although post-burial mutations were observed in both P. megaterium and S. lydicus populations, they remained at low frequency and did not display parallelism between aChips buried at the same sites, indicating a lack of strong positive selection and/or limited generations of population growth within the aChip. We suggest several improvements to aChip design to facilitate greater evolutionary progression, including a larger within-aChip soil volume and fewer cells initially secured inside the aChip.