novel in-situ microbial enrichment

Cultured microorganisms are integral components in many industries, medicine, agriculture and environmental remediation. Yet, the vast majority of microorganisms remain uncultured, and therefore mostly unexplored and unexploited. Here we present a new in situ incubation system, the MicroCaptureArray, based on paired nutrient and capture pills placed in a 3D printed array. This system creates a chemical and structural microenvironment that facilitates the attraction, capture and growth of microorganisms with particular metabolic functions. The system was used to selectively capture nitrifying, nitrogen fixing and sulfur oxidizing microorganisms from soil and pond sediment by tailoring the nutrient pills to attract species with these specific biogeochemical functions. Most of the retrieved species were undetectable in pure soil and sediment samples. Furthermore, some OTUs could not be allocated beyond the kingdom or phylum level, indicating presence of new microorganisms in these samples. Hopefully, the MicroCaptureArray will allow us to capture and culture more microorganisms from the rare biosphere.