Introduction: Microorganisms occur in an immense variety on earth, that inhabit a wide range of diverse habitats. A significant portion of these microorganisms, collectively termed microbial dark matter (MDM), are still unknown. Since most of these microorganisms do not follow an isolated planktonic lifestyle, cultivating these microorganisms in laboratory settings is challenging. Consequently, there is a great need for matrices that facilitate the cultivation of complex microbial communities.

Goals: Development of a macroporous elastomeric silicon foam (MESIF) as a matrix integrated into a chip with a media reservoir to enable the growth of complex microbial communities.

Methods: MESIF materials with varying pore sizes and chemically modified surfaces were prepared. Integration of MESIF into a chip was followed by a characterization of its colonization by the model organism Escherichia coli. The impact of MESIF on the enrichment of environmental microbiomes was assessed through genomic DNA sequencing and bioinformatics.

Results: The model organism Escherichia coli was used to validate the rapid colonization of the modifiable MESIF in the chip. Environmental microbiomes were enriched in the MESIF chip within a few days. Especially organisms belonging to the Candidate Phyla Radiation could be enriched in chips placed in a moving bed biofilter of a fish tank. From dry air from a chicken coop a variety of biotechnologically interesting Actinobacteriota could be enriched and detected in the chip. Sampling with the herbicide glyphosate as the sole carbon source enriched Desulfobacteria, which are known to include species metabolizing glyphosate.

Summary: The MESIF materials serving as macroporous enrichment matrix, can be easily prepared with reproducible properties. The chip design provides a platform for enriching uncultured microorganisms, facilitating the systematic exploration of microbial dark matter.

Literature:Zoheir AE, Meisch L, Velaz Martín M, Bickmann C, Kiselev A, Lenk F, Kaster A-K, Rabe KS and Niemeyer CM.: Macroporous Silicone Chips for Decoding Microbial Dark Matter in Environmental Microbiomes. ACS Appl. Mater. Interfaces (2022) 14 (44):49592