Macroporous Silicone Chips for Decoding Microbial Dark Matter in Environmental Microbiomes.

Area of Science:

• Microbiology
• Biotechnology
• Environmental Science

Background:

• Vast microbial diversity remains uncharacterized, termed microbial dark matter (MDM).
• Elucidating MDM is crucial for biotechnological applications.
• Existing methods for microbial sampling and cultivation have limitations.

Purpose of the Study:

• To develop and validate a novel chip for decoding microbial dark matter in environmental microbiomes.
• To assess the chip's efficiency in sampling and enriching diverse microorganisms.
• To demonstrate the chip's utility in identifying previously unculturable microbes.

Main Methods:

• Fabrication of a scalable chip integrating macroporous elastomeric silicone foam (MESIF).
• Technical validation using *Escherichia coli* for colonization efficiency.
• Application in diverse environmental habitats including biofilters, wastewater treatment plants, and air.
• Sequencing analysis to identify enriched microbial communities.

Main Results:

• The MESIF chip demonstrated rapid colonization and high sampling robustness across various environments.
• Efficient enrichment of key microbial groups, including *Candidate Phyla Radiation* and *Actinobacteriota*, was achieved.
• The chip facilitated the targeted enrichment of glyphosate-degrading bacteria (*Cyanobacteria*, *Desulfobacteria*) from wastewater.

Conclusions:

• The novel MESIF chip is a low-cost, effective tool for systematic MDM exploration.
• The chip enables rapid detection and enrichment of diverse microbial communities.
• This technology opens new avenues for cultivating previously unculturable microorganisms and discovering novel biotechnological functions.