Optimized DNA Extraction from Coffee Roots Colonized by Arbuscular Mycorrhizal Fungi Using a Commercial Kit

The molecular identification of arbuscular mycorrhizal fungi (AMF) from root tissues can often be limited by the co-extraction of polysaccharides, phenolic compounds, and other PCR inhibitors, particularly in woody or highly lignified roots, where cell lysis is also often difficult. Although commercial extraction kits offer standardized workflows and reduce the handling of harmful reagents, the manufacturer's protocols are insufficient for root samples with high levels of secondary metabolites. This protocol describes the optimization of DNA extraction from coffee (Coffea arabica L.) roots colonized by AMF, based on the use of the commercial ZymoBIOMICS™ Quick-DNA fecal/soil Microbe Kit, designed for the rapid and simple isolation of microbial DNA and host cells from fecal and soil samples, incorporating a pre-maceration and pre-digestion step with proteinase K and β-mercaptoethanol. This modification significantly improves yield, DNA integrity, and PCR amplification of Glomeromycota-specific ribosomal markers (SSU/18S).