Accurate characterization of soil microbial communities depends on both DNA extraction efficiency and primer choice. We compared a CTAB‐based extraction protocol (CTAB+) with a commercial kit (Qiagen DNeasy PowerSoil) across five major microbial groups, Bacteria, Archaea, Fungi, arbuscular mycorrhizal fungi (AMF), and Oomycetes, amplified with eight primer pairs. Unlike most studies using mock communities, our comparison was performed on DNA from 12 field soils spanning broad physicochemical and climatic gradients, providing a realistic test of methodological performance. While Qiagen kit generally yielded higher richness and diversity for archaea, fungi, and oomycetes, CTAB + improved recovery of taxa with robust cell walls or membranes, including Gram‐positive Bacteria such as Firmicutes and archaeal lineages such as Thermoplasmatota and Nanoarchaeota. Primer selection also shaped outcomes: ITS1 and ITS2 provided complementary fungal profiles, with ITS2 enhancing detection of Glomeromycota; Archaea‐specific primers with CTAB + improved recovery of low‐abundance taxa, whereas oomycete primers showed variable sensitivity to inhibitors. AMF communities were largely consistent across methods, indicating methodological resilience. These findings demonstrate that extraction chemistry and primer design introduce group‐specific biases and emphasize the need to tailor methodological choices to target taxa when designing field‐based soil microbiome studies.
Cardoni et al. (Thu,) studied this question.