Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition

High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic like snow algae. DNA extraction significantly impacts these analyses, often introducing more variation than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, inconsistencies in DNA extraction remain a major challenge, and no recommended method exists for assessing their community composition and richness. Here, we compared three common extraction methods (DNeasy PowerSoil Pro, DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of resilient cells, including mature-phase snow algae likely due to improved cell lysis step. This is the first systematic comparison of DNA extraction methods for snow algae, highlighting how methodological choices affect microbial community analyses. Our findings provide insights to improve standardization, enhancing the reliability of future studies in snow and ice environments.