Comparison of Methods to Characterize the Microbiota of Myxomycete Plasmodia

Myxomycetes are valuable models for studying interactions between single-celled eukaryotes and bacteria; however, little is known about their microbiota or optimal DNA extraction methods. We analyzed the bacterial community of Claustria didermoides plasmodia using commercial and noncommercial DNA extraction methods. A total of 218 amplicon sequence variants (ASVs) were identified, dominated by Pseudomonadota (78%), Bacillota (10%), and Actinomycetota (9%). Achromobacter denitrificans was the most abundant species, with 3-7 codominant ASVs, including opportunistic pathogens. The commercial kit captured higher diversity, while the noncommercial method favored Gram-negatives and preserved DNA integrity longer when phenol was added.