2026/01/01 by Camille Thomas, Aliisa K. Laakkonen, Rast Regina Deborah +4 · 1 voice
Environmental Science · Biochemistry, Genetics and Molecular Biology · #Microbial Community Ecology and Physiology #Genomics and Phylogenetic Studies #Environmental DNA in Biodiversity Studies
paper · doi:10.1093/femsle/fnag072
Abstract Microbial communities in the subsurface biosphere remain poorly characterized because many taxa lack cultured representatives and genomic references, limiting the accuracy of taxonomy inferred from short-read 16S ribosomal RNA gene sequencing. We tested the hypothesis that long-read 16S sequencing improves taxonomic resolution and detection of rare lineages compared with short-read approaches in low-biomass, diversity-rich sediments. Microbial communities from a sediment core of Lake Arnon (Switzerland) were analyzed using both long-and short-read sequencing, and community composition, diversity metrics, and taxonomic resolution were compared. Sequencing technology influenced observed community structure, but sediment depth also exerted a strong effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, whereas archaeal diversity was underrepresented in long-read datasets due to primer mismatches. When detected, long reads provided higher taxonomic resolution, frequently to species level, improving ecological interpretation and inference of metabolic potential. Finer-scale analyses, including species contributions to beta diversity and co-occurrence networks, showed greater specificity with long reads. These results demonstrate that long-read sequencing can substantially enhance subsurface microbial characterization, provided that primer design is optimized, and highlight its potential to improve assessments of microbial identity, structure, and function in low-biomass environments.