Abstract
Long-term agricultural conversion is known to shift soil microbial diversity and abundance in soils that formerly supported native grassland, but whether these shifts reflect uniform suppression across a bacterial genus or selective filtering of specific evolutionary lineages remains poorly understood. We addressed this question in
Candidatus
Udaeobacter, a globally abundant member of the phylum Verrucomicrobiota and a model oligotrophic soil bacterium. We collected 40 soil samples for RNA-Seq metatranscriptome analysis across three paired native prairie and long-term agricultural sites in Missouri and mapped transcriptional recruitment against a taxonomically curated consensus reference built from 36 concordant NCBI and GTDB
Candidatus
Udaeobacter genome assemblies. Total transcriptional recruitment to
Candidatus
Udaeobacter was nearly eleven-fold higher in prairie soils, and recruitment composition remained significantly distinct between land uses even after normalizing for this difference, indicating that land use reshapes which lineages remain active rather than uniformly reducing activity across the genus. This land use-associated recruitment showed strong phylogenetic signal, with closely related genomes exhibiting similar responses to land use. Genome architecture tracked this pattern and prairie-enriched lineages carried consistently smaller genomes and expressed a larger share of their coding capacity than agriculture-enriched lineages. These results show that environmental selection in Candidatus Udaeobacter operates below the genus level. Combining curated reference genomes with metatranscriptomic recruitment offers a scalable framework for resolving lineage-level ecological responses in other abundant, poorly characterized microbial taxa.