Unraveling fitness landscapes in plant-associated Bacteroidota

Members of the bacterial phylum Bacteroidota inhabit diverse ecosystems, yet environmental species remain poorly understood compared to clinically relevant ones. Although Bacteroidota are dominant in crop-associated microbiomes, the mechanisms enabling them to thrive in plant and soil environments remain unclear. A key obstacle in understanding gene fitness in Bacteroidota is the lack of genome-wide functional studies, largely due to their inherent resistance to antibiotics, which hinders genetic manipulation. Here, we applied randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) to measure gene fitness in a plant-associated Bacteroidota, Mucilaginibacter yixingensis YX-36. Our data sheds light on pathways involved in rhizosphere colonization, gliding motility, stress tolerance, and carbon metabolism. Notably, we found that phylum-specific genes such as polysaccharide utilization loci and carbohydrate-active enzymes are needed for fitness in the plant niche. Overall, this work advances our understanding of gene functions in environmental Bacteroidota species and provides a foundation for future research on their roles in plant-microbe interactions.