Unraveling fitness landscapes in plant-associated Bacteroidota

Abstract Members of the bacterial phylum Bacteroidota inhabit a wide range of ecosystems. Although significant progress has been made over the past decade in understanding the metabolic functions of clinically relevant Bacteroidota , far less is known about the environmental species. Despite being one of the dominant phyla linked to crops, there is limited information on the mechanisms that enable Bacteroidota to thrive in plant and soil environments. 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 complicates genetic manipulation. In this study, we used 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 (PULs) and Carbohydrate-Active enzymes (CAZymes) 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.