Plant-associated bacteria offer a sustainable alternative to chemical inputs in agriculture, yet the field performance of microbial inoculants remains inconsistent. A central but frequently overlooked cause is that bioprospecting pipelines still select strains on the basis of plant-growth-promoting activities, while the bacterial genetic traits that determine whether a strain can reach, colonise and persist in a given root compartment are rarely assessed. Previous reviews have largely catalogued growth-promoting functions or described root microbiome assembly from the plant's perspective, here we take the bacterium's. We trace the journey of a bacterium from bulk soil to its final niche and, at each stage, identify the genes and pathways (genetic determinants) that encode key bacterial traits involved, such as chemotaxis and motility, nutrient acquisition and metabolic independence, competitive and defensive arsenals, attachment and biofilm formation, evasion of plant immunity, and endophytic entry and persistence. Throughout, we use evidence from comparative genomics and metagenomics, (meta)transcriptomics, targeted mutagenesis and genome-wide screens such as Tn-seq, obtained in systems ranging from binary interactions to synthetic communities and natural soils. For each stage we examine the current state of knowledge, identify critical gaps, and propose avenues to deepen our mechanistic understanding of the bacterial traits involved in plant colonisation. We argue that this mechanistic understanding is the missing foundation for developing inoculants with more consistent and robust performance across diverse agroecosystems.

Myxobacteria are renowned producers of structurally diverse bioactive natural products. Motivated by a comprehensive inventory of myxobacterial biosynthetic gene clusters (BGCs), we develop efficient genetic toolkits and construct a robust heterologous expression chassis. We identify a pair of Myxococcus-derived recombinases, designated MxRecET, that enables efficient genome editing in the model strain Myxococcus xanthus DK1622. The synergistic combination of MxRecET recombineering with the transposon-associated nuclease TnpB (ISDra2) enables versatile genetic manipulations, including seamless deletion of large DNA fragments (up to 200 kb), tandem editing of dual loci, and flexible single-nucleotide substitutions within a streamlined two-week workflow. This integrated technology, termed MxDIRECT, facilitates the rational engineering of DK1622 into a plug-and-play chassis designated MxPKS, featuring enhanced growth properties, elimination of competing pathways, an improved precursor sup

COBRA Webinar Series, September 1, 2026

Discovering exoplanets and satellites in habitable zones within and beyond our solar system has sparked intrigue in planetary setting varieties that could support life. Based on our understanding of l...