Microbial communities including bacteria, archaea, viruses and fungi are present in all environments, often associated with macroorganisms. Bacterial populations can colonise plant components and thrive in and on plant cells and express gene functions sometimes at a greater level than plant cells, constituting the so-called secondary genome. Plant-associated bacterial communities are important drivers for host growth, health and fitness (Berg et al., 2016; Lakshmanan et al., 2014) and function as a first line defence against phytopathogens (Berendsen et al., 2012; Ghosh and Jha, 2023). Recent technological advances in the identification and characterisation of beneficial plant-associated bacteria have opened a myriad of opportunities for their exploitation as microbial biological control agents (MBCAs) for crop protection. Comparative genome analyses in host-associated microbiomes suggest that bacterial assemblies have taxonomic and functional overlaps among plant organs, but microbiota specialise to spatial niches (Bai et al., 2015). Insights into the native functional roles of MBCAs and their interactions within the microbial community across plant compartments such as rhizosphere, endosphere and the phyllosphere are essential for the selection and design of effective microbiome engineering solutions. However, such considerations have been significantly understudied, also for keystone taxa with far-reaching metabolic potential like Actinobacteria.