Recent Advances and Developments in Bacterial Endophyte Identification and Application: A 20-Year Landscape Review

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity.