A decade of citrus Huanglongbing management with native endophytes in China

Abstract Citrus Huanglongbing (HLB), caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus ( C Las), is the most devastating citrus disease worldwide, with no efficient cure currently available. C Las pathogen exhibits seasonal variations in China and adversely affects the native citrus endophytic microbiome. Recent research on the citrus endophytic microbiome has identified the promising biocontrol strategies for mitigating HLB, particularly through the manipulation of plant–microbe–pathogen interactions. Here, we provide empirical evidence from a decade (2015–2025) of research focusing on indigenous citrus endophyte, notably Bacillus subtilis L1-21, which demonstrates remarkable efficacy in reducing C Las in the diseased citrus fields with biocontrol effect exceeding 95% in successive HLB-affected citrus plants (> 200 acres of infected field). Further, we demonstrate several mechanisms, such as colonization inside phloem, host immune modulation, and interkingdom signalling-through which pathogen reduction is achieved in greenhouse experiments. Across different scenarios, surfactin lipopeptides were found to play a multifaceted role in colonization, acting as a defense elicitor, and a quorum sensing molecule involved in regulating Bacillus community behaviour. Next, multi-omics approaches (metabolomics, transcriptomics, and metagenomics) have elucidated metabolic crosstalk between citrus hosts and endophytes, highlighting the importance of upregulated defense pathways and enrichment of potential endophytic microbiome. However, several challenges remain in translating laboratory findings to field applications, including scalability of endophyte formulations, environmental stability, and ecological impacts of microbiome manipulation. Overall, we propose that integrating citrus microbiome engineering with plant breeding and precision agriculture could bridge the gap between lab discoveries and field applications in long-term. Finally, we highlight the biocontrol potential of native endophyte-based strategies for HLB management and advocate for interdisciplinary collaboration to address knowledge gaps in microbial ecology, host genetics, and sustainable agriculture strategies.