UC Riverside

Evolutionary selection between plants and microorganisms contributes to the system's stability. Microorganisms are beneficial to plants in promoting plant growth and alleviating biotic and abiotic stress. Using the microbiome at work provides a viable path toward establishing a more sustainable agriculture. Citrus, a vital part of California's cuisine, landscape, and economy, is threatened by an incurable and fatal plant disease, Huanglongbing (HLB). Recent advances in understanding the citrus microbiome included the composition and function of the microbiome in the different citrus bio compartments and HLB-infected citrus. However, additional work and research are necessary prior to their application in the field. This study is a comprehensive, culture-independent microbial study of citrus that includes previously unknown plant niches, flushes, and flowers. The citrus microbiome was dominated by Acinetobacter, Sphingomonas, Streptomyces, Actinoplanes, Burkholderia, Neocosmospora, Cladosporium, Solicoccozyma, Mortierella, and Fusarium. The fungi Alternaria, Cladosporium and Neocosmospora and bacteria Actinoplanes, Bacillus, Burkholderia, Firmicutes and Sphingomonas represented ubiquitous taxa capable of colonizing all five biocompartments analyzed (root, rhizosphere, soil, flush and flower). This research also provided insightful information about citrus AMF dynamics related to geographic location, management strategy, and Huanglongbing disease. We have found a core microbiome (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and biomarkers for healthy trees (Glomeraceae VTX00323 and Dominikia VTX00132 were significantly depleted as HLB symptoms became more severe). Finally, we have developed a bioassay to screen for potential PGPR microbes on citrus rootstock seedlings. ‘Carrizo’ citrange seeds were inoculated with 10 potential PGPR and all were able to colonize the host plant root/rhizosphere. Three Bacillus species significantly increased the seed germination rate. Two Bacillus species and one Rhizobium species significantly increased the plant height, leaf number, and shoot biomass of seedlings. In conclusion, this study reveals the bacteriome and mycobiome within citrus, ranging from symbiotic to pathogenic, deepening our understanding of the microbe-host interaction in perennial agroecosystems and mining the microbiome for novel approaches to HLB management.