Rhizosphere Microbiomes of Citrus Plants in Historically Undisturbed 100-Year-Old Groves Appear to Mitigate Susceptibility to Citrus Greening Disease

Microbiome studies aimed at combating the citrus greening devastation caused by <i>Liberibacter asiaticus</i> abound. However, the role of farming practices, such as the massive use of herbicides, pesticides, and inorganic fertilizers on specific taxa and plant population immunity remains an important inquiry. To test our hypothesis that agricultural practices in managed Citrus groves induce root microbiome dysbiosis, potentially rendering citrus readily susceptible to citrus greening disease (CGD), we compared the CGD and root microbiome status of citrus plants in a rare > 130-year-old grove (no anthropogenic influence) to those of managed Valencia groves (symptomatic and asymptomatic). Citrus greening disease was detected by qPCR using the HLBa/HLBs/HLBp primer/probe combination, while root microbiome community structure was determined using 16S rDNA amplicon sequencing. The prevalence of CGD among citrus growing in the undisturbed, healthy soils was zero (Ct values > 36), while symptomatic and asymptomatic Valencia from managed groves was 100% positive (Ct < 34). Known beneficial plant symbionts (Actinomycetales, <i>Bradyrhizobium</i>, Verrucomicrobia, etc.) from Phylum Actinobacteria and Proteobacteria were depleted in the rhizosphere of the managed sites. This dysbiotic shift was characterized by enrichment with <i>Acidobacterium</i>, <i>Nitrospira,</i> and <i>Sphingomonas</i> spp. In highly infected Valencia oranges, beneficial taxa of the Alphaproteobacteria declined significantly (from 20-25% to 10-15%), while <i>Bacillus</i> sp. (a Firmicutes) was enriched 13-fold. Simpson and Shannon diversity indices were similar for all plant microbiomes except the heavily infected Valencia, which exhibited low diversity (<i>p</i> < 0.05), indicating that diversity indices alone are not reliable measures of soil health or rhizobiome homeostasis. Large reservoirs of known and novel putative beneficial rhizosphere microbes in undisturbed sites supported zero CGD, despite proximity to the managed sites where diverse non-beneficial taxa coincided with high disease rates. Supplementing the use of agrochemicals with carefully designed microbial products for plant disease control and sustainable soil health deserves acute attention.