Shifts in the structure of rhizosphere bacterial communities of avocado after Fusarium dieback

The rhizosphere microbiome is critical for plant growth and protection against plant pathogens. However, rhizosphere microbial communities are likely to be restructured upon plant infection by fungal pathogens. Our objective was to determine the shifts in rhizosphere bacterial communities of avocado trees (Persea americana Mill.) after Fusarium dieback (FD), a disease triggered by the symbiotic fungi of invasive ambrosia beetles (Euwallacea kuroshio and Euwallacea sp. nr. fornicatus), using 16S rDNA gene amplicon sequencing and a culture-dependent approach. Rhizosphere soil samples were collected from five asymptomatic and five FD-symptomatic avocado trees in a Californian orchard. Sequence analysis showed that diversity metrics of the rhizosphere bacterial communities associated with asymptomatic avocado trees were larger than those of communities from FD-symptomatic trees. Moreover, FD produced significant shifts in rhizobacterial community structure, which were mainly caused by rare OTUs. Bacterial taxa such as Armatimonadetes, Sporocytophaga or Cellvibrio were exclusively associated with the rhizosphere of asymptomatic trees and may act as an insurance mechanism against fungal invasions. Conversely, genera such as Myxococcus or Lysobacter, which have been described as effective biocontrol agents against Fusarium oxysporum, Colletotrichum gloeosporioides or Rhizoctonia spp., among other phytopathogens, were only found in the rhizosphere of FD-symptomatic trees. The culturable bacterial communities in the rhizosphere of both FD-symptomatic and asymptomatic trees were dominated by isolates from the Bacillus and Pseudomonas genera, indicating that potential biocontrol agents against FD may be isolated from healthy and diseased avocado trees. Altogether, our results showed that FD elicited shifts in the avocado rhizosphere microbiome, which could potentially affect soil microbial processes, and provide a basis for the selection of biocontrol agents that could be used for FD prevention.
This research was funded by a 2015 UC MEXUS −CONACYT collaborative research grant and by a CONACYT postgraduate fellowship awarded to the first author.