Bacterial citrus microbiomes described using uncultured and cultured approaches.

The untapped diversity of host-associated bacteria as a source of benefits.

A collection of potentially beneficial bacteria for citrus is now available.

These bacteria could provide future agricultural probiotics required for the citrus industry.

Citrus is the most cultivated fruit crop worldwide. The modern citrus industry needs new bioproducts to overcome phytopathological threats, tolerate stresses and increase yield and quality. Mutualistic microbes from roots significantly impact host physiology and health and are a potentially beneficial resource. The bacterial microbiome can be surveyed to select potentially host-beneficial microbes. To achieve this goal, a prevalent “core-citrus” bacterial microbiome was obtained by picking those operational taxonomic units (OTUs) shared among samples within and across two Citrus rootstock genotypes grown in the same soil for more than 20 years. A sub-selection of main OTUs from the defined "core-citrus" microbiome was made based on abundance, host-enriched versus bulk soil, and rhizosphere-indicator species. In parallel, an extensive census of the cultivable microbiota was performed to collect a large number of bacterial citrus isolates. Metataxonomic data were linked to cultured microbes, matching 16S rRNA gene sequences from bacterial isolates with those counterpart OTU reference sequences from the selected bacterial "core-citrus" microbiome. This approach allowed selection of potentially host-beneficial bacteria to mine for agricultural probiotics in future biotechnological applications required for the citrus industry.

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Workflow used for the selection of bacteria potentially beneficial for citrus. It is the first microbial culture collection theoretically enriched in host-beneficial microbes from a woody fruit crop selected by linking metataxonomic and culturomic analyses of rhizospheric bacterial microbiomes. The untapped diversity of bacterial citrus microbiomes has provided a citrus-adapted and host-selected bacteria that is a source to mine for agricultural probiotics for future biotechnological applications required for the citrus industry.

operational taxonomic unit

Valencian Institute for Agricultural Research

Citrus microbiomes

Metataxonomics

Culturomics

Rhizospheric bacteria

Beneficial bacteria

Agricultural probiotics

© 2022 The Author(s). Published by Elsevier B.V.