Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum

Arbuscular mycorrhizal fungi (AMF) remain understudied in perennial cropping systems. Citrus is a globally grown fruit tree and under threat by the pandemic Huanglongbing (HLB) disease. Here, we assessed in what capacity geographical location, management strategies and disease affect AMF citrus root communities. Root samples were collected from 88 trees in ten orchards located in the two major citrus producing states in the US. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. We used AMF-specific amplicon sequencing primers to capture community composition and diversity. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF references sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples with taxa belonging to six known (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and unknown Glomeraceae genera. Geographical location affected AMF community composition but not richness, whereas management practice and disease influenced both richness and composition. Our approach indicated that perennial agroecosystems share a set of AMF generalist and specialist taxa. Some taxa could improve environmental fitness and be exploited for agricultural purposes.