The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.

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The benefits of arbuscular mycorrhizal fungi (AMF) to agroecosystems have been well recognized. Citrus is a globally grown fruit tree commonly found in association with AMF. Global citrus production is currently under the threat of the pandemic huanglongbing (HLB) disease. Since its introduction in the United States, the disease has devastated the Florida citrus industry and is now at the doorsteps of commercial orchards in California. Here, we tested how the two distinct climatic zones within the continental United States where citrus is mostly grown (California and Florida) influenced AMF community diversity and composition. We also assessed in what capacity low-input organic farming and HLB disease affected the AMF communities colonizing the citrus roots. Root samples were collected from 88 trees across 10 orchards. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. AMF communities were characterized using high-throughput sequencing of the small-subunit ribosomal RNA gene. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF reference sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples, with taxa belonging to six genera ( Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, and Septoglomus) and unknown Glomeraceae genera. Geographical location, management practice, and disease affected AMF community composition. We provide evidence that perennial agroecosystems are composed of generalist and specialist AMF taxa comparable with other ecosystems and identified ubiquitous taxa that could potentially be exploited for agricultural purposes.

No abstract

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.