SUMMARYTaxonomic status: Bacteria, Proteobacteria, gamma subdivision, Xanthomodales, Xanthomonas group, axonopodis DNA homology group, X. axonopodis pv. citri (Hasse) Vauterin et al .Microbiological properties: Gram negative, slender, rodshaped, aerobic, motile by a single polar flagellum, produces slow growing, non-mucoid colonies in culture, ecologically obligate plant parasite.Host range: Causal agent of Asiatic citrus canker on most Citrus spp. and close relatives of Citrus in the family Rutaceae.Disease symptoms: Distinctively raised, necrotic lesions on fruits, stems and leaves.Epidemiology: Bacteria exude from lesions during wet weather and are disseminated by splash dispersal at short range, windblown rain at medium to long range and human assisted movement at all ranges.Crop loss: Severe infections cause defoliation, blemished fruit, premature fruit drop, die-back of twigs and general debilitation of the tree.Distribution: Citrus canker is not present in all subtropical to tropical regions of citriculture in the world, so considerable regulatory efforts are expended to prevent the introduction and spread of X. axonopodis pv. citri into areas in the Americas, Australia and elsewhere, with climates conducive to the disease.Importance: Limited strategies exist for suppression of citrus canker on more susceptible cultivars. Blemished fruit are unmarketable and exposed fruit are restricted in market access. The economic impact of loss of markets is much greater than that from yield and quality reductions of the crop.

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Partial sequence analysis of the ribosomal operon in Xanthomonas axonopodis allowed discrimination among strains causing the A, B, and C types of citrus bacterial canker (CBC) and quantification of the relationship of these organisms with other species and pathovars in the same genus. Sets of primers based on sequence differences in the internally transcribed spacer and on a sequence from the plasmid gene pthA involved in virulence were designed for specific identification of xanthomonads causing CBC diseases. The two sets were validated with a collection of Xanthomonas strains associated with citrus species. The primer set based on ribosomal sequences had a high level of specificity for X. axonopodis pv. citri, whereas the set based on the pthA gene was universal for all types of CBC organisms. Moreover, the relationships among worldwide Xanthomonas strains causing CBC were analyzed by amplification of repetitive sequences (enterobacterial repetitive intergenic consensus and BOX elements). Under specific conditions, pathotypes of these Xanthomonas strains could be discerned, and subgroups of the pathotypes were identified. Subgroups of strains were associated with certain geographic areas of the world, and on this basis the origin of type A strains introduced into Florida could be inferred.Xanthomonas axonopodis pv. citri and X. axonopodis pv. aurantifolii cause citrus bacterial canker (CBC), a serious disease of most citrus species and cultivars in many citrus-producing areas worldwide (1). Distinct forms of CBC based on different pathogenicities of the bacteria have been described. The Asiatic form or A type, caused by X. axonopodis pv. citri, is the most virulent form and affects the widest range of hosts, including Citrus spp. and many closely related rutaceous plants. The CBC B and C types are caused by X. axonopodis pv. aurantifolii. Pathotype B strains affect primarily lemon (Citrus limon (L.) Burm f.), but they also affect some other citrus species and are found only in Argentina and neighboring Uruguay and Paraguay. Pathotype C strains have been isolated in a small area of Sao Paulo State in Brazil and infect Key or Mexican lime (Citrus aurantifolia (Christm.) Swingle) (21). The symptoms induced by the three forms of canker organisms are similar and consist of erumpent and corky lesions surrounded by oily or water-soaked margins on leaf, fruit, and stem tissues (1). A new strain of X. axonopodis pv. citri, designated A*, was identified in southwest Asia and has a host range restricted naturally to Key or Mexican lime; this strain is closely related to type A strains (24). Another strain (type A w ), which behaves similarly, has recently been discovered in Florida; this strain has a restricted host range that includes Key or Mexican lime and alemow (Citrus macrophylla Wester)