Resolution of the Identity of 'Candidatus Liberibacter' Species From Huanglongbing-Affected Citrus in East Africa

Identification and Distribution of the 'Candidatus Liberibacter asiaticus'-Asian Citrus Psyllid Pathosystem in Saudi Arabia

Citrus greening disease was first reported in Saudi Arabia during the 1970s when characteristic foliar and fruit symptoms were observed in commercial citrus groves. However, 'Candidatus Liberibacter asiaticus' (CLas) was not detected in symptomatic trees until 1981 to 1984 when CLas-like cells were observed by transmission electron microscopy in leaves collected from symptomatic citrus groves in southwestern Saudi Arabia. Despite the anticipated establishment of the CLas-Asian citrus psyllid (ACP) (Diaphorina citri Kuwayama) pathosystem, CLas presence has not been verified in suspect trees nor have ACP infestations been documented. Given the recent expansion of citrus production in Saudi Arabia, a systematic country-wide survey was carried out to determine the potential CLas distribution in the 13 citrus-growing regions of the country. Citrus trees were surveyed for the presence of CLas-psyllid vector(s) and characteristic disease symptoms in commercial and urban citrus trees. Adult psyllids collected from infested citrus trees were identified as ACP based on morphological characteristics. Real-time quantitative PCR amplification (qPCR) of the CLas β-subunit of the ribonucleotide reductase (RNR) gene from citrus leaf and fruit samples and/or ACP adults revealed that trees were positive for CLas detection in 10 of the 13 survey regions; however, CLas was undetectable in ACP adults. Phylogenetic and single nucleotide polymorphism (SNP) analyses of a PCR-amplified, cloned fragment of the CLas 16S rRNA gene (∼1.1 kbp) indicated Saudi Arabian isolates were most closely related to Florida, U.S.A., isolates. Analysis of climate variables indicated that the distribution of the ACP-CLas pathosystem observed in Saudi Arabia was consistent with published predictions of terrains most likely to support establishment.

Cultural Management of Huanglongbing: Current Status and Ongoing Research

Huanglongbing (HLB), formerly known as greening, is a bacterial disease restricted to some Asian and African regions until two decades ago. Nowadays, associated bacteria and their vectors have spread to almost all citrus-producing regions, and it is currently considered the most devastating citrus disease. HLB management can be approached in terms of prevention, limiting or avoiding pathogen and associated vectors to reach an area, or in terms of control, trying to reduce the impact of the disease by adopting different cultural strategies depending on infestation/infection levels. In both cases, control of psyllid populations is currently the best way to stop HLB spread. Best cultural actions (CHMAs, TPS system) to attain this goal and, thus, able to limit HLB spread, and ongoing research in this regard is summarized in this review.

A Review of the 'Candidatus Liberibacter africanus' Citrus Pathosystem in Africa

It has been nearly 100 years since citrus growers in two distinct regions in the northern provinces of South Africa noticed unusual symptoms in their citrus trees, causing significant crop losses. They had no idea that these symptoms would later become part of an almost global pandemic of a disease called greening or huanglongbing (HLB). The rapid spread of the disease indicated that it might be caused by a transmissible pathogen, but it took >50 years to identify the causative agent as 'Candidatus Liberibacter africanus'. Recently, the disease appeared in more African countries, spreading by both infected planting material and Trioza erytreae. To date, five 'Ca. L. africanus' subspecies have been identified in various rutaceous species, with 'Ca. L. africanus subsp. clausenae' the only subspecies for which a biovar was detected in citrus. Efforts to detect and differentiate HLB-causing Liberibacter species are ongoing, and recent developments are discussed here. This review focuses on aspects of the African form of HLB, including its specific bacterial species and subspecies, its main insect vector, its geographic distribution, and current management strategies.

Pest categorisation of Diaphorina citri

The EFSA Panel on Plant Health performed a pest categorisation of Diaphorina citri (Hemiptera: Liviidae) (Asian citrus psyllid) for the EU. D. citri is a key pest of citrus in several countries as it is a vector of serious bacterial pathogens, the putative causal agents of Huanglongbing (HLB) also known as citrus greening. Eggs are laid on tips of growing shoots on and between unfurling leaves. Females may lay more than 800 eggs during their lives. Nymphs pass through five instars. The life cycle requires from 14 to 49 days, depending upon the season. There is no diapause, but populations are low in winter. It overwinters as an adult which may live for several months. The species completes 9-10 generations/year; however, under protected conditions, up to 16 generations have been recorded. Commission Implementing Regulation (EU) 2019/2072 (Annex IIA) regulates D. citri, as a quarantine pest not known to occur in the EU territory. Fruits and plants for planting provide potential pathways for entry into the EU. Climatic conditions and the availability of host plants provide conditions to support establishment in the EU. The introduction of D. citri would have an economic impact in the EU through direct but mainly indirect effects due to potential transmission of HLB. Phytosanitary measures are available to reduce the likelihood of entry. D. citri satisfies the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest. D. citri does not meet the criteria of occurring in the EU, nor plants for planting being the principal means of spread, for it to be regarded as a potential Union regulated non-quarantine pest.

Enhanced Serologically Based Detection of Liberibacters Associated with Citrus Huanglongbing

'Candidatus Liberibacter spp.' are associated with the most devastating disease of citrus Huanglongbing (HLB). In previous work, we established an in situ tissue print method for the detection of 'Ca. L. asiaticus' (CLas) in sweet orange. We optimized the protocol by preincubation of the anti-Omp antibody with 5% (w/v) extract of healthy rough lemon. This simple process eliminated cross reactions between citrus and the antibody. The optimized protocol enhanced the application of the polyclonal antibody, and we demonstrate detection of CLas from all parts of the world, including isolates from Japan, Thailand, Vietnam, Pakistan, Saudi Arabia, Brazil, the United States, and a selection of strains from China representative of the diversity extant there. The assay also was used to detect four isolates of 'Ca. L. africanus' (CLaf) representative of the diversity present in South Africa. The corresponding outer membrane genes of representative isolates were cloned and sequenced. The coding sequences were highly conserved, and isolates of CLas and CLaf shared 53.8 to 55.9% identity between species at the amino acid level. The optimized protocol is efficient for recognition of both CLas and CLaf in phloem cells of different citrus tissues regardless of geographic origin of the HLB samples. The method is simple and scales well to match the urgent need for accurate, sensitive, and high-throughput screening of HLB bacteria, and may play an important role especially for plant inspection and quarantine programs.

Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae

Trioza erytreae is the main vector for ‘Candidatus Liberibacter africanus’, the causative agent of African Citrus Greening disease. The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences for T. erytreae, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes of T. erytreae from Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure of T. erytreae was assessed using genetic clustering and pairwise distances, based on a dataset of public COI sequences recorded as T. erytreae. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya on Clausena anisata belonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified as T. erytreae belong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity of T. erytreae, with potential implications for the epidemiology of African Citrus Greening disease.

Distribution of Candidatus Liberibacter species in Eastern Africa, and the First Report of Candidatus Liberibacter asiaticus in Kenya

Huanglongbing (HLB) is a serious disease of Citrus sp. worldwide. In Africa and the Mascarene Islands, a similar disease is known as African citrus greening (ACG) and is associated with the bacterium Candidatus Liberibacter africanus (Laf). In recent years, Candidatus Liberibacter asiaticus (Las) associated with the severe HLB has been reported in Ethiopia. Thus, we aimed to identify the Liberibacter species affecting citrus, the associated vectors in Eastern Africa and their ecological distribution. We assessed the presence of generic Liberibacter in symptomatic leaf samples by quantitative PCR. Subsequently, we sequenced the 50 S ribosomal protein L10 (rplJ) gene region in samples positive for Liberibacters and identified the species by comparison with public sequence data using phylogenetic reconstruction and genetic distances. We detected generic Liberibacter in 26%, 21% and 66% of plants tested from Uganda, Ethiopia and Kenya, respectively. The rplJ sequences revealed the most prevalent Liberibacters in Uganda and Ethiopia were LafCl (22%) and Las (17%), respectively. We detected Las in Kenya for the first time from three sites in the coastal region. Finally, we modelled the potential habitat suitability of Las in Eastern Africa using MaxEnt. The projection showed large areas of suitability for the pathogen in the three countries surveyed. Moreover, the potential distribution in Eastern Africa covered important citrus-producing parts of Ethiopia, Kenya, Uganda and Tanzania, and included regions where the disease has not been reported. These findings will guide in the development of an integrated pest management strategy to ACG/HLB management in Africa.

African Citrus Greening Disease in East Africa: Incidence, Severity, and Distribution Patterns

African citrus greening disease (ACGD) is considered as one of the major diseases of citrus threatening citrus production in East Africa. Our study aimed for the first time to assess the incidence, severity, and distribution patterns of ACGD in Kenya and Tanzania. In total, 105 citrus orchards were assessed in 13 regions representing low, mid, and high altitude areas. In each backyard and orchard, trees were randomly selected and rated for visual ACGD symptoms; then leaves and insect samples collected for analysis of 'Candidatus Liberibacter africanus' (CLaf), the presumptive causal agent of ACGD. Endpoint PCR, sequencing, and molecular phylogenetic tools were employed to confirm the identity of potential circulating pathogens. Incidence and severity of ACGD varied significantly among the different regions. Both Trioza erytreae (Del Guerico) (Hemiptera: Triozidae) and the invasive Asian citrus psyllid vector Diaphorina citri (Kuwayama) (Hemiptera: Liviidae) were found to co-occur in upper and lower midland regions. Molecular characterization identified 'Candidatus Liberibacter africanus spp. Clausenae' (CLafCl) as the main causal agent of ACGD in most of the citrus plants and insect samples. No instances of Candidatus Liberibacter asiaticus infection were found. These findings provide valuable insights into understanding and management of ACGD by employing stringent and early disease detection tools to curb the spread of the disease.

Genetic Diversity of 'Candidatus Liberibacter asiaticus' Revealed by Short Tandem Repeats and Prophage Typing Indicates Population Homogeneity in Brazil

'Candidatus Liberibacter asiaticus' is the most common huanglongbing-associated bacteria, being present in Asia, South, Central, and North America. Genomic approaches enabled sequencing of 'Ca. L. asiaticus' genomes, allowing for a broader assessment of its genetic variability with the application of polymerase chain reaction (PCR)-based tools such as microsatellite or short tandem repeat (STR) analysis. Although these tools contributed to a detailed analysis of strains from Japan, China, and the United States, Brazilian strains were analyzed in either too few samples with several STRs or in several strains with only a single microsatellite and a single PCR marker. We used 573 'Ca. L. asiaticus' strains, mainly collected from São Paulo State (SPS), in our genetic analyses, employing three STRs and several prophage PCR markers. STR revealed a homogeneous population regardless of sampling year or geographic regions of SPS. Thirty-eight haplotypes were recognized with a predominance of VNTR_005 higher than 10 repeats, with VNTR_002 and VNTR_077 containing 11 and 8 repeats, respectively. This haplotype is indicated as class HE, which comprised 80.28% of strains. Classes HA and HB, predominant in Florida, were not found. A new genomic organization in the junction of prophages SC2 and SC1 is prevalent in Brazilian strains, indicating gene rearrangement and a widespread occurrence of a type 1 prophage as well as the presence of a type 2-like prophage. Our results indicate that 'Ca. L. asiaticus' populations are homogeneous and harbor a new genomic organization in prophages type 1 and 2.

Molecular Characterization and Detection of 16SrIII Group Phytoplasma Associated with Huanglongbing Symptoms

When huanglongbing (HLB) was found in Brazil in 2004, 'Candidatus Liberibacter americanus' was infecting most of the trees while 'Ca. L. asiaticus' was present in a minor proportion. Currently, 'Ca. L. asiaticus' is the predominant bacterium associated with HLB in citrus trees in São Paulo (SP) and Minas Gerais (MG) States, the major citrus-growing regions in Brazil. A phytoplasma from the 16SrIX group was associated with HLB symptoms in Brazil in 2007, in plants free of Liberibacter spp. In this report, HLB samples testing negative for 'Ca. L. asiaticus', 'Ca. L. americanus', and 16SrIX phytoplasma were infected with 16SrIII phytoplasmas. Coinfection with 'Ca. L. asiaticus' and 16SrIII was also found. The 16S ribosomal RNA (rRNA) gene sequences from 22 samples were obtained and sequenced, confirming that the 16SrIII group phytoplasma is associated with HLB symptoms in SP and MG States. Ten single-nucleotide polymorphisms (SNPs) were found in the 1,427-bp 16S rRNA gene sequences from 16SrIII phytoplasmas from citrus, whereas none was detected in 16S rRNA gene sequences among 16SrIX phytoplasma from citrus. Ribosomal protein (rp) rpsSrplVrpsC gene sequences were amplified with 16SrIII group-specific primers, sequenced from a subset of nine samples, and assembled into three groups based on eight SNPs. SNPs in 16S rRNA gene and rp gene sequences are common in 16SrIII phytoplasmas from other hosts and this phytoplasma group is widespread in South America. 16SrIII phytoplasmas highly related are commonly found in Melia azedarach, a widespread tree in Brazil and Argentina. The finding of a new phytoplasma associated with HLB symptoms belonging to the 16SrIII group reinforces the need to develop diagnostic tools to assess HLB-associated microbiomes.