Publications

4470

Malakand Division in northwest Pakistan is known for delicious sweet orange, locally called Malta (Citrus sinensis). However, both quality and quantity of the citrus produce has seen a decline over the past few decades. Among production constraints, Huanglongbing (HLB) caused by phloem-limited alpha proteobacterium Candidatus Liberibacter asiaticus (CLas) -an endosymbiont of Asian Citrus Psyllid (Diaphorina citri), is of great economic significance. Therefore, we assessed HLB incidence through symptom-based surveys in major citrus growing areas of Khyber Pakhtunkhwa (KP), Northwest Pakistan. The presence or absence of CLas in the collected citrus samples was confirmed by PCR (Polymerase Chain Reaction) using three set of primers (LSS/LAS606, OI1/OI2C “16S rDNA” and MH353/MH354 “operon “nusG-rplK”). An average disease incidence of 92% and severity of 34% were recorded from main production zones in district Swat, KP. Likewise, in district Lower Dir, HLB had disease incidence and severity of 64% and 24%, respectively. Molecular diagnostics using 16S rDNA-specific primer LSS/LAS606 and OI1/OI2C, yielded characteristic bands of 500 bp and 1160 bp, from all five pooled samples from Swat district, while only two samples of Dir tested positive for both primers. Using an alternative primer MH353/MH354 (nusG-rplK) showed positive amplification for four samples from Swat and two samples of Dir with an amplicon of 631 bp. To assess the molecular diversity of the CLas, Sanger sequencing was carried out based on16S rDNA gene. Sequence analysis of 16S rDNA gene from all samples revealed maximum similarity with C. Liberibacter asiaticus. Among studied isolates, SwKjuPk-5 (MH374503) and SwMtaPk-2 (MH374500) isolates appeared to be more divergent and grouped in separate clad as compared to remaining isolates of Swat and Dir. 

AbstractBois noir, a disease of the grapevine yellows complex, is associated with ‘CandidatusPhytoplasma solani’ and transmitted to grapevines in open fields by the cixiidsHyalesthes obsoletusandReptalus panzeri. In vine-growing areas where the population density of these vectors is low within the vineyard, the occurrence of bois noir implies the existence of alternative vectors. The aim of this study was to identify alternative vectors through screening of the Auchenorrhyncha community, phytoplasma typing bystampgene sequence analyses, and transmission trials. During field activities, conducted in Northern Italy in a vineyard where the bois noir incidence was extremely high, nine potential alternative insect vectors were identified according to high abundance in the vineyard agro-ecosystem, high infection rate, and harbouring phytoplasma strains characterized bystampgene sequence variants found also in symptomatic grapevines. Transmission trials coupled with molecular analyses showed that at least eight species (Aphrodes makarovi,Dicranotropis hamata,Dictyophara europaea,Euscelis incisus,Euscelidius variegatus,Laodelphax striatella,Philaenus spumarius, andPsammotettix alienus/confinis) are alternative vectors of ‘CandidatusPhytoplasma solani’ to grapevines. These novel findings highlight that bois noir epidemiology in vineyard agro-ecosystems is more complex than previously known, opening up new perspectives in the disease management.

Potato psyllid (Bactericera cockerelli) is one of the most important pests in potatoes (Solanum tuberosum L.) due to its feeding behavior and the transmission of a bacterium (Candidatus Liberibacter solanacearum) that causes zebra chip disease, altering the quality of the potato tuber and the fried potato chip or french fry. This pest is thus a threat to the chip potato industry and often requires preventive measures including the use of costly insecticides. The objectives of this research were to monitor the variation in B. cockerelli adult abundance and to evaluate the risk of zebra chip disease in northwestern New Mexico, USA. Yellow sticky traps were used to collect the pest at the Agricultural Experiment Station at Farmington, NM and in nearby commercial fields at the Navajo Agricultural Products Industry (NAPI) and Navajo Mesa Farms during the 2017–2019 period. The collected adult pests were analyzed at Texas A & M University for the presence of Candidatus L. solanacearum (Lso). The results showed field infestation by B. cockerelli in early June and that the population peaked during the second half of July and decreased as the potato growing season progressed. However, a second less important peak of the pest was revealed around mid- to late-August, depending on the growing season and field. While the B. cockerelli population increased linearly with average air temperature, it showed strong third order polynomial relationships with the accumulated thermal units and the Julian days. The test of B. cockerelli for the Lso infection revealed a low incidence of the pathogen varying from 0.22% to 6.25% and the infected adult B. cockerelli were collected during the population peak period. The results of this study may be helpful to potato growers in pest management decision-making and control. However, more study is needed to evaluate zebra chip disease in terms of its prevention and economic impact, and to develop economic thresholds and pest management programs for northwestern New Mexico and neighboring regions.

Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “ Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “ Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “ Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “ Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “ Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “ Ca. Liberibacter asiaticus.”

“ Candidatus Liberibacter solanacearum” is a pathogen transmitted by the potato psyllid Bactericera cockerelli (Šulc) (Hemiptera: Triozidae) in a persistent manner. In this study, we investigated the molecular interaction between “ Ca. Liberibacter solanacearum” and the potato psyllid at the gut interface. Specifically, we focused on the apoptotic response of potato psyllids to the infection by two “ Ca. Liberibacter solanacearum” haplotypes, LsoA and LsoB.

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

ABSTRACTThe presences of ammonia tolerant ammonia-oxidizing archaea (AOA) in environments are always underestimated and their adaption to complex habitats has also rarely been reported. Here we present the physiological and genomic characteristics of an ammonia tolerant soil AOA strainCandidatusNitrosocosmicus agrestis. This strain was able to form aggregates and adhere on the surface of hydrophobic matrix. Ammonia-oxidizing activities were still observed at 200 mM NH4+(> 1500 μM of free ammonia) and 50 mM NO2-. Urea could be used as sole energy source but exogenous organics had no significant effect on the ammonia oxidation. Besides the genes involving in ammonia oxidation, carbon fixation and urea hydrolysis, the genome also encodes a full set of genes (GTs, GHs, CEs, MOP, LPSE, etc) that responsible for polysaccharide metabolism and secretion, suggesting the potential production of extracellular polymeric substances (EPS). Moreover, a pathway connecting urea cycle, polyamines synthesis and excretion was identified in the genome, which indicates the NH4+in cytoplasm could potentially be converted into polyamines and excreted out of cell, and then contributes to the high ammonia tolerance. Genes encoding the cytoplasmic carbonic anhydrase and putative polyamine exporter are unique inCa. Nitrosocosmicus agrestis or the genusCa. Nitrosocosmicus, suggesting the prevalence of ammonia tolerance in this clade. The proposed mechanism of ammonia tolerance via polyamines synthesis and export was verified by using transcriptional gene regulation and polyamines determination.IMPORTANCEAOA are ubiquitous in different environments and play a major role in nitrification. Though AOA have higher affinities for ammonia, their maximum specific cell activity and ammonia tolerance are usually much lower than AOB, resulting in low contribution to the global ammonia oxidation and N2O production. However, in some agricultural soils, the AOA activity would not be suppressed by the fertilization with high concentration of ammonium nitrogen, suggesting the presence of some ammonia tolerant species. This study provides some physiological and genomic characteristics for an ammonia tolerant soil AOA strainCa. Nitrosocosmicus agrestis and proposes some mechanisms of this AOA adapting to a variety of environments and tolerating to high ammonia. Ammonia tolerance of AOA was always underestimated in many previous studies, physiological and genomic analyses of this AOA clade are benefit to uncover the role of AOA playing in global environmental patterns.

AbstractRickettsiales bacteria in arthropods play a significant role in both public health and arthropod ecology. However, the extensive genetic diversity of Rickettsiales endosymbionts of arthropods is still to be discovered. In 2016, 515 arthropods belonging to 9 species of four classes (Insecta, Chilopoda, Diplopoda and Arachnida) were collected in Serbia. The presence and genetic diversity of Rickettsiales bacteria were evaluated by characterizing the 16S rRNA (rrs), citrate synthase (gltA) and heat shock protein (groEL) genes. The presence of various Rickettsiales bacteria was identified in the majority of tested arthropod species. The results revealed co-circulation of five recognized Rickettsiales species including Rickettsia, Ehrlichia and Wolbachia, as well as four tentative novel species, including one tentative novel genus named Neowolbachia. These results suggest the remarkable genetic diversity of Rickettsiales bacteria in certain arthropod species in this region. Furthermore, the high prevalence of spotted fever group Rickettsia in Ixodes ricinus ticks highlights the potential public health risk of human Rickettsia infection.