Publications

4713

AbstractBackgroundCitrushuanglongbing(HLB) disease is caused by endogenous, phloem-restricted, Gram negative, uncultured bacteria namedCandidatusLiberibacter africanus (CaLaf),Ca.L. asiaticus (CaLas), andCa.L. americanus (CaLam), depending on the continent where the bacteria were first detected. The Asian citrus psyllid vector,Diaphorina citri, transmits CaLas and CaLam and both Liberibacter species are present in Brazil. Several studies of the transcriptional response of citrus plants manifesting HLB symptoms have been reported, but only for CaLas infection. This study evaluated the transcriptional reprogramming of a susceptible genotype of sweet orange challenged with CaLam, using a customized 385K microarray containing approximately 32,000 unigene transcripts. We analyzed global changes in gene expression of CaLam-infected leaves of sweet orange during the symptomatic stage of infection and compared the results with previously published microarray studies that used CaLas-infected plants. Twenty candidate genes were selected to validate the expression profiles in symptomatic and asymptomatic PCR-positive leaves infected with CaLas or CaLam.ResultsThe microarray analysis identified 633 differentially expressed genes during the symptomatic stage of CaLam infection. Among them, 418 (66%) were upregulated and 215 (34%) were down regulated. Five hundred and fourteen genes (81%) were orthologs of genes fromArabidopsis thaliana. Gene set enrichment analysis (GSEA) revealed that several of the transcripts encoded transporters associated with the endomembrane system, especially zinc transport. Among the most biologically relevant gene transcripts in GSEA were those related to signaling, metabolism and/or stimulus to hormones, genes responding to stress and pathogenesis, biosynthesis of secondary metabolites, oxidative stress and transcription factors belonging to different families. Real time PCR of 20 candidate genes validated the expression pattern of some genes in symptomatic and asymptomatic leaves infected with CaLam or CaLas.ConclusionsMany gene transcripts and biological processes are significantly altered upon CaLam infection. Some of them had been identified in response to CaLas infection, while others had not been previously reported. These data will be useful for selecting target genes for genetic engineering to control HLB.

‘Candidatus Liberibacter asiaticus’ is the most prevalent Liberibacter sp. associated with huanglongbing (HLB) in Brazil. Within São Paulo state (SP), HLB has spread more rapidly to and reached higher incidence in regions with relatively mild (cooler) summer temperatures. This suggests that climate can influence disease spread and severity. ‘Ca. L. asiaticus’ titers on soft, immature leaves from infected ‘Valencia’ sweet orange plants exposed to different temperature regimes and adult Diaphorina citri fed for 48 h on these plants for ‘Ca. L. asiaticus’ acquisition were determined by quantitative polymerase chain reaction in two experiments. The first experiment included plants with three levels of infection, three incubation periods (IPs), and air temperatures favorable (14.6 to 28°C) and unfavorable (24 to 38°C) to ‘Ca. L. asiaticus’. The second included plants with severe late-stage infections, 10 IPs (based on 3-day intervals over 27 days), and three air temperature regimes (12 to 24, 18 to 30, and 24 to 38°C). Overall, ‘Ca. L. asiaticus’ titers and the percentages of ‘Ca. L. asiaticus’-positive psyllids were lower in plants maintained at the warmer temperature regime (24 to 38°C) than in plants maintained in the cooler regimes. The results suggest that the lower incidence and slower spread of ‘Ca. L. asiaticus’ to warmer regions of SP are related to the influence of ambient temperatures on titers of ‘Ca. L. asiaticus’ in leaves.

In May of 2012, eggplant (Solanum melongena) plants in an experimental research plot located at Zamorano in the Department of Francisco Morazán, Honduras, were observed with symptoms that included leaf chlorosis and cupping, overall stunting, and production of small and malformed fruits. The research plot was planted next to a commercial tomato field heavily infested with the psyllid Bactericera cockerelli, a vector of ‘Candidatus Liberibacter solanacearum’ (1,2,3). This bacterium severely affects potato and other solanaceous species and is the putative causal agent of zebra chip disease (2,3). The plot was planted with the eggplant variety ‘China’ and about 25% of the plants were symptomatic. A total of 10 eggplant samples, including five symptomatic and five asymptomatic plants, were collected from the plot. Total DNA was extracted from the leaf tissue of each of the collected plants with the cetyltrimethylammonium bromide (CTAB) buffer extraction method (1). The DNA samples were then tested by PCR using specific primer sets OA2/OI2c and OMB 1482f/2086r to amplify a portion of 16S rDNA and the outer membrane protein (OMB) genes, respectively, of ‘Ca. L. solanacearum’ (1,2). OMB gene and 16S rDNA fragments of 605 and 1,168 bp, respectively, were amplified from the DNA of two of the five (40%) symptomatic plants with each primer set, indicating the presence of ‘Ca. L. solanacearum.’ No ‘Ca. L. solanacearum’ was detected in the five asymptomatic plants with either primer sets. DNA amplicons with both primer sets were cloned from the DNA of the two ‘Ca. L. solanacearum’-positive plant samples and four clones of each of the four amplicons were sequenced. BLASTn analysis of the 16S rDNA resulted in two independent but related consensus sequences (deposited in GenBank as Accession Nos. KF188224 and KF188225) and were 99% similar to each other. The two sequences showed 99 to 100% identity to a number of 16S rDNA sequences of ‘Ca. L. solanacearum’ in Genbank, including accessions HM245242, FJ811596, and KC768319. For the OMB amplicons, a single consensus sequence was obtained following clone sequencing and was deposited in GenBank as accession KF188229. BLASTn analysis of the sequence indicated that it was 100% identical to several OMB sequences of ‘Ca. L. solanacearum’ in GenBank, including accessions KC768331 and CP002371. To our knowledge, this is the first report of ‘Ca. L. solanacearum’ associated with eggplant in Honduras. Eggplant is an economically important commodity in Central America and serious damage to this crop due to this plant pathogen could expand throughout the region, especially if its insect vector B. cockerelli is not properly managed. ‘Ca. L. solanacearum’ has also caused millions of dollars in losses to potato and several other solanaceous crops in the United States, Mexico, Central America, and New Zealand (2,3). In addition, this bacterium severely damages carrot crops in Europe, where it is transmitted to carrot by the psyllids Trioza apicalis and B. trigonica (3,4). It is imperative that both ‘Ca. L. solanacearum’ and its insect vectors be effectively monitored and managed to minimize their threat to economically important vegetable crops in many parts of the world. References: (1) J. M. Crosslin et al. Southwest. Entomol. 36:125, 2011. (2) L. W. Liefting et al. Plant Dis. 93:208, 2009. (3) J. E. Munyaneza. Am. J. Pot. Res. 89:329, 2012. (4) J. E. Munyaneza et al. J. Econ. Entomol. 103:1060, 2010.

Abstract Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80–90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.

AbstractBackgroundHuanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. Previously, we reported a combination of Penicillin G and Streptomycin was effective in eliminating or suppressing the associated bacterium, ‘CandidatusLiberibacter asiaticus’ (Las).ResultsHere we report the bacterial composition and community structure in HLB-affected citrus plants during a growing season and while being treated with antibiotic combinations PS (Penicillin G and Streptomycin) and KO (Kasugamycin and Oxytetracycline) using the Phylochip™ G3 array. Both antibiotic treatments resulted in significantly lower Las bacterial titers (Pr<0.05) and hybridization scores. Of the 50,000+ available operational taxonomic units (OTUs) on PhyloChip™ G3, 7,028 known OTUs were present in citrus leaf midribs. These OTUs were from 58 phyla, of which five contained 100 or more OTUs,Proteobacteria(44.1%), Firmicutes(23.5%),Actinobacteria(12.4%),Bacteroidetes(6.6%) andCyanobacteria(3.2%). In the antibiotic treated samples, the number of OTUs decreased to a total of 5,599. The over-all bacterial diversity decreased with the antibiotic treatments, as did the abundance of 11 OTUs withinProteobacteria,Firmicutes,BacteroidetesandPlanctomycetes. Within theProteobacteria, ten OTUs representing the classγ-proteobacteria increased in abundance after four months of treatment, when the Las bacterium was at its lowest level in the HLB-affected citrus field plants.ConclusionsOur data revealed thatProteobacteriawas constantly the dominant bacterial phylum recovered from citrus leaf midribs, with the α-proteobacterial and the γ-proteobacterial classes vying for prevalence. In addition, the level of bacterial diversity found in the leaf midribs of field citrus was greater than previously described. Bacterial cells in close proximity may be able to modify their microenvironment, making the composition of the microbial community an important factor in the ability of Las to cause HLB progression. A low Las level was seen as an annual fluctuation, part of the bacterial population dynamics, and as a response to the antibiotic treatments.