Publications

4561

ABSTRACTHere we investigated the bacterial endosymbionts of weevils of the genusCurculio. From all four species ofCurculioweevils examined, a novel group of bacterial gene sequences were consistently identified. Molecular phylogenetic analyses demonstrated that the sequences formed a distinct clade in theGammaproteobacteria, which was not related to previously known groups of weevil endosymbionts such asNardonellaspp. andSodalis-allied symbionts. In situ hybridization revealed that the bacterium was intracellularly harbored in a bacteriome associated with larval midgut. In adult females, the bacterium was localized in the germalia at the tip of each overiole, suggesting vertical transmission via ovarial passage. Diagnostic PCR surveys detected high prevalence of the bacterial infection in natural host populations. Electron microscopy identified the reduced cell wall of the bacterial cells, and the bacterial genes exhibited AT-biased nucleotide composition and accelerated molecular evolution, which are suggestive of a long-lasting endosymbiotic association. On the basis of these results, we conclude that the novel endocellular bacteria represent the primary symbiont ofCurculioweevils and proposed the designation “CandidatusCurculioniphilus buchneri.” In addition to “Ca.Curculioniphilus,” we identifiedSodalis-allied gammaproteobacterial endosymbionts from the chestnut weevil,Curculio sikkimensis, which exhibited partial infection frequencies in host insect populations and neither AT-biased nucleotide composition nor accelerated molecular evolution. We suggest that suchSodalis-allied secondary symbionts in weevils might provide a potential source for symbiont replacements, as has occurred in an ancestor ofSitophilusgrain weevils.

Abstract Background Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. Results To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. Conclusion This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.

Huanglongbing (HLB) is a devastating disease of citrus and threatens the citrus industry worldwide. The suspected causal agent of the disease is a phloem-limited bacterium of the genus Candidatus Liberibacter transmitted through insect vector or grafting with diseased budwood. Currently, most seed source trees for citrus rootstock propagation are located outdoors and unprotected from disease transmission. In addition, fruit from HLB-affected scion varieties in Florida containing seeds enter the commercial trade and move into other citrus-growing areas. The objective of this study was to determine how Ca. L. asiaticus infection affects seed quality and seedling development and whether the disease appears in seedlings grown from infected fruit. Two experiments were conducted involving thousands of seedlings produced from seeds from infected rootstock seed source trees and ‘Valencia’ sweet orange trees, respectively. Infection of trees and fruit with Ca. L. asiaticus significantly reduced seed weight, seed germination, and seedling height. Seedlings did not develop symptoms typical of HLB throughout the experiment. Polymerase chain reaction (PCR) analysis initially identified two of 686 rootstock seedlings and three of 431 sweet orange seedlings positive for the pathogen when they were very young. Resampling and PCR analysis of these five seedlings at older ages consistently indicated they were negative for the pathogen and none of these plants ever developed symptoms of HLB. It is suggested that Ca. L. asiaticus may have been translocated into some part of the embryo during seed development but that it was not present in cells or tissue, which permitted replication or disease development as the seedling grew.