Publications

4500

Abstract The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time: faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed phylogenetic history of these endosymbionts with divergence dates for closely related species. This allows for genome evolution to be studied in detail and rates of change to be estimated in a phylogenetic framework. Here, we sequenced the genome of the chimpanzee louse endosymbiont (Candidatus Riesia pediculischaeffi) and compared it with the closely related genome of the human body louse endosymbiont. From this comparison, we found evidence for recent genome erosion leading to gene loss in these endosymbionts. Although gene loss was detected, it was not significantly greater than in older endosymbionts from aphids and ants. Additionally, we searched for genes associated with B-vitamin synthesis in the two louse endosymbiont genomes because these endosymbionts are believed to synthesize essential B vitamins absent in the louse’s diet. All of the expected genes were present, except those involved in thiamin synthesis. We failed to find genes encoding for proteins involved in the biosynthesis of thiamin or any complete exogenous means of salvaging thiamin, suggesting there is an undescribed mechanism for the salvage of thiamin. Finally, genes encoding for the pantothenate de novo biosynthesis pathway were located on a plasmid in both taxa along with a heat shock protein. Movement of these genes onto a plasmid may be functionally and evolutionarily significant, potentially increasing production and guarding against the deleterious effects of mutation. These data add to a growing resource of obligate endosymbiont genomes and to our understanding of the rate and mode of genome erosion in obligate animal-associated bacteria. Ultimately sequencing additional louse p-endosymbiont genomes will provide a model system for studying genome evolution in obligate host associated bacteria.

ABSTRACT We report here the draft genome sequence of “ Candidatus Liberibacter asiaticus” strain HHCA, collected from a lemon tree in California. The HHCA strain has a genome size of 1,150,620 bp, 36.5% G+C content, 1,119 predicted open reading frames, and 51 RNA genes.

ABSTRACT Phytoplasmas are unculturable plant-pathogenic bacteria causing devastating damage to agricultural production worldwide. Here, we report the draft genome sequence of “ Candidatus Phytoplasma asteris” strain OY-V. Most of the known virulence factors and host-interacting proteins were conserved in OY-V. This genome furthers our understanding of genetic diversity and pathogenicity of phytoplasmas.

A set of experiments was carried out to characterize how temperature affects the spread of chrysanthemum yellows phytoplasma (CYP), a strain of Candidatus Phytoplasma asteris, in Chrysanthemum carinatum plants transmitted by the Macrosteles quadripunctulatus leafhopper. Experiments provided data on CYP latency period in insect and plant host, M. quadripunctulatus adult mortality rate, and epidemics progression in plants under controlled conditions inside climatic chambers. Experiments were conducted at temperatures ranging between 15 and 30°C. Empirical laws for temperature-dependent epidemiological parameters were next derived and used in a dynamical model of the epidemics progression. Experiments showed that CYP epidemics was faster at higher temperatures and the model could replicate these observations with relatively high accuracy (correlation >98.03% and residuals <14.5%). The epidemics spreading rate increased linearly from 0.2 plants infected per day at 15°C to about 0.7 plants per day at 30°C, possibly due to: i) faster CYP multiplication in the host plants and ii) higher frequency of feeding bouts of M. quadripunctulatus at higher temperatures.

A phylogenetically novel proteobacterium, strain Shr3T, was isolated from sand gravels collected from the eastern margin of the Sahara Desert. The isolation strategy targeted bacteria filterable through 0.2-µm-pore-size filters. Strain Shr3T was determined to be a Gram-negative, aerobic, non-motile, filamentous bacterium. Oxidase and catalase reactions were positive. Strain Shr3T showed growth on R2A medium, but poor or no growth on nutrient agar, trypticase soy agar and standard method agar. The major isoprenoid quinone was menaquinone-7. The dominant cellular fatty acids detected were C16 : 1ω5c and C16 : 0, and the primary hydroxy acid present was C12 : 0 3-OH. The DNA G+C content was 54.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Shr3T was affiliated with an uncultivated lineage of the phylum Proteobacteria ; the nearest known type strain, with 83 % sequence similarity, was Desulfomicrobium orale DSM 12838T in the class Deltaproteobacteria . The isolate and closely related environmental clones formed a novel class-level clade in the phylum Proteobacteria with high bootstrap support (96–99 %). Based on these results, the novel class Oligoflexia classis nov. in the phylum Proteobacteria and the novel genus and species Oligoflexus tunisiensis gen. nov., sp. nov. are proposed for strain Shr3T, the first cultivated representative of the Oligoflexia. The type strain of Oligoflexus tunisiensis is Shr3T ( = JCM 16864T = NCIMB 14846T). We also propose the subordinate taxa Oligoflexales ord. nov. and Oligoflexaceae fam. nov. in the class Oligoflexia.

In March of 2014, carrot plants (Daucus carota L. var. Mascot) exhibiting symptoms of yellowing, purpling, and curling of leaves, proliferation of shoots, formation of hairy secondary roots, general stunting, and plant decline were observed in commercial fields in the Gharb region of Morocco. The symptoms resembled those caused by phytoplasmas, Spiroplasma citri, or ‘Candidatus Liberibacter solanacearum’ infection (1,2,3). About 30% of the plants in each field were symptomatic and plants were infested with unidentified psyllid nymphs; some psyllids are known vectors of ‘Ca. L. solanacearum.’ A total of 10 symptomatic and 2 asymptomatic plants were collected from three fields. Total DNA was extracted from petiole and root tissues of each of the carrots, using the CTAB buffer extraction method (3). The DNA samples were tested for phytoplasmas and spiroplasmas by PCR (3) but neither pathogen was detected in the samples. The DNA extracts were tested for ‘Ca. L. solanacearum’ by PCR using specific primer pairs OA2/OI2c, Lso adkF/R, and CL514F/R, to amplify a partial fragment of the 16S rDNA, the adenylate kinase gene, and rpIJ/rpIL50S rDNA ribosomal protein genes, respectively (1,2,5). DNA samples from all 10 symptomatic carrots yielded specific bands; 1,168 bp for the 16S rDNA fragment, 770 bp for the adk fragment, and 669 bp for rpIJ/rpIL, indicating the presence of ‘Ca. L. solanacearum.’ No ‘Ca. L. solanacearum’ was detected in asymptomatic plants. DNA amplicons of three plant samples (one plant/field) for each primer pair were directly sequenced (Macrogen Inc., Amsterdam). Sequencing results identified two distinct products for the OA2/OI2c primer pair (GenBank Accession Nos. KJ740159 and KJ740160), and BLAST analysis of the 16S rDNA amplicons showed 99 and 100% identity to ‘Ca. L. solanacearum’ (KF737346 and HQ454302, respectively). Two different sequences of the adk amplicon were obtained (KJ740162 and KJ740163), both of which were 98% identical to ‘Ca. L. solanacearum’ (CP002371). Sequencing results also identified two distinct products for the CL514F/R primer pair (KJ754506 and KJ754507), and BLAST analysis of the 50S rDNA ribosomal protein showed 99 and 100% identity to ‘Ca. L. solanacearum’ (KF357912 and HQ454321, respectively). The differences in our 16S and 50S rDNA sequences identified the presence of both ‘Ca. L. solanacearum’ haplotypes D and E (4). To our knowledge, this is the first report of the occurrence of ‘Ca. L. solanacearum’ in Morocco and Africa, suggesting a wider distribution of the bacterium in carrot crops in the Mediterranean region, including North Africa. ‘Ca. L. solanacearum’ has caused economic damages to carrot and celery crops in the Canary Islands and mainland Spain, France, Sweden, Norway, and Finland (3). This bacterium 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 (1,2,5). Given the economic impact of ‘Ca. L. solanacearum’ on numerous important crops worldwide, it is imperative that preventive measures be taken to limit its spread. References: (1) L. W. Liefting et al. Plant Dis. 93:208, 2009. (2) J. E. Munyaneza et al. Plant Dis. 93:552, 2009. (3) J. E. Munyaneza et al. J. Plant Pathol. 93:697, 2011. (4) W. R. Nelson et al. Eur. J. Plant Pathol. 135:633, 2013. (5) A. Ravindran et al. Plant Dis. 95:1542, 2011.