Microbiology

AbstractBackground"CandidatusPhytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifoliaL.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia".ResultsWe carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection.ConclusionThe present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "CandidatusPhytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen.

Abstract By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named ‘Candidatus Fodinabacter communificans.’ Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase–PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.

ABSTRACT The sequence of the genome of “ Candidatus Tremblaya princeps” strain PCVAL, the primary endosymbiont of the citrus mealybug Planococcus citri , has been determined. “ Ca . Tremblaya princeps” presents an unusual nested endosymbiosis and harbors a gammaproteobacterial symbiont within its cytoplasm in all analyzed mealybugs. The genome sequence reveals that “ Ca . Tremblaya princeps” cannot be considered an independent organism but that the consortium with its gammaproteobacterial symbiotic associate represents a new composite living being.

ABSTRACT Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, “ Candidatus Nitrosopumilus koreensis” MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.

In addition to the grapevine flavescence dorée phytoplasmas, other members of taxonomic group 16SrV phytoplasmas infect grapevines, alders and species of the genera Clematis and Rubus in Europe. In order to investigate which phytoplasmas constitute discrete, species-level taxa, several strains were analysed by comparing their 16S rRNA gene sequences and a set of five housekeeping genes. Whereas 16S rRNA gene sequence similarity values were >97.5 %, the proposed threshold to distinguish two ‘Candidatus Phytoplasma’ taxa, phylogenetic analysis of the combined sequences of the tuf, rplV-rpsC, rplF-rplR, map and uvrB-degV genetic loci showed that two discrete phylogenetic clusters could be clearly distinguished. The first cluster grouped flavescence dorée (FD) phytoplasmas, alder yellows (AldY) phytoplasmas, Clematis (CL) phytoplasmas and the Palatinate grapevine yellows (PGY) phytoplasmas. The second cluster comprised Rubus stunt (RS) phytoplasmas. In addition to the specificity of the insect vector, the Rubus stunt phytoplasma contained specific sequences in the 16S rRNA gene. Hence, the Rubus stunt phytoplasma 16S rRNA gene was sufficiently differentiated to represent a novel putative taxon: ‘Candidatus Phytoplasma rubi’.

A novel bacterium of the genusPasteuriawas discovered parasitizing bacterivorous nematodes of the genusBursilla, in selected bermudagrass (Cynodon) field plots in Davie, FL, USA. Soil containing this bacterium was sampled and supplied with bi-weekly inoculations of cultured species of the genusBursillain order to build and maintain a source of endospores for continuousin vivoconservation of the bacteria for further study and characterization. 16S rRNA gene sequence similarities supported its congeneric ranking with other members of the genusPasteuriathat have been identified from nematodes and cladocerans. There were, however, no clear sister candidates for this organism, which supported the evidence of endospore ultrastructure and host-range studies, suggesting it belonged to a novel taxon. Because members of the genusPasteuriacannot yet be isolated, definitive type strains could not be maintained; therefore, the name ‘CandidatusPasteuria aldrichii’ is proposed for this organism.

The taxonomic status of the families Actinosynnemataceae and Pseudonocardiaceae was assessed based on 16S rRNA gene sequence data available for the 151 taxa with validly published names, as well as chemotaxonomic and morphological properties available from the literature. 16S rRNA gene sequences for the type strains of all taxa within the suborder Pseudonocardineae were subjected to phylogenetic analyses using different algorithms in arb and phylip. The description of many new genera and species within the suborder Pseudonocardineae since the family Actinosynnemataceae was proposed in 2000 has resulted in a markedly different distribution of chemotaxonomic markers within the suborder from that observed at that time. For instance, it is noted that species of the genera Actinokineospora and Allokutzneria contain arabinose in whole-cell hydrolysates, which is not observed in the other genera within the Actinosynnemataceae, and that there are many genera within the family Pseudonocardiaceae as currently described that do not contain arabinose. Phylogenetic analyses of 16S rRNA gene sequences for all taxa within the suborder do not provide any statistical support for the family Actinosynnemataceae, nor are signature nucleotides found that support its continued differentiation from the family Pseudonocardiaceae. The description of the family Pseudonocardiaceae is therefore emended to include the genera previously classified within the family Actinosynnemataceae and the description of the suborder Pseudonocardineae is also emended to reflect this reclassification.