Publications

4358

AbstractThe bacterium Candidatus Liberibacter asiaticus (Las) has been strongly associated with huanglongbing, or citrus greening, which is one of the most devastating citrus diseases worldwide. Las is transmitted by the Asian citrus psyllid (ACP) Diaphorina citri (Hemiptera: Psyllidae) in a persistent manner, but its interactions with the psyllid vector, particularly at the organ and cellular levels, are poorly understood. We have tested several fluorescence in situ hybridization (FISH) protocols and three nucleic acid probes for the localization of Las in haemolymph smears and dissected organs of ACP adults that fed on Las‐infected plants in the field or laboratory and in sections from Las‐infected citrus leaves. Las was detected by FISH and confocal laser scanning microscopy in the filter chamber, midgut, Malpighian tubules, haemolymph, salivary glands, ovaries and in muscle and fat tissues of ACP that acquired Las from infected plants, as well as in the phloem of infected citrus leaves. Las appeared as pleiomorphic bodies or short thin rods that were much more dispersed and individually distinct in citrus leaf phloem and in ACP haemolymph, but more densely aggregated in cells of the salivary glands and other ACP organs and tissues. Our results provide the first in situ demonstration of Las infection in various psyllid organs and tissues and show the near‐systemic infection of ACP by Las.

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.

Winter oilseed rape (Brassica napus L.) is widely grown in Poland to produce vegetable oil for industrial processing of human and animal feed. In recent years, according to European Union directives on the use of biofuels (Directive 2003/30/EC), the area under oilseed rape cultivation in Poland has dramatically increased to 810,000 ha in 2009 and is still increasing. Morphological deformations of winter oilseed rape indicative of phytoplasma infection have been observed sporadically in Poland since 2000 (3). Plants exhibiting floral virescence, phyllody, as well as auxiliary bud proliferation, reduced leaves, and malformation of siliques were identified during surveys of research fields in Wielkopolska during May and June of 2009 and 2010. To confirm phytoplasma infection of these plants, inflorescence and leaf tissues were collected from nine diseased and three symptomless plants from three different field locations with 1 to 16% disease incidence. Total DNA was extracted from each plant tissue sample with a modified cetyltrimethylammoniumbromide method (2). Samples were analyzed for phytoplasma DNA with a nested PCR assay employing phytoplasma universal rRNA operon primer pair P1/P7 followed by R16F2n/R16R2, using previously described conditions (1). PCR products of 1.8 and 1.2 kb were obtained from all diseased plants only following PCRs with P1/P7 and nested primer pair R16F2n/R16R2, respectively. PCR products were not obtained from symptomless plants. Eight 1.2-kb amplicons were sequenced (GenBank Accession Nos. JN193475 to JN193482). Comparative analysis of the R16F2n/R16R2 rDNA sequences confirmed the phytoplasma origin of the rDNA sequences that shared 100 to 99% identity with Maize bushy stunt phytoplasma (GenBank Accession No. HQ530152), Alfalfa stunt phytoplasma (GenBank Accession No. GU289675), Primula green yellows phytoplasma (GenBank Accession No. HM590623), and other aster yellows group phytoplasmas. A 1.8-kb amplicon of isolate designated RzW14 was sequenced (GenBank Accession No. HM561990) and had 99% identity with Aster yellow group phytoplasmas from Lithuania (GenBank Accession Nos.GU223208 and AY744071). A virtual restriction fragment length polymorphism analysis of the 16S rDNA sequences from the R16F2n/R16R2 amplicons was performed with iPhyClassifier (4). Restriction profile comparisons identified all aster yellows group phytoplasmas as subgroup 16SrI-B strains. To our knowledge, this is the first report of a ‘Candidatus Phytoplasma asteris’-related strain infecting oilseed rape in Poland. References: (1) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) A. C. Padovan et al. Aust. J. Grape Wine Res. 1:25, 1995. (3) M. Starzycki and E. Starzycka. Oilseed Crops 21:399, 2000. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

Citrus Huanglongbing (HLB) has been threatening citrus production worldwide. In this study, a comparative proteomic approach was applied to understand the pathogenic process of HLB in affected sweet orange leaves. Using the isobaric tags for relative and absolute quantification (iTRAQ) technique, we identified 686 unique proteins in the mature leaves of both mock‐inoculated and diseased ‘Madam Vinous' sweet orange plants. Of the identified proteins, 20 and 10 were differentially expressed in leaves with and without symptoms of HLB (fold change > 2.5), respectively, compared with mock‐inoculated controls. Most significantly, upregulated proteins were involved in stress/defense response, such as four miraculin‐like proteins, chitinase, Cu/Zn superoxide dismutase and lipoxygenase. Microarray analysis also showed that stress‐related genes were significantly upregulated at the transcriptional level. For example, remarkable upregulations of miraculin‐like proteins and Cu/Zn superoxide dismutase transcripts were observed. Moreover, the transcriptional patterns of miraculin‐like protein 1 and Cu/Zn superoxide dismutase were examined at different stages of HLB disease development. Combined with the transcriptomic data, the proteomic data can provide an enhanced understanding of citrus stress/defense responses to HLB.

A sustainable option for nitrogen removal is the anaerobic ammonium-oxidizing (anammox) process in which ammonium is oxidized to nitrogen gas with nitrite as electron acceptor. Application of this process, however, is limited by the availability of anammox biomass. In this study, two Brocadia-like anammox phylotypes were successfully enriched, detected and identified from an activated sludge taken from a domestic wastewater treatment plant (Minas Gerais, Brazil) employing a Sequencing Batch Reactor (SBR). The dominant phylotype was closely related to ‘Candidatus Brocadia sinica’, but one clone seemed to represent a novel species for which we propose the name ‘Candidatus Brocadia brasiliensis’. Based on Fluorescence in situ hybridization (FISH) analysis, this enrichment led to a relative population size of 52.7% (±15.6) anammox bacteria after 6 months of cultivation. The cultivation process can be divided into three phases: phase 1 (approximately 25 days) was characterized by heterotrophic denitrification metabolism, phase 2 was the propagation phase and phase 3 (from the 87th day onwards), in which significant anammox activity was detected. A long-term performance of the SBR showed a near perfect removal of nitrite based on the influent NO2−-N concentration of 61–95 mg L−1. The average ammonia removal efficiency was 90% with the influent NH4+-N concentration of 55–82 mg L−1. Therefore, anammox cultivation and enrichment from activated sludge was possible under a controlled environment within 3 months.

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.

Incidence and severity of Huanglongbing (HLB) disease were assessed in Apr. 2010 among eight citrus cultivars representing diverse scion types growing in commercial groves in Florida's Indian River region, an area with a high incidence of HLB. In each grove, 20 trees of each cultivar were rated for visual HLB symptoms and leaves were collected for quantitative polymerase chain reaction quantification of Candidatus Liberibacter asiaticus (CLas), the presumptive causal agent of HLB. There was a strong correlation between HLB rating and CLas titer (titer represented by Ct, r2 = 0.37 and 0.40, for whole tree and leaf sample, respectively, both with P < 0.0001) across all cultivars and groves. Although incidence and severity of HLB varied considerably among the groves, scion-specific differences were apparent, even when analyses excluded potentially confounding grove effects. ‘Temple’ tangor showed the most consistently low incidence of HLB symptoms and CLas titer; in contrast, ‘Murcott’ tangor and ‘Minneola’ tangelo had the highest incidence of HLB symptoms and highest CLas titer. These results suggest useful resistance to HLB with reduced symptoms and reduced CLas titer may be found in conventional scion cultivars and further work is needed to assess this potential and its commercial value.

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.

An aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium, strain T49T, was isolated from geothermally heated soil at Hell’s Gate, Tikitere, New Zealand. On the basis of 16S rRNA gene sequence similarity, T49T is the first representative of a new class in the newly described phylum Armatimonadetes, formerly known as candidate division OP10. Cells of strain T49T stained Gram-negative and were catalase-positive and oxidase-negative. Cells possessed a highly corrugated outer membrane. The major fatty acids were 16 : 0, i17 : 0 and ai17 : 0. The G+C content of the genomic DNA was 54.6 mol%. Strain T49T grew at 50–73 °C with an optimum temperature of 68 °C, and at pH 4.7–5.8 with an optimum growth pH of 5.3. A growth rate of 0.012 h−1 was observed under optimal temperature and pH conditions. The primary respiratory quinone was MK-8. Optimal growth was achieved in the absence of NaCl, although growth was observed at NaCl concentrations as high as 2 % (w/v). Strain T49T was able to utilize mono- and disaccharides such as cellobiose, lactose, mannose and glucose, as well as branched or amorphous polysaccharides such as starch, CM-cellulose, xylan and glycogen, but not highly linear polysaccharides such as crystalline cellulose or cotton. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain T49T represents a novel bacterial genus and species within the new class Chthonomonadetes classis nov. of the phylum Armatimonadetes. The type strain of Chthonomonas calidirosea gen. nov., sp. nov. is T49T ( = DSM 23976T = ICMP 18418T).