Molecular techniques for pathogen identification and fungus detection in the environment

Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here

Quorum Sensing Signaling Molecules Produced by Reference and Emerging Soft-Rot Bacteria (Dickeya and Pectobacterium spp.)

International audienceBACKGROUND: Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates. METHODOLOGY/PRINCIPAL FINDINGS: Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase. CONCLUSIONS/SIGNIFICANCE: Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the mechanisms of communication via the diffusible molecules. Our results designate autoinducer-1 lactones as the main targets for a global biocontrol of soft-rot bacteria communications, including those of emerging isolates

Mining in Africa after the supercycle:New directions and geographies

Mining in Africa is at a pivotal moment. For most of the period 2000 to 2012, the extractive industries were in a ‘supercycle’ of sustained high commodity prices. Driven by resource-intensive growth in emerging market economies, prices were anticipated to continue for decades to come. However, this ‘supercycle’ ended in 2012 and there followed a severe slump in mineral prices from 2014 onwards. On the one hand, a new era of commodity market dynamics has begun, with changing patterns of economic activity, minerals governance, and environmental regulation. On the other hand, the end of the supercycle has continued or intensified pre-existing trends towards mechanisation, automation, and enclavity while distributive pressures on companies by local communities and host nations increases. We argue that the end of the supercycle has reconfigured the geographies of extraction in ways that are not yet reflected in existing research nor taken into consideration in policy implementation, particularly around corporate strategy, state- business relations and models for mineral-based development strategies. In this paper we map the terrain of research on the supercycle in Africa and identify emerging post-supercycle trends - some of which have overtaken research. The paper is structured around examining four themes: (1) new geographies of investment and extraction, (2) new geographies of struggle, (3) national minerals-based development and (4) labour and livelihoods, for which we identify key trends during the supercycle and post-supercycle and areas for future research and policy development