Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling

Background Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs. Methodology/Principal Findings Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively. Conclusions/Significance A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin.This study was financially supported by GrapeGen Project funded by Genoma España within a collaborative agreement with Genome Canada. The authors also thank The Ministerio de Ciencia e Innovacion for project BIO2008-03892 and a bilateral collaborative grant with Argentina (AR2009-0021). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe

Microorganisms for soil treatment.

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic

Biodegradability of HCH in agricultural soils from Guadeloupe (French West Indies): identification of the lin genes involved in the HCH degradation pathway

International audienceBanana has been a main agricultural product in the French West Indies (Guadeloupe and Martinique) since the 1960s. This crop requires the intensive use of pesticides to prevent attacks by insect pests. Chlorinated pesticides, such as hexachlorocyclohexane (HCH), chlordecone and dieldrin, were used until the beginning of the 1990s, resulting in a generalized diffuse contamination of the soil and water in the areas of banana production, hence the need to develop solutions for cleanup of the polluted sites. The aims of this work were (i) to assess lindane degradation in soil slurry microcosms treated with lindane at 10 mg/L and (ii) to detect the catabolic genes involved in the HCH degradation pathway. The soil slurry microcosm system showed a 40 % lindane degradation efficiency at the end of a 30-day experiment. Lower lindane removal was also detected in the abiotic controls, probably caused by pesticide adsorption to soil particles. Indeed, the lindane concentration decreased from 6000 to 1330 ng/mL and from 800 to 340 ng/mL for the biotic and abiotic soils, respectively. Nevertheless, some of the genes involved in the HCH degradation pathway were amplified by polymerase chain reaction (PCR) from crude deoxyribonucleic acid (DNA) extracted from the Guadeloupe agricultural soil, suggesting that HCH degradation is probably mediated by bacteria closely related to the family Sphingomonadaceae

Evidence for extensice anaerobic dechlorination and transformation of chlordecone from soil microcosm from Guadeloupe study and comparison with field sample

International audienceThe use of chlordecone as the active ingredient in pesticide formulations has resulted in extensive pollution of large land areas in the French West Indies. These areas were treated with pesticides to control the banana black weevil. Although the use of these pesticides is currently banned, chlordecone strongly adsorbs to soil and is highly recalcitrant due to its complex bis-homocubane structure. In order to investigate the biodegradability of chlordecone, microcosms were constructed anaerobically from chlordecone impacted Guadeloupe soil and sludge. The microcosms were incubated and repeatedly amended with chlordecone and electron donor (ethanol and acetone) over a period of 7 years. DNA was extracted from some of the microcosms, and the microbial community was analyzed using 16S amplicon sequencing (Illumina MiSeq). Degradation products of chlordecone were detected in all the biologically active microcosms. Observed products include monohydro- and dihydrochlordecone derivatives (C10H10-nO2Hn+1 n= 1,2), as well as C10- and C9- polychloroindene compounds (C9Cl5-nH3+n n=0,1) and carboxylic indene derivatives (C10Cl4-nO2H4+n, n=0-4) assumed to be “open cage” structures with significant dechlorination also characterized in other studies (1,2,3) but which are not present in sterile controls. Chlordecone concentrations decreased in active microcosms. Results from microbial community analysis show enrichment of several organisms possibly involved in chlordecone biodegradation. In two microcosms with no methanogenesis we see high relative abundance of Desulfovibrio and Sporomusa, while in two of the microcosms with methane production, we see enrichment of two highly similar Anaerolinaceae species (Pelolinea and Leptolinea), Bathyarchaeota, and two methanogens (Methanoregula and Methanosaeta). The metabolites identified in this study are also detected in the field, showing that a bioremediation process could be envisioned. Stimulatation pf dechlorination in farmer’s fields can be considered by inducing reducing conditions with substrate addition and restricting oxygen entry

Evidence for extensice anaerobic dechlorination and transformation of chlordecone from soil microcosm from Guadeloupe study and comparison with field sample

International audienceThe use of chlordecone as the active ingredient in pesticide formulations has resulted in extensive pollution of large land areas in the French West Indies. These areas were treated with pesticides to control the banana black weevil. Although the use of these pesticides is currently banned, chlordecone strongly adsorbs to soil and is highly recalcitrant due to its complex bis-homocubane structure. In order to investigate the biodegradability of chlordecone, microcosms were constructed anaerobically from chlordecone impacted Guadeloupe soil and sludge. The microcosms were incubated and repeatedly amended with chlordecone and electron donor (ethanol and acetone) over a period of 7 years. DNA was extracted from some of the microcosms, and the microbial community was analyzed using 16S amplicon sequencing (Illumina MiSeq). Degradation products of chlordecone were detected in all the biologically active microcosms. Observed products include monohydro- and dihydrochlordecone derivatives (C10H10-nO2Hn+1 n= 1,2), as well as C10- and C9- polychloroindene compounds (C9Cl5-nH3+n n=0,1) and carboxylic indene derivatives (C10Cl4-nO2H4+n, n=0-4) assumed to be “open cage” structures with significant dechlorination also characterized in other studies (1,2,3) but which are not present in sterile controls. Chlordecone concentrations decreased in active microcosms. Results from microbial community analysis show enrichment of several organisms possibly involved in chlordecone biodegradation. In two microcosms with no methanogenesis we see high relative abundance of Desulfovibrio and Sporomusa, while in two of the microcosms with methane production, we see enrichment of two highly similar Anaerolinaceae species (Pelolinea and Leptolinea), Bathyarchaeota, and two methanogens (Methanoregula and Methanosaeta). The metabolites identified in this study are also detected in the field, showing that a bioremediation process could be envisioned. Stimulatation pf dechlorination in farmer’s fields can be considered by inducing reducing conditions with substrate addition and restricting oxygen entry