Impact de la variation du niveau d'eau d'un marais du lac Saint-Pierre (Québec, Canada) sur les concentrations et les flux d'hydrogène, monoxyde de carbone, méthane et dioxyde de carbone

Le but de la présente étude était d'étudier l'impact de la variation des niveaux d'eau d'un marais d'eau douce (Baie Saint-François, Québec) sur l'évolution des concentrations et des flux d'hydrogène, monoxyde de carbone, méthane et dioxyde de carbone. Une approche originale impliquant l'association d'un gradient de concentration de ces composés sur un profil vertical de 1,5 m au transfert de flux turbulent micrométéorologique fut utilisée pour la détermination des flux. L'étude démontre qu'une hausse du niveau d'eau d'un bassin versant alimentant une zone humide influence les flux de méthane, de monoxyde de carbone d'hydrogène et de dioxyde de carbone. En conditions submergées, le marais émettait du méthane et du monoxyde de carbone et consommait moins d'hydrogène troposphérique. Ainsi, cette étude démontre que des mesures in situ peuvent servir à inférer des scénarios d'impacts possibles des changements climatiques et des variations des niveaux d'eau sur les émissions des gaz à effets de serre dans l'écosystème du fleuve Saint-Laurent.Wetlands are known for their great biodiversity and the important carbon reservoir that they represent. Moreover, in the global warming context, these ecosystems represent net sources or sinks for different greenhouse gases depending of their conditions. For instance, flooded conditions favour methane production whereas they prevent hydrogen and carbon monoxide soil consumption. Baie Saint-François is a freshwater wetland that opens onto Lake Saint-Pierre (St. Lawrence River) where water levels are subject to important fluctuations due to natural processes and human activities (hydroelectricity and navigation). This study was done in order to assess the impact of the Lake Saint-Pierre water level variations on the tropospheric methane, carbon monoxide, hydrogen and carbon dioxide dynamics over the wetland. Knowledge of these dynamics should provide indications about the possible effects of the decreasing or increasing water level associated with the global warming on the production or consumption of these trace gases.Studies were carried out between June and August 2003 in Baie Saint-François where soil was subjected to successions of flooded and dry conditions. Water and carbon dioxide fluxes were obtained with a Bowen ratio micrometeorological station including a high frequency single infrared gas analyser. Hydrogen, carbon monoxide and methane fluxes were estimated with the modified Bowen method, their vertical concentration gradients (1.5 m) were measured over the plant canopy. The Bowen Ratio station was equipped with different probes to measure parameters such as net radiations, soil heat fluxes and vertical temperature gradients. The turbulent transfer coefficient (k) obtained every 20 min was assumed equal for heat, water vapour and trace gases. Hence, fluxes calculations were done by the multiplication of the turbulent transfer coefficients with the vertical concentration gradients of hydrogen, carbon monoxide and methane.The instrument used to detect hydrogen, carbon monoxide and methane was a RGA5. This analyser has two detectors: the reductive gas detector (RGD) for hydrogen and carbon monoxide and a flame ionisation detector (FID) for methane. The RGD contains an HgO bed wherein oxygen reacts with reductive gases resulting in Hg° releases detectable by differential UV absorbance. Chemicals were detected continuously in 10 min cycles with an analytical reproducibility of ±0.2, 0.3 and 2% for hydrogen, carbon monoxide and methane. Generally, vertical concentration gradients measured were greater than these limits. A calibration gas containing hydrogen, carbon monoxide and methane at 4940, 1000 and 1000 ppbv respectively in nitrogen was analysed daily to verify calibration. To ensure data integrity, linearity of the instrument was assayed by several dilutions of the standard gas and the integration of the curves gave a correction factor for hydrogen (18%) and carbon monoxide (13%). An intercomparison with NOAA (National Oceanic and Atmospheric Administration) was done to corroborate these correction factors.Background carbon monoxide, methane and carbon dioxide levels were in agreement with literature values. However, hydrogen was low, as observed by other investigators in summertime, since this season is related to minimal concentrations. Methane followed a diurnal cycle where maximum levels were observed during nighttime. In wet conditions, these nocturnal peaks reached occasionally 4000 ppbv and could be explained by specific production mechanisms and diurnal changes of vertical mixing in the boundary layer. Sensitivity of the processes responsible for methane and carbon monoxide cycling was seen between July 21st and 26th where a rain episode (total precipitation of 33.2 mm) increased their background concentrations. It seems that this precipitation was enough to favour methanogenesis and inhibit tropospheric CO and CH4 consumptions by a reduction of the diffusion of these chemicals into the soil.Our results demonstrated that four to eleven days following a variation of the Lake Saint-Pierre water level, a change in the tropospheric hydrogen, carbon monoxide and methane concentrations was observed. This lag might be explained by the distance between the lake and the research station (about 1.5 km) and the required time for the adaptation of soil microorganisms to the disruption of their environment. The concentration variations of these chemicals resulted from the inhibition of the processes responsible for their consumption or the activation of the processes accountable for their production.In June, the wetland was flooded and the CO2 median flux was -56.5 g m-2 d-1. Fluxes increased significantly (Mann-Whitney, α=0.01) in July to 5.30 g m-2 d-1, possibly due to dry conditions. Indeed, absence of water favours the activity of soil aerobic microorganisms which might produce more carbon dioxide than the quantity used by plants during photosynthesis.Methane was produced in June where the median flux was 54 mg m-2 d-1. These emissions were caused by the presence of water which maintained anaerobic conditions in the sediments, a suitable environment for methanogenic microorganisms. July was characterised by dry conditions, which generated aerobic environments in soils, an unfavourable microniche for methanogens. Therefore, methane median fluxes decreased significantly (Mann-Whitney, α=0.05) to 0.011 mg m-2 d-1 in July. In August, before the end of the investigation period, water levels had increased but methane fluxes were not significantly higher than in July. Moreover, in this period, methane concentrations tended to increase, showing that after an augmentation of the Lake Saint-Pierre water level, Baie Saint-François flooding area could represent a methane source.During summer 2003, Baie Saint-François acted as a net source of carbon monoxide. In June, the median flux was 21 µg m-2 d-1 due to presence of water which inhibited consumption by soil. Emissions were significantly (Mann-Whitney, α=0.05) lower in July (15 µg m-2 d-1) due to the absence of water, which represented a suitable environment for microorganisms consuming tropospheric carbon monoxide. In August, the median carbon monoxide flux attained 65 µg m-2 d-1 due to an increase of the Lake Saint-Pierre water level. Net carbon monoxide emissions observed in wet and dry conditions might be due to the high organic content in soil and water in addition to the presence of plants since all of these are subjected to photooxidation, generating this pollutant. Therefore, an increase of the Lake Saint-Pierre water level is associated with an augmentation of tropospheric carbon monoxide due to the inhibition of the processes responsible of its consumption.A decline in the water level might result in the activation of the soil microorganisms (or abiotic hydrogenases) able to consume tropospheric hydrogen. At the beginning of the campaign (June), the median hydrogen flux was weak (-1.37 g m-2 d-1) due to the presence of water. However, a net soil consumption was seen in July, where the median hydrogen flux decreased to -125 g m-2 d-1. The Lake Saint-Pierre water level increase observed in August was associated with a significant (Mann-Whitney, α=0.05) augmentation of the hydrogen median flux to 299 g m-2 d-1. Consequently, a rise in the Lake Saint-Pierre water levels induced an inhibition of the processes responsible of the tropospheric hydrogen consumption.This study illustrated that the water level fluctuations of the Lake Saint-Pierre have an impact on the H2, CO, CH4 and CO2 dynamics over the surrounding wetlands. When the Lake Saint-Pierre water level decreased, the wetlands acted as a carbon monoxide and carbon dioxide source, but as a consumer of tropospheric hydrogen and a minor source of methane

Manganese and cobalt redox cycling in laterites; Biogeochemical and bioprocessing implications

This research was developed during the PhD studies of Agustín Solano Arguedas in the University of Manchester, United Kingdom. PhD scholarship was funded by the Ministerio de Ciencia, Tecnología y Telecomunicaciones (MICITT) of the Government of Costa Rica and the Universidad de Costa Rica (UCR). Agustín Solano Arguedas is a researcher at the Unidad de Recursos Forestales (Reforesta, Unit of Forest Resources) of the Instituto de Investigaciones en Ingeniería (INII, Engineering Research Institute), UCR.Cobalt is essential for the modern technology that underpins the decarbonisation of our economies, but its supply is limited leading to its designation as a critical metal. Cobalt biogeochemistry is poorly understood, yet knowledge of how biogeochemical cycling impacts cobalt behaviour could assist the development of new techniques to recover cobalt from ores, and so improve the security of supply. Laterites are an important source of cobalt, they are primarily processed for nickel using energy or chemical intensive processes, with cobalt recovered as a by-product. Metal-reducing conditions were stimulated in laterite sediment microcosms by the addition of simple and cheaply available organic substrates (acetate or glucose). At the end of the experiment the amount of easily recoverable cobalt (aqueous or extractable with acetic acid) increased from < 1% to up to 64%, which closely mirrored the behaviour of manganese, while only a small proportion of iron was transformed into an easily recoverable phase. Sequencing of the microbial community showed that the addition of organic substrates stimulated the growth of indigenous prokaryotes closely related to known manganese(IV)/iron(III)-reducers, particularly from the Clostridiales, and that fungi assigned to Penicillium, known to produce organic acids beneficial for leaching cobalt and nickel from laterites, were identified. Overall, the results indicate that the environmental behaviour of cobalt in laterites is likely to be controlled by manganese biogeochemical cycling by microorganisms. These results are compelling given that similar behaviour was observed in four laterites (Acoje, Çaldağ, Piauí and Shevchenko) from different continents. A new bioprocessing strategy is proposed whereby laterites are treated with an organic substrate to generate metal-reducing conditions, then rinsed with acetic acid to remove the cobalt. Not only are organic substrates environmentally-friendly and potentially sourced from waste carbon substrates, a minimal amount of iron oxides was mobilised and consequently less waste generated.Natural Environment Research Council/[CoG3 NE/M011518/1]/NERC/Reino UnidoDiamond Light Source/[SP16735]//Reino UnidoDiamond Light Source/[SP17313]//Reino UnidoOffice of Science User Facility/[DE-AC02-05CH11231]//Estados UnidosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Instituto Investigaciones en Ingeniería (INII

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Apport du polymorphisme alloenzymatique à l'identification variétale de l'olivier (Olea europaea L)

L'identification des variétés d'olivier (Olea europaea L) est réalisée à partir du polymorphisme alloenzymatique des feuilles obtenu par électrophorèse sur gel d'amidon. L'analyse a porté sur 47 variétés représentant une large distribution de l'olivier dans le bassin méditerranéen. Vingt et un allèles ont été observés pour l'ensemble des 9 loci polymorphes étudiés (7 systèmes enzymatiques différents). Trente-huit génotypes multiloci ont permis l'identification de 35 variétés sur les 47 analysées. À partir de ces génotypes, les méthodes d'analyses multivariées ont abouti à classer les variétés en 6 groupes dont une minorité seulement représentait une région géographique précise (un groupe de 3 variétés françaises), 10 des 11 variétés originaires d'Afrique du Nord se retrouvant dans un même groupe. La composition très cosmopolite des autres groupes atteste de l'ampleur des diverses migrations humaines qui ont favorisé la dispersion de l'olivier sur l'ensemble du bassin méditerranéen. La combinaison de ces marqueurs enzymatiques avec des caractères morphologiques, physiologiques et agronomiques pourrait contribuer à la mise en place d'une classification systématique fiable des variétés d'olivier. La possibilité de l'utilisation des marqueurs alloenzymatiques pour l'amélioration variétale de l'olivier est également suggérée.Contribution of allozyme polymorphism to varietal identification in the olive tree (Olea europaea L). Allozyme polymorphism of leaf proteins was used to characterize 47 olive varieties widely distributed in the Mediterranean basin. Twenty-one alleles were observed at 9 polymorphic loci corresponding to 7 enzyme systems. Thirty-five of the 47 varieties could be identified by one of the 38 multiloci genotypes observed. Six groups of varieties were constituted using multivariate analysis of the multiloci genotypes. A single group gathered together varieties from a specific geographic area, namely France. Ten of the 11 varieties from North Africa were grouped together. Most of the groups contained varieties from various geographic origins, which was assumed to be the result of the occurrence of numerous human migrations which favoured olive dispersion throughout the Mediterranean basin. A combination of enzyme markers with morphological, physiological and agronomic characteristics may provide a consistent systematic classification of olive varieties. The possibility of using allozyme markers for olive breeding is also suggested

A New Framework to Accurately Quantify Soil Bacterial Community Diversity From DGGE

International audienceDenaturing gradient gel electrophoresis (DGGE) has been and remains extensively used to assess and monitor the effects of various treatments on soil bacterial communities. Considering only abundant phylotypes, the diversity estimates produced by this technique have been proven to be uncorrelated to true community diversity. The aim of this paper was to develop a framework to estimate a community's true diversity from DGGE. Developed using in silico DGGE profiles generated from published pyrosequencing datasets, this framework elongates the rank-abundance distributions (RADs) drawn by band quantification using the peak-to-signal ratio (PSR) parameter, which was proven to be related to bacterial richness. The ability to compare DGGE-based diversity estimates to the true diversity of communities led to a unique opportunity to identify potential pitfalls when analyzing DGGE gels with commercial analysis software programs and gain insight into the process of DNA band clustering in the profiles. Bacterial diversity was compared through richness, Shannon, and Simpson's 1/D indices. Intermediate results demonstrated that, even though commercial gel analysis software programs were unable to produce consistent results throughout all samples, a newly developed Matlab-based framework unraveled the dominance profiles of communities from band quantification. Elongating these partial RADs using the PSRs extracted from the DGGE profiles chiefly made it possible to accurately estimate the true diversity of communities. For all the samples analyzed, the estimated Shannon and Simpson's 1/D were accurate at ±10 %. Richness estimations were less accurate, ranging from -11 to 31 % of the expected values. The framework showed great potential to study the structure and diversity of soil bacterial communities