Relation entre la richesse du sol en phosphore et la concentration en phosphore de l'eau de drainage dans deux agro-écosystèmes

Des concentrations en P excédant le seuil d'eutrophisation sont fréquemment mesurées dans l'eau des affluents du fleuve Saint-Laurent au Québec, Canada. Un enrichissement excessif en P des sols agricoles en serait la source. Une norme relative à la saturation en P des sols a été proposée comme critère de risque de contamination en P des eaux de surface. L'objectif de ce travail est d'étudier le lien entre la richesse en P du sol et la teneur en P de l'eau de drainage dans deux agro-écosystèmes du Québec. Le bassin versant de la rivière Boyer (BVB), dominé par des sols en pente, une forte densité animale et des productions fourragères et les Basses Terres de Montréal (BTM), dominées par des sols plats utilisés pour la production intensive de maïs et une faible densité animale sont étudiés. Le degré de saturation en P des sols du BVB est de 8 à 10 % alors que celui des BTM dépasse très souvent 15 %. Le pool du P organique est plus faible dans les sols des BTM que dans le BVB. La concentration moyenne en P de l'eau de drainage est plus élevée dans les sols du BVB (171 µg L-1) que dans ceux des BTM (98 µg L-1). Elle est corrélée à la teneur en P extrait à l'oxalate des sols argileux et à la teneur en P soluble dans l'eau ou à l'index de sorption en P des sols grossiers. Ces relations sont plus étroites pour la couche 0-5 cm de sol que pour les couches plus profondes. Les résultats de cette étude démontrent qu'il est difficile de prédire la concentration en P de l'eau de drainage de sols contrastants. Regrouper les sols selon leur texture améliore la précision de la prédiction de la teneur en P de l'eau de drainage à partir de leurs propriétés.Concentrations of P higher than the recognised threshold for eutrophication are often measured in the tributaries of the St. Lawrence river, Quebec, Canada. An excessive P enrichment of agricultural soils was identified as the potential cause of this phenomenon. This enrichment results in a decrease in the P sorption capacity of soils and an increased risk of P contamination of surface waters. A norm based on soil P saturation degree (DSPS) was proposed as an agro-environmental criterion to reduce this risk. Relationships between DSPS and other soil P attributes and surface runoff P concentration have been reported in the literature but not for tile-drainage water. The objective of this work is to study the relationship between soil P attributes and drainage water P in two agro-ecosystems of Quebec.The Boyer watershed (BW), which is dominated by soils with significant slopes, a high animal density and forage production, and the Montreal lowlands (ML), dominated by flat soils, low animal density and mostly used for corn (Zea mays L.), were studied. The A, B and C horizons from soils from the BW were sampled at three locations in tile-drained fields from farms in surplus or not of manure N in regards to crop needs. Soils were sampled in the ML according to a gradient in clay content with the same procedures. Soils were characterised for their pH, particle size distribution, Mehlich 3-extractable P (Pm3) and Al, water-soluble P (Pw), organic P (Po) and oxalate-extractable P (Pox), Al (Alox) and Fe (Feox) contents. Grab tile-drainage samples were taken in triplicate and characterised for total (TP), particulate (PP) and dissolved reactive P (RP) and unreactive P (UP).The soils of the BW are more acidic and have higher P retention capacities than ML soils. The Pw content of BW soils is lower than in ML ones in spite of comparable Pm3 contents. The DSPS (Pox /Alox + Feox) of BW soils is moderate (8 to 10 %) whereas DSPS in ML soils is often >15 %. The soil P organic pool is much smaller in the ML soils than in those from BW, probably because of more frequent tillage and lower manure C inputs.The average P concentration (TP) in drainage water was higher in soils from the BW (171 µg L-1) than from ML soils (98 µg L-1). The PP was the main P fraction in drainage water from the two ecosystems. The RP was on average 44 % of TP whereas UP was much less. The TP concentration in drainage waters was higher than 0.03 mg L-1 in most cases. The TP concentration was higher in tile-drainage waters from the BW than in the ML even though comparable Pm3 and lower DSPS were found in the BW than in ML soils. These results suggest that other criteria should be included in the prediction of the risk of P contamination of drainage waters. The results of the present study indicate that agricultural practices (crop species, manure inputs, tillage type and frequency) could have a greater influence than soil P status on the TP concentration in tile-drainage waters.A linear correlation analysis between the logarithm of the TP (TP + 0.5) and that of the different soil P attributes indicated that TP was related to the P extracted by oxalate from clay soils and by water in coarse-textured soils. These relationships were closer in the 0-5 cm soil layer than in deeper strata. Multiple regression analysis between the logarithms of drainage water P concentrations and soil attributes revealed that, when soils were grouped by texture, the prediction of TP was much more accurate than when all soils were considered. The present regulatory approach of assessing the risk of water P contamination by using the soil Pm3 and DSPS only was inadequate in the two considered agroecosystems.The results of this study indicate that the prediction of the drainage water P concentration with P attributes from contrasting soils is difficult. Grouping soils by texture improves the prediction of Pt from soil P attributes

Contrasted Reactivity to Oxygen Tensions in Frankia sp. Strain CcI3 throughout Nitrogen Fixation and Assimilation

Reconciling the irreconcilable is a primary struggle in aerobic nitrogen-fixing bacteria. Although nitrogenase is oxygen and reactive oxygen species-labile, oxygen tension is required to sustain respiration. In the nitrogen-fixing Frankia, various strategies have been developed through evolution to control the respiration and nitrogen-fixation balance. Here, we assessed the effect of different oxygen tensions on Frankia sp. strain CcI3 growth, vesicle production, and gene expression under different oxygen tensions. Both biomass and vesicle production were correlated with elevated oxygen levels under both nitrogen-replete and nitrogen-deficient conditions. The mRNA levels for the nitrogenase structural genes (nifHDK) were high under hypoxic and hyperoxic conditions compared to oxic conditions. The mRNA level for the hopanoid biosynthesis genes (sqhC and hpnC) was also elevated under hyperoxic conditions suggesting an increase in the vesicle envelope. Under nitrogen-deficient conditions, the hup2 mRNA levels increased with hyperoxic environment, while hup1 mRNA levels remained relatively constant. Taken together, these results indicate that Frankia protects nitrogenase by the use of multiple mechanisms including the vesicle-hopanoid barrier and increased respiratory protection

Agent-Based Modeling of Host-Pathogen Systems: The Successes and Challenges

Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host-pathogen systems and discuss their contributions to our understanding of biological processes. We then point out some limitations and challenges of agent-based models and encourage efforts towards reproducibility and model validation.Comment: LaTeX, 12 pages, 1 EPS figure, uses document class REVTeX 4, and packages hyperref, xspace, graphics, amsmath, verbatim, and SIunit

Quantifying mechanistic traits of influenza viral dynamics using in vitro data.

When analysing in vitro data, growth kinetics of influenza virus strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mathematical models for epidemics, the growth rate can be defined as a function of mechanistic traits: the basic reproduction number (the average number of cells each infected cell infects) and the mean generation time (the average length of a replication cycle). Fitting a model to previously published and newly generated data from experiments in human lung cells, we compared estimates of growth rate, reproduction number and generation time for six influenza A strains. Of four strains in previously published data, A/Canada/RV733/2003 (seasonal H1N1) had the lowest basic reproduction number, followed by A/Mexico/INDRE4487/2009 (pandemic H1N1), then A/Indonesia/05/2005 (spill-over H5N1) and A/Anhui/1/2013 (spill-over H7N9). This ordering of strains was preserved for both generation time and growth rate, suggesting a positive biological correlation between these quantities which have not been previously observed. We further investigated these potential correlations using data from reassortant viruses with different internal proteins (from A/England/195/2009 (pandemic H1N1) and A/Turkey/05/2005 (H5N1)), and the same surface proteins (from A/Puerto Rico/8/34 (lab-adapted H1N1)). Similar correlations between traits were observed for these viruses, confirming our initial findings and suggesting that these patterns were related to the degree of human adaptation of internal genes. Also, the model predicted that strains with a smaller basic reproduction number, shorter generation time and slower growth rate underwent more replication cycles by the time of peak viral load, potentially accumulating mutations more quickly. These results illustrate the utility of mathematical models in inferring traits driving observed differences in in vitro growth of influenza strains

Alteration of As-bearing phases in a small watershed located on a high grade arsenic-geochemical anomaly (French Massif Central)

International audienceAt a watershed scale, sediments and soil weathering exerts a control on solid and dissolved transport of trace elements in surface waters and it can be considered as a source of pollution. The studied subwatershed (1.5 km2) was located on an As geochemical anomaly. The studied soil profile showed a significant decrease of As content from 1500 mg.kg-1 in the 135-165 cm deepest soil layer to 385 mg.kg-1 in the upper 0-5 cm soil layer. Directly in the stream, suspended matter and the <63 μm fraction of bed sediments had As concentrations greater than 400 mg.kg-1. In all these solid fractions, the main representative As-bearing phases were determined at two different observation scales: bulk analyses using X-ray absorption structure spectroscopy (XAS) and microanalyses using scanning electron microscope (SEM) and associated electron probe microanalyses (EPMA), as well as micro-Raman spectroscopy and synchrotron-based micro-scanning X-ray diffraction (μSXRD) characterization. Three main As-bearing phases were identified: (i) arsenates (mostly pharmacosiderite), the most concentrated phases As in both the coherent weathered bedrock and the 135-165 cm soil layer but not observed in the river solid fraction, (ii) Fe-oxyhydroxides with in situ As content up to 15.4 wt.% in the deepest soil layer, and (iii) aluminosilicates, the least concentrated As carriers. The mineralogical evolution of As-bearing phases in the soil profile, coupled with the decrease of bulk As content, may be related to pedogenesis processes, suggesting an evolution of arsenates into As-rich Fe-oxyhydroxides. Therefore, weathering and mineralogical evolution of these As-rich phases may release As to surface waters

Determination of trace elements in natural water samples by air-segmented flow-injection/ICP-MS after preconcentration with a chitosan-based chelating resin

本法では,各種天然水中の極微量金属成分を同時定量する目的で空気分節試料導入/ICP-MSシステムを用いて,微少量試料(数十μl)を前処理せずにネブライザーに送り込み,多数の金属成分の定量が可能であった。共存主成分による質量干渉を受ける一部遷移金属や直接試料導入では感度の足りない元素については,イミノ二酢酸型キトサンキレート樹脂充填カラムによる分離·濃縮操作の併用によって更に信頼性の高いデータが得られることが分かった。前処理においては,体積1mlのミニカラムを用いて50mlの溶液試料から50倍濃縮を行い,試料·試薬·廃液すべてを少量化することができた。本ICP-MSシステムでは試料導入量は80μlで十分であり,1mlでも数回繰り返し測定が可能で,しかも多元素同時分析ができた。確立した分析法を用いて河川水や市販のミネラルウォーターに応用し,希土類を含め45種の微量元素の定量が可能となった。Ultratrace elements in natural water samples were determined simultaneously by air-segmented flow-injection/inductively coupled plasma-mass spectrometry(SFI/ICP-MS).A small volume of the sample solutions(80μl) was introduced into a nebulizer by an air-segmented flow-injection(SFI) system, and a maximum of fifteen elements were measured during each run.A chitosan-based chelating resin containing functional groups of iminodiacetate was used to separate and enrich analyte metal ions.A 50-fold preconcentration using 50ml of sample solutions was achieved by the proposed method, where 1ml of 0.1M nitric acid was added to residues after drying the chelating column effluent.At pH6, several heavy metals(Fe, Ni, Co, Cu, Zn, Ag, Cd, Pb and U) and rare earth elements(REEs) were quantitatively retained on the chelating resin column, whereas alkali and alkaline earth metals were eluted from the column by rinsing with 5ml of a 0.2M ammonium acetate solution.Metals adsorbed on the chelating resin column were recovered by elution with 10ml of 1M nitric acid.The proposed method was applied to the determination of trace elements in several natural water samples, such as river water and mineral drinking water

A Polymerase-chain-reaction Assay for the Specific Identification of Transcripts Encoded by Individual Carcinoembryonic Antigen (CEA)-gene-family Members

Carcinoembryonic antigen (CEA) is a tumor marker that belongs to a family of closely related molecules with variable expression patterns. We have developed sets of oligonucleotide primers for the specific amplification of transcripts from individual CEA-family members using the reverse transcriptase/ polymerase chain reaction (RT/PCR). Specific primer sets were designed for CEA, non-specific cross-reacting antigen (NCA), biliary glycoprotein (BGP), carcinoembryonic antigen gene-family members 1, 6 and 7 (CGMI, CGM6 and CGM7), and one set for all pregnancy-specific glycoprotein (PSG) transcripts. Primers were first tested for their specificity against individual cDNA clones and product-hybridization with internal, transcript-specific oligonucleotides. Total RNA from 12 brain and 63 gynecological tumors were then tested for expression of CEA-related transcripts. None were found in tumors located in the brain, including various mesenchymal and neuro-epithelial tumors. CEA and NCA transcripts were, however, present in an adenocarcinoma located in the nasal sinuses. In ovarian mucinous adenocarcinomas, we always found co-expression of CEA and NCA transcripts, and occasionally BGP mRNA. CEA-related transcripts were also found in some serous, endometrioid and clear-cell ovarian carcinomas. CEA, NCA and BGP transcripts were present in endometrial carcinomas of the uterus and cervical carcinomas, whereas uterine leiomyomas were completely negative. No transcripts were found from CGM 1, CGM6, CGM7 or from PSG genes in any of the tumors tested. The PCR data were compared with immunohistochemical investigations of ovarian tumors at the protein level using CEA (26/3/13)-, NCA-50/90 (9A6FR) and NCA-95 (80H3)-specific monoclonal antibodies

Permanent draft genome sequence of Nocardia sp. BMG111209, an actinobacterium isolated from nodules of Casuarina glauca

Nocardia sp. strain BMG111209 is a non-Frankia actinobacterium isolated from root nodules of Casuarina glauca in Tunisia. Here, we report the 9.1-Mbp draft genome sequence of Nocardia sp. strain BMG111209 with a G + C content of 69.19% and 8,122 candidate protein-encoding genes