Le bactériome des mousses et sa fixation d'azote en forêt boréale : caractérisation et influence de l'environnement

Dans la forêt boréale, les mousses sont des végétaux abondants ayant des fonctions écologiques et biogéochimiques majeures, telles que la régulation de la température et de l’humidité du sol et le stockage du carbone atmosphérique. Les mousses abritent diverses bactéries jouant des rôles clés dans le cycle des nutriments, comme l’oxydation du méthane et la décomposition de la matière organique. Certaines bactéries, notamment les cyanobactéries, sont également capables d’établir des associations avec les mousses et de réaliser la fixation biologique de l’azote (FBN). La FBN par le bactériome (i.e., ensemble des communautés bactériennes) des mousses est particulièrement importante car elle représente une des principales sources de nouvel azote en forêt boréale et contribue ainsi à soutenir la productivité primaire de la mousse et des plantes supérieures. Ainsi, étudier comment l’environnement (e.g., climat et nutriments) affectent le bactériome des mousses et sa FBN est essentiel pour mieux comprendre et prédire l’influence du changement climatique sur le cycle global de l’azote en forêt boréale. La FBN étant directement liée à la quantité de cyanobactéries colonisant les mousses, le premier objectif de cette thèse (Chapitre 2) était de développer une méthode rapide et robuste pour déterminer la biomasse cyanobactérienne associée aux mousses. En adaptant une technique employée pour les cyanobactéries aquatiques, nous avons montré que l’extraction et la quantification de la phycocyanine (i.e., pigment photosynthétique cyanobactérien) par spectrofluorimétrie permet d’estimer rapidement et à moindre coût la biomasse de cyanobactéries vivant sur les mousses. Cette méthode s’est révélée être répétable, efficace avec un haut taux de recouvrement, et ne présente pas d’effets de matrice détectables. Le deuxième objectif de cette thèse (Chapitre 3) était de déterminer les principaux facteurs environnementaux contrôlant in situ la biomasse cyanobactérienne et la FBN de deux espèces de mousses dominantes dans la forêt boréale de l’est Canadien. En réalisant un échantillonnage au Québec, sur un transect latitudinal de 1000 km constituant un gradient climatique et de dépôts atmosphériques en nutriments (e.g., azote, métaux), nous avons démontré que la température, les précipitations et le phosphore contrôlaient la biomasse de cyanobactéries associées aux mousses, alors que la température, le molybdène et le vanadium contrôlaient la FBN. Nous avons aussi montré que l’espèce de mousse et son rapport carbone/azote avaient des effets importants sur la biomasse de cyanobactéries et la fixation d’azote. Le troisième objectif de cette thèse (Chapitre 4) était de caractériser le bactériome actif global et diazotrophique (i.e., bactéries capables de réaliser la FBN) des mousses et d’évaluer comment ce bactériome est affecté par les conditions environnementales. Grâce au séquençage d’amplicons des gènes 16S et nifH à partir d’ARN provenant d’échantillons de mousses similaires à l’objectif 2, nous avons montré que les cyanobactéries dominaient le bactériome des mousses et représentaient 65 % des communautés de diazotrophes. Nous avons également pu déterminer que, en plus des cyanobactéries, certains méthanotrophes (i.e., bactéries oxydant le méthane) étaient présents sur les mousses et contribuaient activement à la fixation d’azote. D’autre part, en réalisant des sections le long du brin de mousse, nous avons observé que les bactéries occupaient des niches écologiques liées à leurs fonctions : les bactéries favorisant la croissance de la mousse étant localisées sur la partie verte apicale du brin et les bactéries aidant à la décomposition étant localisées sur la partie basale et sénescente du brin. Enfin, nous avons mis en évidence que le climat, les nutriments (i.e., azote, phosphore, molybdène, vanadium et fer), la densité d’arbres et l’espèce de mousse influençaient la structure et la composition du bactériome des mousses, affectant potentiellement ses fonctions microbiennes associées. En conclusion, les résultats de cette thèse permettent d’identifier les genres de cyanobactéries et de méthanotrophes qui contribuent activement à la FBN et qui constituent donc des acteurs clés du cycle de l’azote en forêt boréale. Ces résultats montrent aussi que le bactériome des mousses et sa FBN sont fortement contrôlés par leur environnement (i.e., espèce de mousse, climat, macro- et micro-nutriments) et seront donc certainement affectés positivement ou négativement par le changement global, particulièrement intense dans les écosystèmes boréaux. Ces résultats invitent donc à effectuer des études complémentaires pour estimer plus précisément les effets du changement climatique et atmosphérique sur la structure du bactériome des mousses et la FBN

On the effect of temperature on the insertion of zinc into hydroxyapatite.

International audienceRietveld analysis on X-ray powder diffraction patterns recorded from 28 hydroxyapatite samples containing various amount of zinc (0, 1.6, 3.2 and 6.1 wt. Zn %) and heat treated at various temperatures (between 500°C and 1100°C) have allowed to finely characterize the Zn insertion mechanism into the HAp crystal structure. The formation of Zn-doped HAp was achieved above 900°C only. Zn-doped HAp has the Ca10Znx(PO4)6(OH)2-2xO2x (0 < x ≤ 0.25) chemical composition with a constant Ca/P ratio of 1.67 due to the insertion mechanism into the hexagonal channel (partial occupancy of the 2b Wyckoff site with formation of linear OZn- O entities). Samples heat treated at 500 °C were almost single phase, HAp did not incorporate Zn and about half of the Zn atoms incorporated during the synthesis are not observable by X-ray powder diffraction (contained in an amorphous compound or physisorbed at the HAp surface). The reversible formation of Zn-doped β-TCP phase was observed at 600°C, reached its maximum content at 900°C and almost vanished at 1100°C. The results presented here strengthen the recently described mechanism of Zn insertion in the interstitial 2b Wyckoff position of the HAp structure, and explain the origin of the contradictory reports in the corresponding literature

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Structural characterization of Sol-Gel derived Sr-substituted calcium phosphates with anti-osteoporotic and anti-inflammatory properties.

International audienceSol-Gel chemistry has been successfully used to prepare un-doped and Sr-doped calcium phosphate ceramics exhibiting a porous structure. The samples composition is very close to the nominal one. All samples present phase mixtures mainly Hydroxyapatite (HAp) and Tri Calcium Phosphate (Β-TCP). Doping with Sr2+ ions has a clear effect on the proportions of the different phases, increasing the amount of Β-TCP. An amorphous phase is also observed incorporating some 40 % of the total amount of strontium. Strontium ions also substitute for calcium both in HAp and Β-TCP in specific sites that have been determined from Rietveld refinement on synchrotron powder diffraction data. The soluble amorphous and TCP phases are responsible for a beneficial partial release of strontium ions in solution during interactions between the material and biological fluids. Preliminary in vitro study demonstrates anti-inflammatory effect of strontium for human monocytes cultured in contact with calcium phosphates

Preparation and characterization of functionalized hybrid hydroxyapatite from phosphorite and its potential application to Pb2+ remediation

International audienceCalcium hydroxyapatite-aspartate (CaHAp-Asp) and calcium hydroxyapatite-glutamate (CaHAp-Glu) hybrid materials were prepared by the dissolution of Tunisian Phosphate Rocks in concentrated nitric acid and re-precipitation in basic solution in the presence of aspartic and glutamic acids. Chemical analyses, X-Ray Powder Diffraction, Infrared spectroscopy, 13C MAS-NMR spectroscopy, ThermoGravimetry and Scanning Electron Microscopy were used to characterize the materials and also the organic-inorganic interfaces. All techniques converge to the formation of hybrid organic-inorganic compounds composed of hydroxyapatite solids with organic anions incorporated at the surface. XRPD and SEM observations showed that not only was the crystallinity significantly affected by the presence of organic anions, but also the structural and morphological properties. The presence of organic anions has been confirmed by IR and 13C MS-NMR spectroscopies, and their amount has been evaluated by TG and chemical analyses. The three CaHAp, CaHAp-Asp and CaHAp-Glu materials were evaluated for Pb2+ sorption from aqueous solutions. Sorption isotherms have been analyzed using Langmuir and Freundlich models showing that the Pb2+ sorption capacity is increased for CaHAp-Asp and CaHAp-Glu. The comparison of the two models indicates a single active site corresponding to a homogeneous interface between Pb2+ aqueous adsorbate and the solid adsorbent surface

Oesophagite à éosinophiles : une maladie d’actualité

L’œsophagite à éosinophiles est définie comme une maladie chronique, médiée par des réponses immunologiques à des antigènes (allergènes), caractérisée cliniquement par les symptômes liés à un dysfonctionnement œsophagien, et histologiquement par une infiltration à éosinophiles prédominante de la muqueuse (Eos> 15/ champ 400) (Liacouras, 2011). Elle constitue une entité isolée, distincte de l’oesophagite par reflux gastro-oesophagien, et non intégrable dans les affections gastro-intestinales et coliques à éosinophiles (Sherrill, 2011). Elle touche l’adulte comme l’enfant, quoique 8 fois plus fréquente en population pédiatrique où l’acmé du diagnostic se situe dans les trois premières années. On estime sa prévalence à 4 sur 10 000 dans la population pédiatrique. Est-elle en accroissement ? Oui, pour certain (Potter, 2004). Non, pour d’autres auteurs…Eosinophilic esophagitis can be defined as a chronic disease, mediated by immunological responses to antigens (allergens), clinically characterized by symptoms related to esophageal disorders, and histologically by a mucosa predominantly infiltrated by eosinophils (Eos> 15/ field 400) (Liacouras, 2011). It is an isolated entity, distinct from esophagitis by gastro esophageal reflux, and it cannot be integrated to gastrointestinal and colic eosinophilic pathologies (Sherrill, 2011).The disease occurs in adults as well as in children, although it is 8 times more frequent in a pediatric population where the peak of the diagnosis arises during the first three years. Its prevalence is estimated at 4 out of 10 000 in a pediatric population. Is it increasing? Some say yes (Potter, 2004); other authors say no

The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome

<p>Abstract</p> <p>Background</p> <p><it>Spiroplama citri</it>, the causal agent of citrus stubborn disease, is a bacterium of the class <it>Mollicutes </it>and is transmitted by phloem-feeding leafhopper vectors. In order to characterize candidate genes potentially involved in spiroplasma transmission and pathogenicity, the genome of <it>S. citri </it>strain GII3-3X is currently being deciphered.</p> <p>Results</p> <p>Assembling 20,000 sequencing reads generated seven circular contigs, none of which fit the 1.8 Mb chromosome map or carried chromosomal markers. These contigs correspond to seven plasmids: pSci1 to pSci6, with sizes ranging from 12.9 to 35.3 kbp and pSciA of 7.8 kbp. Plasmids pSci were detected as multiple copies in strain GII3-3X. Plasmid copy numbers of pSci1-6, as deduced from sequencing coverage, were estimated at 10 to 14 copies per spiroplasma cell, representing 1.6 Mb of extrachromosomal DNA. Genes encoding proteins of the TrsE-TraE, Mob, TraD-TraG, and Soj-ParA protein families were predicted in most of the pSci sequences, in addition to members of 14 protein families of unknown function. Plasmid pSci6 encodes protein P32, a marker of insect transmissibility. Plasmids pSci1-5 code for eight different <it>S. citri </it>adhesion-related proteins (ScARPs) that are homologous to the previously described protein P89 and the <it>S. kunkelii </it>SkARP1. Conserved signal peptides and C-terminal transmembrane alpha helices were predicted in all ScARPs. The predicted surface-exposed N-terminal region possesses the following elements: (i) 6 to 8 repeats of 39 to 42 amino acids each (sarpin repeats), (ii) a central conserved region of 330 amino acids followed by (iii) a more variable domain of about 110 amino acids. The C-terminus, predicted to be cytoplasmic, consists of a 27 amino acid stretch enriched in arginine and lysine (KR) and an optional 23 amino acid stretch enriched in lysine, aspartate and glutamate (KDE). Plasmids pSci mainly present a linear increase of cumulative GC skew except in regions presenting conserved hairpin structures.</p> <p>Conclusion</p> <p>The genome of <it>S. citri </it>GII3-3X is characterized by abundant extrachromosomal elements. The pSci plasmids could not only be vertically inherited but also horizontally transmitted, as they encode proteins usually involved in DNA element partitioning and cell to cell DNA transfer. Because plasmids pSci1-5 encode surface proteins of the ScARP family and pSci6 was recently shown to confer insect transmissibility, diversity and abundance of <it>S. citri </it>plasmids may essentially aid the rapid adaptation of <it>S. citri </it>to more efficient transmission by different insect vectors and to various plant hosts.</p

Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests

Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its active site. Vanadium (V) and iron-only Nases have been suggested as viable alternatives to countering Mo limitation of BNF; however, field data supporting this long-standing hypothesis have been lacking. Here, we elucidate the contribution of vanadium nitrogenase (V-Nase) to BNF by cyanolichens across a 600-km latitudinal transect in eastern boreal forests of North America. Widespread V-Nase activity was detected (∼15–50% of total BNF rates), with most of the activity found in the northern part of the transect. We observed a 3-fold increase of V-Nase contribution during the 20-wk growing season. By including the contribution of V-Nase to BNF, estimates of new N input by cyanolichens increase by up to 30%. We find that variability in V-based BNF is strongly related to Mo availability, and we identify a Mo threshold of ∼250 ng·glichen−1 for the onset of V-based BNF. Our results provide compelling ecosystem-scale evidence for the use of the V-Nase as a surrogate enzyme that contributes to BNF when Mo is limiting. Given widespread findings of terrestrial Mo limitation, including the carbon-rich circumboreal belt where global change is most rapid, additional consideration of V-based BNF is required in experimental and modeling studies of terrestrial biogeochemistry

Kidney allograft rejection is associated with an imbalance of B cells, regulatory T cells and differentiated CD28-CD8+ T cells: analysis of a cohort of 1095 graft biopsies

IntroductionThe human immune system contains cells with either effector/memory or regulatory functions. Besides the well-established CD4+CD25hiCD127lo regulatory T cells (Tregs), we and others have shown that B cells can also have regulatory functions since their frequency and number are increased in kidney graft tolerance and B cell depletion as induction therapy may lead to acute rejection. On the other hand, we have shown that CD28-CD8+ T cells represent a subpopulation with potent effector/memory functions. In the current study, we tested the hypothesis that kidney allograft rejection may be linked to an imbalance of effector/memory and regulatory immune cells.MethodsBased on a large cohort of more than 1000 kidney graft biopsies with concomitant peripheral blood lymphocyte phenotyping, we investigated the association between kidney graft rejection and the percentage and absolute number of circulating B cells, Tregs, as well as the ratio of B cells to CD28-CD8+ T cells and the ratio of CD28-CD8+ T cells to Tregs. Kidney graft biopsies were interpreted according to the Banff classification and divided into 5 biopsies groups: 1) normal/subnormal, 2) interstitial fibrosis and tubular atrophy grade 2/3 (IFTA), 3) antibody-mediated rejection (ABMR), 4) T cell mediated-rejection (TCMR), and 5) borderline rejection. We compared group 1 with the other groups as well as with a combined group 3, 4, and 5 (rejection of all types) using multivariable linear mixed models.Results and discussionWe found that compared to normal/subnormal biopsies, rejection of all types was marginally associated with a decrease in the percentage of circulating B cells (p=0.06) and significantly associated with an increase in the ratio of CD28-CD8+ T cells to Tregs (p=0.01). Moreover, ABMR, TCMR (p=0.007), and rejection of all types (p=0.0003) were significantly associated with a decrease in the ratio of B cells to CD28-CD8+ T cells compared to normal/subnormal biopsies. Taken together, our results show that kidney allograft rejection is associated with an imbalance between immune cells with effector/memory functions and those with regulatory properties

Refractory anaphylaxis: Data from the European Anaphylaxis Registry

Refractory anaphylaxis (unresponsive to treatment with at least two doses of minimum 300 μg adrenaline) is a rare and often fatal hypersensitivity reaction. Comprehensive data on its definition, prevalence, and risk factors are missing. Using the data from the European Anaphylaxis Registry (11,596 cases in total) we identified refractory anaphylaxis cases (n = 42) and analyzed these in comparison to a control group of severe anaphylaxis cases (n = 4,820). The data show that drugs more frequently elicited refractory anaphylaxis (50% of cases, p < 0.0001) compared to other severe anaphylaxis cases (19.7%). Cases elicited by insects (n = 8) were more often due to bees than wasps in refractory cases (62.5 vs. 19.4%, p = 0.009). The refractory cases occurred mostly in a perioperative setting (45.2 vs. 9.05, p < 0.0001). Intramuscular adrenaline (as a first line therapy) was administered in 16.7% of refractory cases, whereas in 83.3% of cases it was applied intravenously (significantly more often than in severe anaphylaxis cases: 12.3%, p < 0.0001). Second line treatment options (e.g., vasopression with dopamine, methylene blue, glucagon) were not used at all for the treatment of refractory cases. The mortality rate in refractory anaphylaxis was significantly higher (26.2%) than in severe cases (0.353%, p < 0.0001). Refractory anaphylaxis is associated with drug-induced anaphylaxis in particular if allergens are given intravenously. Although physicians frequently use adrenaline in cases of perioperative anaphylaxis, not all patients are responding to treatment. Whether a delay in recognition of anaphylaxis is responsible for the refractory case or whether these cases are due to an overflow with mast cell activating substances—requires further studies. Reasons for the low use of second-line medication (i.e., methylene blue or dopamine) in refractory cases are unknown, but their use might improve the outcome of severe refractory anaphylaxis cases