Variations inter journalières dans la structure des communautés de poissons : implications pour le développement de modèles de qualité d'habitats

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

The evolution of inter-genomic variation in arbuscular mycorrhizal fungi

Contexte: Les champignons mycorhiziens à arbuscules (AMF) établissent des relations symbiotiques avec la plupart des plantes grâce à leurs réseaux d’hyphes qui s’associent avec les racines de leurs hôtes. De précédentes études ont révélé des niveaux de variation génétique extrêmes pour des loci spécifiques permettant de supposer que les AMF peuvent contenir des milliers de noyaux génétiquement divergents dans un même cytoplasme. Si aucun processus de reproduction sexuée n’a jusqu’ici été observé chez ces mycorhizes, on constate cependant que des niveaux élevés de variation génétique peuvent être maintenus à la fois par l’échange de noyaux entre hyphes et par des processus fréquents de recombinaison entre noyaux. Les AMF se propagent par l’intermédiaire de spores qui contiennent chacune un échantillon d’une population initiale de noyaux hétérogènes, directement hérités du mycélium parent. À notre connaissance les AMF sont les seuls organismes qui ne passent jamais par un stade mononucléaire, ce qui permet aux noyaux de diverger génétiquement dans un même cytoplasme. Ces aspects singuliers de la biologie des AMF rendent l’estimation de leur diversité génétique problématique. Ceci constitue un défi majeur pour les écologistes sur le terrain mais également pour les biologistes moléculaires dans leur laboratoire. Au-delà même des problématiques de diversité spécifique, l’amplitude du polymorphisme entre noyaux mycorhiziens est mal connue. Le travail proposé dans ce manuscrit de thèse explore donc les différents aspects de l’architecture génomique singulière des AMF. Résultats L’ampleur du polymorphisme intra-isolat a été déjà observée pour la grande sous-unité d’ARN ribosomal de l’isolat Glomus irregulare DAOM-197198 (précédemment identifié comme G. intraradices) et pour le gène de la polymerase1-like (PLS) de Glomus etunicatum isolat NPI. Dans un premier temps, nous avons pu confirmer ces résultats et nous avons également pu constater que ces variations étaient transcrites. Nous avons ensuite pu mettre en évidence la présence d’un goulot d’étranglement génétique au moment de la sporulation pour le locus PLS chez l’espèce G. etunicatum illustrant les importants effets d’échantillonnage qui se produisaient entre chaque génération de spore. Enfin, nous avons estimé la différentiation génétique des AMF en utilisant à la fois les réseaux de gènes appliqués aux données de séquençage haut-débit ainsi que cinq nouveaux marqueurs génomiques en copie unique. Ces analyses révèlent que la différenciation génomique est présente de manière systématique dans deux espèces (G. irregulare et G. diaphanum). Conclusions Les résultats de cette thèse fournissent des preuves supplémentaires en faveur du scénario d’une différenciation génomique entre noyaux au sein du même isolat mycorhizien. Ainsi, au moins trois membres du genre Glomus, G. irregulare, G. diaphanum and G. etunicatum, apparaissent comme des organismes dont l’organisation des génomes ne peut pas être décrit d’après un modèle Mendélien strict, ce qui corrobore l’hypothèse que les noyaux mycorhiziens génétiquement différenciés forment un pangenome.

La dynamique spatio-temporelle des flux d’oxyde nitreux (N2O) des lacs, rivières, et étangs boréaux

L’oxyde nitreux (N2O), un puissant gaz à effet de serre (GES) ayant plus de 300 fois le potentiel de réchauffement du dioxyde de carbone (CO2), est produit par des processus microbiens du cycle de l’azote (N). Bien que les eaux de surface continentales soient reconnues comme des sites actifs de transformations de l’azote, leur intégration dans les budgets globaux de N2O comporte de nombreuses incertitudes, dont l’absence des lacs dans ces modèles. Le biome boréal est caractérisé par une des plus grandes densités d’eaux douces au monde, pourtant aucune évaluation exhaustive des émissions aquatiques de N2O n’a à date été conduite dans cette région. Dans la présente étude, nous avons mesuré les concentrations de N2O à travers une large gamme de lacs, rivières, et étangs, dans quatre régions boréales du Québec (Canada), et nous avons calculé les flux eau-air résultants. Les flux nets fluctuent entre -23.1 et 177.9 μmol m-2 J-1, avec une grande variabilité inter-système, inter-régionale, et saisonnière. Étonnamment, 40% des systèmes échantillonnés agissaient en tant que puits de N2O durant l’été, et le réseau d’eaux de surfaces d’une des régions était un net consommateur de N2O. Les concentrations maximales de N2O ont été mesurées en hiver dû à l’accumulation de ce gaz sous la glace. Nous avons estimé que l’émission qui en résulte lors de la fonte des glaces représente 20% des émissions annuelles des eaux douces. Parmi les types d’eaux douces échantillonnées, les lacs sont les principaux responsables du flux aquatique net (jusqu’à 90%), et doivent donc être intégrés dans les budgets globaux de N2O. En se basant sur les données empiriques de la littérature, nous avons éstimé l’émission globale de N2O des eaux douces à 0.78 Tg N (N2O) an-1. Ce chiffre est influencé par les émissions des régions de hautes latitudes (tel que le biome boréal) dont les flux nets varient de positif à négatif constituant -9 à 27 % du total.

Sea Surface Temperature-Convection Relationship in Tropical Oceans with Special Emphasis to Intraseasonal Variability of Indian Summer Monsoon

The SST convection relation over tropical ocean and its impact on the South Asian monsoon is the first part of this thesis. Understanding the complicated relation between SST and convection is important for better prediction of the variability of the Indian monsoon in subseasonal, seasonal, interannual, and longer time scales. Improved global data sets from satellite scatterometer observations of SST, precipitation and refined reanalysis of global wind fields have made it possible to do a comprehensive study of the SST convection relation. Interaction of the monsoon and Indian ocean has been discussed. A coupled feedback process between SST and the Active-Break cycle of the Asian summer monsoon is a central theme of the thesis. The relation between SST and convection is very important in the field of numerical modeling of tropical rainfall. It is well known that models generally do very well simulating rainfall in areas of tropical convergence zones but are found unable to do satisfactory simulation in the monsoon areas. Thus in this study we critically examined the different mechanisms of generation of deep convection over these two distinct regions.The study reported in chapter 3 has shown that SST - convection relation over the warm pool regions of Indian and west Pacific oceans (monsoon areas) is in such a way that convection increases with SST in the SST range 26-29 C and for SST higher than 29-30 C convection decreases with increase of SST (it is called Waliser type). It is found that convection is induced in areas with SST gradients in the warm pool areas of Indian and west Pacific oceans. Once deep convection is initiated in the south of the warmest region of warm pool, the deep tropospheric heating by the latent heat released in the convective clouds produces strong low level wind fields (Low level Jet - LLJ) on the equatorward side of the warm pool and both the convection and wind are found to grow through a positive feedback process. Thus SST through its gradient acts only as an initiator of convection. The central region of the warm pool has very small SST gradients and large values of convection are associated with the cyclonic vorticity of the LLJ in the atmospheric boundary layer. The conditionally unstable atmosphere in the tropics is favorable for the production of deep convective clouds.

Enhancement of ENSO variability by a weakened Atlantic thermohaline circulation in a coupled GCM

A coupled ocean–atmosphere general circulation model is used to investigate the modulation of El Niño–Southern Oscillation (ENSO) variability due to a weakened Atlantic thermohaline circulation (THC). The THC weakening is induced by freshwater perturbations in the North Atlantic, and leads to a well-known sea surface temperature dipole and a southward shift of the intertropical convergence zone (ITCZ) in the tropical Atlantic. Through atmospheric teleconnections and local coupled air–sea feedbacks, a meridionally asymmetric mean state change is generated in the eastern equatorial Pacific, corresponding to a weakened annual cycle, and westerly anomalies develop over the central Pacific. The westerly anomalies are associated with anomalous warming of SST, causing an eastward extension of the west Pacific warm pool particularly in August–February, and enhanced precipitation. These and other changes in the mean state lead in turn to an eastward shift of the zonal wind anomalies associated with El Niño events, and a significant increase in ENSO variability. In response to a 1-Sv (1 Sv ≡ 106 m3 s−1) freshwater input in the North Atlantic, the THC slows down rapidly and it weakens by 86% over years 50–100. The Niño-3 index standard deviation increases by 36% during the first 100-yr simulation relative to the control simulation. Further analysis indicates that the weakened THC not only leads to a stronger ENSO variability, but also leads to a stronger asymmetry between El Niño and La Niña events. This study suggests a role for an atmospheric bridge that rapidly conveys the influence of the Atlantic Ocean to the tropical Pacific and indicates that fluctuations of the THC can mediate not only mean climate globally but also modulate interannual variability. The results may contribute to understanding both the multidecadal variability of ENSO activity during the twentieth century and longer time-scale variability of ENSO, as suggested by some paleoclimate records.

Variability in clear-sky longwave radiative cooling of the atmosphere

The longwave radiative cooling of the clear-sky atmosphere (Q(LWc)) is a crucial component of the global hydrological cycle and is composed of the clear-sky outgoing longwave radiation to space (OLRc) and the net downward minus upward clear-sky longwave radiation to the surface (SNLc). Estimates of QLWc from reanalyses and observations are presented for the period 1979-2004. Compared to other reanalyses data sets, the European Centre for Medium-range Weather Forecasts 40-year reanalysis (ERA40) produces the largest Q(LWc) over the tropical oceans (217 W m(-2)), explained by the least negative SNLc. On the basis of comparisons with data derived from satellite measurements, ERA40 provides the most realistic QLWc climatology over the tropical oceans but exhibits a spurious interannual variability for column integrated water vapor (CWV) and SNLc. Interannual monthly anomalies of QLWc are broadly consistent between data sets with large increases during the warm El Nino events. Since relative humidity ( RH) errors applying throughout the troposphere result in compensating effects on the cooling to space and to the surface, they exert only a marginal effect on QLWc. An observed increase in CWV with surface temperature of 3 kg m(-2) K-1 over the tropical oceans is important in explaining a positive relationship between QLWc and surface temperature, in particular over ascending regimes; over tropical ocean descending regions this relationship ranges from 3.6 to 4.6 +/- 0.4 W m(-2) K-1 for the data sets considered, consistent with idealized sensitivity tests in which tropospheric warming is applied and RH is held constant and implying an increase in precipitation with warming.

Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in-situ optical nitrate sensor and dual nitrate isotopes

We investigated diurnal nitrate (NO3-) concentration variability in the San Joaquin River using an in situ optical NO3- sensor and discrete sampling during a 5-day summer period characterized by high algal productivity. Dual NO3- isotopes (delta N-15(NO3) and delta O-18(NO3)) and dissolved oxygen isotopes (delta O-18(DO)) were measured over 2 days to assess NO3- sources and biogeochemical controls over diurnal time-scales. Concerted temporal patterns of dissolved oxygen (DO) concentrations and delta O-18(DO) were consistent with photosynthesis, respiration and atmospheric O-2 exchange, providing evidence of diurnal biological processes independent of river discharge. Surface water NO3- concentrations varied by up to 22% over a single diurnal cycle and up to 31% over the 5-day study, but did not reveal concerted diurnal patterns at a frequency comparable to DO concentrations. The decoupling of delta N-15(NO3) and delta O-18(NO3) isotopes suggests that algal assimilation and denitrification are not major processes controlling diurnal NO3- variability in the San Joaquin River during the study. The lack of a clear explanation for NO3- variability likely reflects a combination of riverine biological processes and time-varying physical transport of NO3- from upstream agricultural drains to the mainstem San Joaquin River. The application of an in situ optical NO3- sensor along with discrete samples provides a view into the fine temporal structure of hydrochemical data and may allow for greater accuracy in pollution assessment.

Stratospheric temperature trends: impact of ozone variability and the QBO

In most climate simulations used by the Intergovernmental Panel on Climate Change 2007 fourth assessment report, stratospheric processes are only poorly represented. For example, climatological or simple specifications of time-varying ozone concentrations are imposed and the quasi-biennial oscillation (QBO) of equatorial stratospheric zonal wind is absent. Here we investigate the impact of an improved stratospheric representation using two sets of perturbed simulations with the Hadley Centre coupled ocean atmosphere model HadGEM1 with natural and anthropogenic forcings for the 1979–2003 period. In the first set of simulations, the usual zonal mean ozone climatology with superimposed trends is replaced with a time series of observed zonal mean ozone distributions that includes interannual variability associated with the solar cycle, QBO and volcanic eruptions. In addition to this, the second set of perturbed simulations includes a scheme in which the stratospheric zonal wind in the tropics is relaxed to appropriate zonal mean values obtained from the ERA-40 re-analysis, thus forcing a QBO. Both of these changes are applied strictly to the stratosphere only. The improved ozone field results in an improved simulation of the stepwise temperature transitions observed in the lower stratosphere in the aftermath of the two major recent volcanic eruptions. The contribution of the solar cycle signal in the ozone field to this improved representation of the stepwise cooling is discussed. The improved ozone field and also the QBO result in an improved simulation of observed trends, both globally and at tropical latitudes. The Eulerian upwelling in the lower stratosphere in the equatorial region is enhanced by the improved ozone field and is affected by the QBO relaxation, yet neither induces a significant change in the upwelling trend.

Diurnal cycle of land surface temperature in a desert encroachment zone as observed from satellites

Climate variability in the African Soudano-Sahel savanna zone has attracted much attention because of the persistence of anomalously low rainfall. Past efforts to monitor the climate of this region have focused on rainfall and vegetation conditions, while land surface temperature (LST) has received less attention. Remote sensing of LST is feasible and possible at global scale. Most remotely sensed estimates of LST are based on the National Oceanic and Atmospheric Administration (NOAA) Advanced Very High Resolution Radiometer (AVHRR) that are limited in their ability to capture the full diurnal cycle. Although more frequent observations are available from past geostationary satellites, their spatial resolution is coarser than that of polar orbiting satellites. In this study, the improved capabilities of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) on the METEOSAT Second Generation (MSG) instrument are used to remotely sense the LST in the African Soudano-Sahel savanna zone at a resolution of 3 km and 15 minutes. In support of the Radiative Atmospheric Divergence using the ARM Mobile Facility (AMF), GERB and AMMA Stations (RADAGAST) project, African Monsoon Multidisciplinary Analyses (AMMA) project and the Department of Energy's Atmospheric Radiation Measurement (ARM) program, the ARM Mobile Facility was deployed during 2006 in this climatically sensitive region, thereby providing a unique opportunity to evaluate remotely sensed algorithms for deriving LST.

Cloud properties and their seasonal and diurnal variability from TOVS path-B

Eight years of cloud properties retrieved from Television Infrared Observation Satellite-N (TIROS-N) Observational Vertical Sounder (TOVS) observations aboard the NOAA polar orbiting satellites are presented. The relatively high spectral resolution of these instruments in the infrared allows especially reliable cirrus identification day and night. This dataset therefore provides complementary information to the International Satellite Cloud Climatology Project (ISCCP). According to this dataset, cirrus clouds cover about 27% of the earth and 45% of the Tropics, whereas ISCCP reports 19% and 25%, respectively. Both global datasets agree within 5% on the amount of single-layer low clouds, at 30%. From 1987 to 1995, global cloud amounts remained stable to within 2%. The seasonal cycle of cloud amount is in general stronger than its diurnal cycle and it is stronger than the one of effective cloud amount, the latter the relevant variable for radiative transfer. Maximum effective low cloud amount over ocean occurs in winter in SH subtropics in the early morning hours and in NH midlatitudes without diurnal cycle. Over land in winter the maximum is in the early afternoon, accompanied in the midlatitudes by thin cirrus. Over tropical land and in the other regions in summer, the maximum of mesoscale high opaque clouds occurs in the evening. Cirrus also increases during the afternoon and persists during night and early morning. The maximum of thin cirrus is in the early afternoon, then decreases slowly while cirrus and high opaque clouds increase. TOVS extends information of ISCCP during night, indicating that high cloudiness, increasing during the afternoon, persists longer during night in the Tropics and subtropics than in midlatitudes. A comparison of seasonal and diurnal cycle of high cloud amount between South America, Africa, and Indonesia during boreal winter has shown strong similarities between the two land regions, whereas the Indonesian islands show a seasonal and diurnal behavior strongly influenced by the surrounding ocean. Deeper precipitation systems over Africa than over South America do not seem to be directly reflected in the horizontal coverage and mesoscale effective emissivity of high clouds.

The diurnal cycle of convection and atmospheric tides in an aquaplanet

The diurnal cycle of tropical convection and its relationship to the atmospheric tides is investigated using an aquaplanet GCM. The diurnal and semidiurnal harmonics of precipitation are both found to contribute significantly to the total diurnal variability of precipitation in the model, which is broadly consistent with observations of the diurnal cycle of convection over the open ocean. The semidiurnal tide is found to be the dominant forcing for the semidiurnal harmonic of precipitation. In contrast the diurnal tide plays only a small role in forcing the diurnal harmonic of precipitation, which is dominated by the variations in shortwave and longwave heating. In both the diurnal and semidiurnal harmonics, the feedback onto the convection by the humidity tendencies due to the convection is found to be important in determining the phase of the harmonics. Further experiments show that the diurnal cycle of precipitation is sensitive to the choice of closure in the convection scheme. While the surface pressure signal of the simulated atmospheric tides in the model agree well with both theory and observations in their magnitude and phase, sensitivity experiments suggest that the role of the stratospheric ozone in forcing the semidiurnal tide is much reduced compared to theoretical predictions. Furthermore, the influence of the cloud radiative effects seems small. It is suggested that the radiative heating profile in the troposphere, associated primarily with the water vapor distribution, is more important than previously thought for driving the semidiurnal tide. However, this result may be sensitive to the vertical resolution and extent of the model.

El Nino-mean state-seasonal cycle interactions in a multi-model ensemble

The modelled El Nino-mean state-seasonal cycle interactions in 23 coupled ocean-atmosphere GCMs, including the recent IPCC AR4 models, are assessed and compared to observations and theory. The models show a clear improvement over previous generations in simulating the tropical Pacific climatology. Systematic biases still include too strong mean and seasonal cycle of trade winds. El Nino amplitude is shown to be an inverse function of the mean trade winds in agreement with the observed shift of 1976 and with theoretical studies. El Nino amplitude is further shown to be an inverse function of the relative strength of the seasonal cycle. When most of the energy is within the seasonal cycle, little is left for inter-annual signals and vice versa. An interannual coupling strength (ICS) is defined and its relation with the modelled El Nino frequency is compared to that predicted by theoretical models. An assessment of the modelled El Nino in term of SST mode (S-mode) or thermocline mode (T-mode) shows that most models are locked into a S-mode and that only a few models exhibit a hybrid mode, like in observations. It is concluded that several basic El Nino-mean state-seasonal cycle relationships proposed by either theory or analysis of observations seem to be reproduced by CGCMs. This is especially true for the amplitude of El Nino and is less clear for its frequency. Most of these relationships, first established for the pre-industrial control simulations, hold for the double and quadruple CO2 stabilized scenarios. The models that exhibit the largest El Nino amplitude change in these greenhouse gas (GHG) increase scenarios are those that exhibit a mode change towards a T-mode (either from S-mode to hybrid or hybrid to T-mode). This follows the observed 1976 climate shift in the tropical Pacific, and supports the-still debated-finding of studies that associated this shift to increased GHGs. In many respects, these models are also among those that best simulate the tropical Pacific climatology (ECHAM5/MPI-OM, GFDL-CM2.0, GFDL-CM2.1, MRI-CGM2.3.2, UKMO-HadCM3). Results from this large subset of models suggest the likelihood of increased El Nino amplitude in a warmer climate, though there is considerable spread of El Nino behaviour among the models and the changes in the subsurface thermocline properties that may be important for El Nino change could not be assessed. There are no clear indications of an El Nino frequency change with increased GHG.

Equatorial waves in the lower stratosphere. II: Annual and interannual variability

The annual and interannual variability of idealized, linear, equatorial waves in the lower stratosphere is investigated using the temperature and velocity fields from the ECMWF 15-year re-analysis dataset. Peak Kelvin wave activity occurs during solstice seasons at 100 hPa, during December-February at 70 hPa and in the easterly to westerly quasi-biennial oscillation (QBO) phase transition at 50 hPa. Peak Rossby-gravity wave activity occurs during equinox seasons at 100 hPa, during June-August/September-November at 70 hPa and in the westerly to easterly QBO phase transition at 50 hPa. Although neglect of wind shear means that the results for inertio-gravity waves are likely to be less accurate, they are still qualitatively reasonable and an annual cycle is observed in these waves at 100 hPa and 70 hPa. Inertio-gravity waves with n = 1 are correlated with the QBO at 50 hPa, but the eastward inertio-gravity n = 0 wave is not, due to its very fast vertical group velocity in all background winds. The relative importance of different wave types in driving the QBO at 50 hPa is also discussed. The strongest acceleration appears to be provided by the Kelvin wave while the acceleration provided by the Rossby-gravity wave is negligible. Of the higher-frequency waves, the westward inertio-gravity n = 1 wave appears able to contribute more to the acceleration of the 50 hPa mean zonal wind than the eastward inertio-gravity n = 1 wave.

Decadal-scale rainfall variability in Ethiopia recorded in an annually laminated, Holocene-age, stalagmite

An annually laminated, uranium-series dated, Holocene stalagmite from southeast Ethiopia has been analysed for growth rate and δ13C and δ18O variations at annual to biennial resolution, in order to provide the first long duration proxy record of decadal-scale rainfall variability in this climatically sensitive region. Our study site (10°N) is climatically influenced by both summer (June—August) and spring (March—May) rainfall caused by the annual movement of the Inter-Tropical Convergence Zone (ITCZ) and modulated by large-scale anomalies in the atmospheric circulation and in ocean temperatures. Here we show that stalagmite growth, episodic throughout the last 7800 years, demonstrates decadal-scale (8—25 yr) variability in both growth rate and δ 18O. A hydrological model was employed and indicates that this decadal variability is due to variations in the relative amounts of rainfall in the two rain seasons. Our record, unique in its combination of length (a total of ~1000 years), annual chronology and high resolution δ18O, shows for the first time that such decadal-scale variability in rainfall in this region has occurred through the Holocene, which implies persistent decadal-scale variability for the large-scale atmospheric and oceanic driving factors.

Inter-simple sequence repeat and aggressiveness analyses revealed high genetic diversity, recombination and long-range dispersal in Fusarium culmorum

Inter-simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. 'Armada'. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro- as well as micro-geographical scale. The data suggested a long-range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur.