Structure et dynamique des communautés multi-espèces : le rôle de l’espace

Cette thèse porte sur le rôle de l’espace dans l’organisation et dans la dynamique des communautés écologiques multi-espèces. Deux carences peuvent être identifiées dans les études théoriques actuelles portant sur la dimension spatiale des communautés écologiques : l’insuffisance de modèles multi-espèces représentant la dimension spatiale explicitement, et le manque d’attention portée aux interactions positives, tel le mutualisme, en dépit de la reconnaissance de leur ubiquité dans les systèmes écologiques. Cette thèse explore cette problématique propre à l’écologie des communautés, en utilisant une approche théorique s’inspirant de la théorie des systèmes complexes et de la mécanique statistique. Selon cette approche, les communautés d’espèces sont considérées comme des systèmes complexes dont les propriétés globales émergent des interactions locales entre les organismes qui les composent, et des interactions locales entre ces organismes et leur environnement. Le premier objectif de cette thèse est de développer un modèle de métacommunauté multi-espèces, explicitement spatial, orienté à l’échelle des individus et basé sur un réseau d’interactions interspécifiques générales comprenant à la fois des interactions d’exploitation, de compétition et de mutualisme. Dans ce modèle, les communautés locales sont formées par un processus d’assemblage des espèces à partir d’un réservoir régional. La croissance des populations est restreinte par une capacité limite et leur dynamique évolue suivant des mécanismes simples de reproduction et de dispersion des individus. Ces mécanismes sont dépendants des conditions biotiques et abiotiques des communautés locales et leur effet varie en fonction des espèces, du temps et de l’espace. Dans un deuxième temps, cette thèse a pour objectif de déterminer l’impact d’une connectivité spatiale croissante sur la dynamique spatiotemporelle et sur les propriétés structurelles et fonctionnelles de cette métacommunauté. Plus précisément, nous évaluons différentes propriétés des communautés en fonction du niveau de dispersion des espèces : i) la similarité dans la composition des communautés locales et ses patrons de corrélations spatiales; ii) la biodiversité locale et régionale, et la distribution locale de l’abondance des espèces; iii) la biomasse, la productivité et la stabilité dynamique aux échelles locale et régionale; et iv) la structure locale des interactions entre les espèces. Ces propriétés sont examinées selon deux schémas spatiaux. D’abord nous employons un environnement homogène et ensuite nous employons un environnement hétérogène où la capacité limite des communautés locales évoluent suivant un gradient. De façon générale, nos résultats révèlent que les communautés écologiques spatialement distribuées sont extrêmement sensibles aux modes et aux niveaux de dispersion des organismes. Leur dynamique spatiotemporelle et leurs propriétés structurelles et fonctionnelles peuvent subir des changements profonds sous forme de transitions significatives suivant une faible variation du niveau de dispersion. Ces changements apparaissent aussi par l’émergence de patrons spatiotemporels dans la distribution spatiale des populations qui sont typiques des transitions de phases observées généralement dans les systèmes physiques. La dynamique de la métacommunauté présente deux régimes. Dans le premier régime, correspondant aux niveaux faibles de dispersion des espèces, la dynamique d’assemblage favorise l’émergence de communautés stables, peu diverses et formées d’espèces abondantes et fortement mutualistes. La métacommunauté possède une forte diversité régionale puisque les communautés locales sont faiblement connectées et que leur composition demeure ainsi distincte. Par ailleurs dans le second régime, correspondant aux niveaux élevés de dispersion, la diversité régionale diminue au profit d’une augmentation de la diversité locale. Les communautés locales sont plus productives mais leur stabilité dynamique est réduite suite à la migration importante d’individus. Ce régime est aussi caractérisé par des assemblages incluant une plus grande diversité d’interactions interspécifiques. Ces résultats suggèrent qu’une augmentation du niveau de dispersion des organismes permet de coupler les communautés locales entre elles ce qui accroît la coexistence locale et favorise la formation de communautés écologiques plus riches et plus complexes. Finalement, notre étude suggère que le mutualisme est fondamentale à l’organisation et au maintient des communautés écologiques. Les espèces mutualistes dominent dans les habitats caractérisés par une capacité limite restreinte et servent d’ingénieurs écologiques en facilitant l’établissement de compétiteurs, prédateurs et opportunistes qui bénéficient de leur présence.

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Long-term endemism of two highly divergent lineages of the amphibian-killing fungus in the Atlantic Forest of Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Distribution, composition and seasonality of aquatic birds in the Nhecolandia sub-region of South Pantanal, Brazil

Despite remarkable significance of Pantanal for the conservation of aquatic birds, the status of their populations, the spatiotemporal patterns of distribution and habitat use and structure of communities are little known. Thus, we studied three aquatic environments (Negro river, bays and salines) from 2007 to 2009 in the Nhecolandia Pantanal to verify the distribution and composition of aquatic birds and also if there is significant seasonal influence on these aspects. We adopted the transect method (288 hours of sampling) and recorded 135 species (7.834 individuals). The Negro river showed the highest diversity, while the salines the lowest. The similarity of aquatic bird communities was higher between bays and salines, followed by Negro river and bays and lower between salines and Negro river. The equidistribution is more variable in the salines and more stable in the Negro river. The environments strongly differ from each other in aquatic bird composition in space (habitat use and distribution) and time (seasonal water fluctuations). The diversity of bird community in the dry season varies significantly in the salines, followed by the bays and more stable in the Negro river. The Negro river, regardless of large annual amplitude of flow, is more seasonally stable since its riparian vegetation is continuous (not isolated) and constant. These aspects provide better conditions to stay all year, contributing to decrease the seasonal nomadic tendencies of aquatic birds. Finally, all these data provide strong arguments to the preservation of all phytophysiognomies in the Nhecolandia sub-region of Pantanal, but with special attention to the salines widely used by many flocks of aquatic birds (mainly in the dry season) and migrant and/or rare species restricted to this habitat.

Mechanisms of intrinsic beating variability in cardiac cell cultures and model pacemaker networks

Heart rate variability (HRV) exhibits fluctuations characterized by a power law behavior of its power spectrum. The interpretation of this nonlinear HRV behavior, resulting from interactions between extracardiac regulatory mechanisms, could be clinically useful. However, the involvement of intrinsic variations of pacemaker rate in HRV has scarcely been investigated. We examined beating variability in spontaneously active incubating cultures of neonatal rat ventricular myocytes using microelectrode arrays. In networks of mathematical model pacemaker cells, we evaluated the variability induced by the stochastic gating of transmembrane currents and of calcium release channels and by the dynamic turnover of ion channels. In the cultures, spontaneous activity originated from a mobile focus. Both the beat-to-beat movement of the focus and beat rate variability exhibited a power law behavior. In the model networks, stochastic fluctuations in transmembrane currents and stochastic gating of calcium release channels did not reproduce the spatiotemporal patterns observed in vitro. In contrast, long-term correlations produced by the turnover of ion channels induced variability patterns with a power law behavior similar to those observed experimentally. Therefore, phenomena leading to long-term correlated variations in pacemaker cellular function may, in conjunction with extracardiac regulatory mechanisms, contribute to the nonlinear characteristics of HRV.

Analysis of an ancient global warming event, the Paleocene-Eocene thermal maximum, under examination from ODP Holes 113-689B and 113-690B

Spatiotemporal patterns of carbonate dissolution provide a critical constraint on carbon input during an ancient (~55.5 Ma) global warming event known as the Paleocene-Eocene thermal maximum (PETM), yet the magnitude of lysocline shoaling in the Southern Ocean is poorly constrained due to limited spatial coverage in the circum-Antarctic region. This shortcoming is partially addressed by comparing patterns of carbonate sedimentation at the Site 690 PETM reference section to those herein reconstructed for nearby Site 689. Biochemostratigraphic correlation of the two records reveals that the first ~36 ka of the carbon isotope excursion (CIE) signaling PETM conditions is captured by the Site 689 section, while the remainder of the CIE interval and nearly all of the CIE recovery are missing due to a coring gap. A relatively expanded stratigraphy and higher carbonate content at mid-bathyal Site 689 indicate that dissolution was less severe than at Site 690. Thus, the bathymetric transect delimited by these two PETM records indicates that the lysocline shoaled above Site 689 (~1,100 m) while the calcite compensation depth remained below Site 690 (~1,900 m) in the Weddell Sea region. The ensuing recovery of carbonate sedimentation conforms to a bathymetric trend best explained by gradual lysocline deepening as negative feedback mechanisms neutralized ocean acidification. Further, biochemostratigraphic evidence indicates the tail end of the CIE recovery interval at both sites has been truncated by a hiatus most likely related to vigorous production and advection of intermediate waters.

Induction of inhibitory factor κBα mRNA in the central nervous system after peripheral lipopolysaccharide administration: An in situ hybridization histochemistry study in the rat

In this study we investigate the mRNA expression of inhibitory factor κBα (IκBα) in cells of the rat brain induced by an intraperitoneal (i.p.) injection of lipopolysaccharide (LPS). IκB controls the activity of nuclear factor κB, which regulates the transcription of many immune signal molecules. The detection of IκB induction, therefore, would reveal the extent and the cellular location of brain-derived immune molecules in response to peripheral immune challenges. Low levels of IκBα mRNA were found in the large blood vessels and in circumventricular organs (CVOs) of saline-injected control animals. After an i.p. LPS injection (2.5 mg/kg), dramatic induction of IκBα mRNA occurred in four spatio-temporal patterns. Induced signals were first detected at 0.5 hr in the lumen of large blood vessels and in blood vessels of the choroid plexus and CVOs. Second, at 1–2 hr, labeling dramatically increased in the CVOs and choroid plexus and spread to small vascular and glial cells throughout the entire brain; these responses peaked at 2 hr and declined thereafter. Third, cells of the meninges became activated at 2 hr and persisted until 12 hr after the LPS injection. Finally, only at 12 hr, induced signals were present in ventricular ependyma. Thus, IκBα mRNA is induced in brain after peripheral LPS injection, beginning in cells lining the blood side of the blood–brain barrier and progressing to cells inside brain. The spatiotemporal patterns suggest that cells of the blood–brain barrier synthesize immune signal molecules to activate cells inside the central nervous system in response to peripheral LPS. The cerebrospinal fluid appears to be a conduit for these signal molecules.

Emergence of order in visual system development.

Neural connections in the adult central nervous system are highly precise. In the visual system, retinal ganglion cells send their axons to target neurons in the lateral geniculate nucleus (LGN) in such a way that axons originating from the two eyes terminate in adjacent but nonoverlapping eye-specific layers. During development, however, inputs from the two eyes are intermixed, and the adult pattern emerges gradually as axons from the two eyes sort out to form the layers. Experiments indicate that the sorting-out process, even though it occurs in utero in higher mammals and always before vision, requires retinal ganglion cell signaling; blocking retinal ganglion cell action potentials with tetrodotoxin prevents the formation of the layers. These action potentials are endogenously generated by the ganglion cells, which fire spontaneously and synchronously with each other, generating "waves" of activity that travel across the retina. Calcium imaging of the retina shows that the ganglion cells undergo correlated calcium bursting to generate the waves and that amacrine cells also participate in the correlated activity patterns. Physiological recordings from LGN neurons in vitro indicate that the quasiperiodic activity generated by the retinal ganglion cells is transmitted across the synapse between ganglion cells to drive target LGN neurons. These observations suggest that (i) a neural circuit within the immature retina is responsible for generating specific spatiotemporal patterns of neural activity; (ii) spontaneous activity generated in the retina is propagated across central synapses; and (iii) even before the photoreceptors are present, nerve cell function is essential for correct wiring of the visual system during early development. Since spontaneously generated activity is known to be present elsewhere in the developing CNS, this process of activity-dependent wiring could be used throughout the nervous system to help refine early sets of neural connections into their highly precise adult patterns.

Sedimentary and carbonate preservation of ODP Sites 1262, 1263 and 1266

Rapid carbon input into the ocean-atmosphere system caused a dramatic shoaling of the lysocline during the Paleocene-Eocene thermal maximum (PETM), a transient (~170 kyr) global warming event that occurred roughly 55 Ma. Carbon cycle models invoking an accelerated carbonate-silicate feedback mechanism to neutralize ocean acidification predict that the lysocline would subsequently deepen to depths below its original position as the marine carbonate system recovered from such a perturbation. To test this hypothesis, records of carbonate sedimentation and preservation for PETM sections in the Weddell Sea (ODP Site 690) and along the Walvis Ridge depth transect (ODP Sites 1262, 1263, and 1266) were assembled within the context of a unified chronostratigraphy. The meridional gradient of undersaturation delimited by these records shows that dissolution was more severe in the subtropical South Atlantic than in the Weddell Sea during the PETM, a spatiotemporal pattern inconsistent with the view that Atlantic overturning circulation underwent a transient reversal. Deepening of the lysocline following its initial ascent is signaled by increases in %CaCO3 and coarse-fraction content at all sites. Carbonate preservation during the recovery period is appreciably better than that seen prior to carbon input with carbonate sedimentation becoming remarkably uniform over a broad spectrum of geographic and bathymetric settings. These congruent patterns of carbonate sedimentation confirm that the lysocline was suppressed below the depth it occupied prior to carbon input, and are consistent with the view that an accelerated carbonate-silicate geochemical cycle played an important role in arresting PETM conditions.

Coarse threat images reveal theta oscillations in the amygdala: a magnetoencephalography study

Neurocognitive models propose a specialized neural system for processing threat-related information, in which the amygdala plays a key role in the analysis of threat cues. fMRI research indicates that the amygdala is sensitive to coarse visual threat relevant information—for example, low spatial frequency (LSF) fearful faces. However, fMRI cannot determine the temporal or spectral characteristics of neural responses. Consequently, we used magnetoencephalography to explore spatiotemporal patterns of activity in the amygdala and cortical regions with blurry (LSF) and normal angry, fearful, and neutral faces. Results demonstrated differences in amygdala activity between LSF threat-related and LSF neutral faces (50-250 msec after face onset). These differences were evident in the theta range (4-8 Hz) and were accompanied by power changes within visual and frontal regions. Our results support the view that the amygdala is involved in the early processing of coarse threat related information and that theta is important in integrating activity within emotion-processing networks.

Relative significance of pelagic, benthic and allochthonous organic matter to microbial carbon cycling in a phosphorus-depleted subtropical estuary (Florida Bay)

Heterotrophic bacteria are important decomposers and transformers of primary production and provide an important link between detritus and the aquatic food web. In seagrass ecosystems, much of seagrass primary production is unavailable through direct grazing and must undergo microbial reworking before seagrass production can enter the aquatic food web. The goal of my dissertation research is to understand better the role heterotrophic bacteria play in carbon cycling in seagrass estuaries. My dissertation research focuses on Florida Bay, a seagrass estuary that has experienced recent changes in carbon source availability, which may have altered ecosystem function. My dissertation research investigates the importance of seagrass, algal and/or cyanobacterial, and allochthonous-derived organic matter to heterotrophic bacteria in Florida Bay and helps establish the carbon base of the estuarine food web. ^ A three tiered approach to the study of heterotrophic bacterial carbon cycling and trophic influences in Florida Bay was used: (1) Spatiotemporal observations of environmental parameters (hydrology, nutrients, extracellular enzymes, and microbial abundance, biomass, and production); (2) Microbial grazing experiments under different levels of top-down and bottom-up influence; and (3) Bulk and compound-specific (bacteria-biomarker fatty acid analysis) stable carbon isotope analysis. ^ In Florida Bay, spatiotemporal patterns in microbial extracellular enzyme (also called ectoenzyme) activities indicate that microorganisms hydrolyzed selectively fractions of the estuarine organic matter pool. The microbial community hydrolyzed organic acids, peptides, and phosphate esters and did not use storage and structural carbohydrates. Organic matter use by heterotrophic bacterioplankton in Florida Bay was co-regulated by bottom-up (resource availability) and top-down (grazer mediated) processes. A bacterial carbon budget based on bacterial, epiphytic, and seagrass production indicates that heterotrophic bacterial carbon cycles are supported primarily through epiphytic production with mixing from seagrass production. Stable carbon isotope analysis of bacteria biomarkers and carbon sources in Florida Bay corroborate the results of the bacterial carbon budget. These results support previous studies of aquatic consumers in Florida Bay, indicating that epiphytic/benthic algal and/or cyanobacterial production with mixing from seagrass-derived organic matter is the carbon base of the seagrass estuarine food web. ^

Tropical seagrass-associated macroalgae distributions and trends relative to water quality

Tropical coastal marine ecosystems including mangroves, seagrass beds and coral reef communities are undergoing intense degradation in response to natural and human disturbances, therefore, understanding the causes and mechanisms present challenges for scientist and managers. In order to protect our marine resources, determining the effects of nutrient loads on these coastal systems has become a key management goal. Data from monitoring programs were used to detect trends of macroalgae abundances and develop correlations with nutrient availability, as well as forecast potential responses of the communities monitored. Using eight years of data (1996–2003) from complementary but independent monitoring programs in seagrass beds and water quality of the Florida Keys National Marine Sanctuary (FKNMS), we: (1) described the distribution and abundance of macroalgae groups; (2) analyzed the status and spatiotemporal trends of macroalgae groups; and (3) explored the connection between water quality and the macroalgae distribution in the FKNMS. In the seagrass beds of the FKNMS calcareous green algae were the dominant macroalgae group followed by the red group; brown and calcareous red algae were present but in lower abundance. Spatiotemporal patterns of the macroalgae groups were analyzed with a non-linear regression model of the abundance data. For the period of record, all macroalgae groups increased in abundance (Abi) at most sites, with calcareous green algae increasing the most. Calcareous green algae and red algae exhibited seasonal pattern with peak abundances (Φi) mainly in summer for calcareous green and mainly in winter for red. Macroalgae Abi and long-term trend (mi) were correlated in a distinctive way with water quality parameters. Both the Abi and mi of calcareous green algae had positive correlations with NO3−, NO2−, total nitrogen (TN) and total organic carbon (TOC). Red algae Abi had a positive correlation with NO2−, TN, total phosphorus and TOC, and the mi in red algae was positively correlated with N:P. In contrast brown and calcareous red algae Abi had negative correlations with N:P. These results suggest that calcareous green algae and red algae are responding mainly to increases in N availability, a process that is happening in inshore sites. A combination of spatially variable factors such as local current patterns, nutrient sources, and habitat characteristics result in a complex array of the macroalgae community in the seagrass beds of the FKNMS.

Simulating Mechanisms for Dispersal, Production and Stranding of Small Forage Fish in Temporary Wetland Habitats

Movement strategies of small forage fish (<8 cm total length) between temporary and permanent wetland habitats affect their overall population growth and biomass concentrations, i.e., availability to predators. These fish are often the key energy link between primary producers and top predators, such as wading birds, which require high concentrations of stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.