Analyse transcriptomique de l'interaction tripartite "Pseudozyma flocculosa-Blumeria graminis f.sp. hordei-Hordeum vulgare"

Afin d’améliorer nos pratiques agricoles dans le contexte d’une agriculture durable, plusieurs agents de lutte biologique (ALB) ont été développés, testés et sont maintenant utilisés dans le monde pour combattre les pertes de rendements causées par les maladies. Blumeria graminis f. sp. hordei ( Bgh) est l’agent pathogène responsable du blanc de l’orge et peut réduire les rendements de cette culture jusqu’à 40%. Un champignon épiphyte, Pseudozyma flocculosa, a été découvert et identifié en 1987 en association étroite avec le blanc du trèfle. Les chercheurs ont alors remarqué que ce champignon exhibait une forte activité antagoniste contre le blanc en détruisant les structures de l’agent pathogène. Suite à d’autres travaux, il est apparu que ce comportement antagoniste était dirigé contre tous les membres des Erysiphales et semblait lié à la synthèse d’un glycolipide antifongique soit la flocculosine. Toutefois, on n’est toujours pas parvenus à associer l’efficacité de l’ALB avec la production de ce glycolipide. Ces observations suggèrent que d’autres facteurs seraient impliqués lorsque les deux protagonistes, l’ALB et le blanc, sont en contact. L’objectif principal de ce projet était donc de chercher d’autres mécanismes moléculaires pouvant expliquer l’interaction P. flocculosa-blanc et orge, en faisant une analyse transcriptomique complète des trois protagonistes en même temps. L’interaction tripartite a été échantillonnée à différents temps suivant l’inoculation de P. flocculosa sur des feuilles d’orge présentant déjà une intensité de blanc d’environ 50%. Les échantillons de feuilles prélevés ont ensuite été utilisés pour l’extraction de l’ARN qui ont été ensuite transformés en ADNc pour la préparation des librairies. Cinq répliquats ont été effectués pour chaque temps et le tout a été séquencé à l’aide de séquençage par synthèse Illumina HiSeq. Les séquences obtenues (reads) ont ensuite été analysées à l’aide du logiciel CLC Genomics Workbench. Brièvement, les séquences obtenues ont été cartographiées sur les trois génomes de référence. Suite à la cartographie, les analyses d’expression ont été conduites et les gènes exprimés de façon différentielle ont été recherchés. Cette étape a été conduite en portant une attention particulière aux gènes codant pour un groupe de protéines appelées CSEP pour “candidate secreted effector proteins” qui seraient possiblement impliquées dans l’interaction tripartite. Parmi les protéines exprimées de façon différentielle en présence du blanc ou en absence de ce dernier, nous avons pu constater que certaines CSEP étaient fortement exprimées en présence du blanc. Ces résultats sont prometteurs et nous offrent une piste certaine pour l’élucidation des mécanismes impliqués dans cette interaction tripartite.

BRACATINGA-de-campo-mourão (Mimosa flocculosa Burkart).

2002

Evaluation of immobilized lipases on poly-hydroxybutyrate beads to catalyze biodiesel synthesis

Five microbial lipase preparations from several sources were immobilized by hydrophobic adsorption on small or large poly-hydroxybutyrate (PHB) beads and the effect of the support particle size on the biocatalyst activity was assessed in the hydrolysis of olive oil, esterification of butyric acid with butanol and transesterification of babassu oil (Orbignya sp.) with ethanol. The catalytic activity of the immobilized lipases in both olive oil hydrolysis and biodiesel synthesis was influenced by the particle size of PHB and lipase source. In the esterification reaction such influence was not observed. Geobacillus thermocatenulatus lipase (BTL2) was considered to be inadequate to catalyze biodiesel synthesis, but displayed high esterification activity. Butyl butyrate synthesis catalyzed by BTL2 immobilized on small PHB beads gave the highest yield (approximate to 90 mmol L-1). In biodiesel synthesis, the catalytic activity of the immobilized lipases was significantly increased in comparison to the free lipases. Full conversion of babassu oil into ethyl esters was achieved at 72 h in the presence of Pseudozyma antarctica type B (CALB), Thermomyces lanuginosus lipase (Lipex (R) 100L) immobilized on either small or large PHB beads and Pseudomonas fluorescens (PFL) immobilized on large PHB beads. The latter preparation presented the highest productivity (40.9 mg of ethyl esters mg(-1) immobilized protein h(-1)). (C) 2012 Elsevier B.V. All rights reserved.

Diatoms, total organic carbon, and total nitrogen of sediment core Dethlingen, Germany

To provide insights into the long-term evolution of aquatic ecosystems without human interference, we here evaluate a decadal- to centennial-scale-resolution diatom record spanning about 12 ka of the Holsteinian interglacial (Marine Isotope Stage 11c). Using a partially varved sediment core from the Dethlingen palaeolake (northern Germany), which has previously been studied for palynological and microfacies signals, we document the co-evolution of the aquatic and surrounding terrestrial environment. The diatom record is dominated by the genera Stephanodiscus, Aulacoseira, Ulnaria and Fragilaria. Based on the diatom assemblages and physical sediment properties, the evolution of the Dethlingen palaeolake can be subdivided into three major phases. During the oldest phase (lasting ~1900 varve years), the lake was ~10-15 m deep and characterized by anoxic bottom-water conditions and a high nutrient content. The following ~5600 years exhibited water depths >20 m, maximum diatom and Pediastrum productivity, and a peak in allochtonous nutrient input. During this phase, water-column mixing became more vigorous, resulting in a breakdown of anoxia. The youngest lake phase (~4000-5000 years) was characterized by decreasing water depth, turbulent water conditions and decreased nutrient loading. Based on our palaeolimnological data, we conclude that the evolution of the Dethlingen palaeolake during the Holsteinian interglacial responded closely to (i) changes within the catchment area (as documented by vegetation and sedimentation) related to the transition from closed forests growing on nutrient-rich soils (mesocratic forest phase) to open forests developing on poor soils (oligocratic forest phase), and (ii) short-term climate variability as reflected in centennial-scale climate perturbations.

Physico-chemical parameters of sediment core PG1972-1 (09-Tik-03) from a Tundra Lake, Northeastern Siberia

Thermokarst lakes in the Siberian Arctic contain sediment archives that can be used for paleoenvironmental inference. Until now, however, there has been no study from the inner Lena River Delta with a focus on diatoms. The objective of this study was to investigate how the diatom community in a thermokarst lake responded to past limnogeological changes and what specific factors drove variations in the diatom assemblage. We analysed fossil diatom species, organic content, grain-size distribution and elemental composition in a sediment core retrieved in 2009 from a shallow thermokarst lake in the Arga Complex, western Lena River Delta. The core contains a 3,000-year record of sediment accumulation. Shifts in the predominantly benthic and epiphytic diatom species composition parallel changes in sediment characteristics. Paleoenvironmental and limnogeological development, inferred from multiple biological and sedimentological variables, are discussed in the context of four diatom zones, and indicate a strong relation between changes in the diatom assemblage and thermokarst processes. We conclude that limnogeological and thermokarst processes such as lake drainage, rather than direct climate forcing, were the main factors that altered the aquatic ecosystem by influencing, for example, habitat availability, hydrochemistry, and water level.

Profiles of diatoms, pollen, XRD, XRF and organic composition of two sediment cores (PG2022 and PG2023) from Lake Kyutyunda in Yakutia, NE Siberia, Russia

Although the climate development over the Holocene in the Northern Hemisphere is well known, palaeolimnological climate reconstructions reveal spatiotemporal variability in northern Eurasia. Here we present a multi-proxy study from north-eastern Siberia combining sediment geochemistry, and diatom and pollen data from lake-sediment cores covering the last 38,000 cal. years. Our results show major changes in pyrite content and fragilarioid diatom species distributions, indicating prolonged seasonal lake-ice cover between ~13,500 and ~8,900 cal. years BP and possibly during the 8,200 cal. years BP cold event. A pollen-based climate reconstruction generated a mean July temperature of 17.8°C during the Holocene Thermal Maximum (HTM) between ~8,900 and ~4,500 cal. years BP. Naviculoid diatoms appear in the late Holocene indicating a shortening of the seasonal ice cover that continues today. Our results reveal a strong correlation between the applied terrestrial and aquatic indicators and natural seasonal climate dynamics in the Holocene. Planktonic diatoms show a strong response to changes in the lake ecosystem due to recent climate warming in the Anthropocene. We assess other palaeolimnological studies to infer the spatiotemporal pattern of the HTM and affirm that the timing of its onset, a difference of up to 3,000 years from north to south, can be well explained by climatic teleconnections. The westerlies brought cold air to this part of Siberia until the Laurentide ice-sheet vanished 7,000 years ago. The apparent delayed ending of the HTM in the central Siberian record can be ascribed to the exceedance of ecological thresholds trailing behind increases in winter temperatures and decreases in contrast in insolation between seasons during the mid to late Holocene as well as lacking differentiation between summer and winter trends in paleolimnological reconstructions.

Distribution of diatoms in surface sediments and some limnological characteristics of studied lakes in the Siberian arctic

The investigation of the species composition and ecology of diatoms of modern bottom sediments in water bodies of arctic polygonal tundra in three subregions of North Yakutiya has been carried out. As a result, 161 taxons of diatoms were determined; the determinant role of the depth, conductivity, pH of the water, and geographic latitude in their distribution was confirmed, and two complexes of species with respect to the leading abiotic factors were distinguished. The diatoms of the first complex prefer shallow water bodies of high latitudes with neutral and slightly alkaline water and relatively high conductivity. The second complex is confined to the water bodies of lower latitudes with small conductivity, as well as neutral and slightly acidic water.

Diatom deposits in the ostpreußischen Haffe

Als man nach dem ersten Weltkrieg im verkleinerten Deutschland nach der Möglichkeit von Neulandgewinnung suchte, dachte man auch an eineTrockenlegung der ostpreußischen Haffe. Aus diesem Anlaß wurden umfangreiche Bohrungen ausgeführt, um ein möglichst genaues Bild vom Untergrunde der Haffe zu bekommen. Auf Veranlassung der Preußischen Geologischen Landesanstalt wurde ich mit der Untersuchung der Diatomeen in den Bohrproben beauftragt. Die Arbeit wurde 1934 begonnen und Ende 1937 wurde der letzte Arbeitsbericht abgeliefert. Die beabsichtigte Veröffentlichung ist bisher unterblieben, weil die Druckvorlagen später verloren gegangen sind. Seitdem sind über die Haffuntersuchungen mehrere Teilergebnisse veröffentlicht worden, von denen hier schon wegen der Terminologie die pollenanalytischen Arbeiten von L. HEIN (1941) und HUGO GROSS (1941) erwähnt seien, auf die im Abschnitt Il 2e näher eingegangen wird. Bei der geologischen Auswertung war Zurückhaltung geboten; denn es wäre gewagt, allein aus der Perspektive der Diatomeenforschung endgültige Aussagen machen zu wollen. Darum habe ich mich bemüht, das Material so weit aufzuschließen, daß es Geologen später auch bei veränderter Fragestellung auswerten können. "Die Theorien wechseln, aber die Tatsachen bleiben." Der Initiative des Herrn Prof. Dr. K. GRIPP und der finanziellen Hilfe der Deutschen Forschungsgemeinschaft ist es zu verdanken, daß die vorliegende Arbeit im Druck erscheinen kann. Zusammenfassung 1. Nur in den alluvialen Schichten des Kurischen Haffs wurden Diatomeen gefunden. 2. Die Diatomeenflora des Kurischen Haffs besteht zur Hauptsache aus Süßwasserformen. 3. Salzwasserformen finden sich in allen Schichten verstreut unter der Süßwasserflora. Wenn sie auch nach Zahl der Arten in manchen Proben einen erheblichen Prozentsatz der Flora ausmachen, so ist doch die Zahl der Individuen stets so gering, daß man nirgends von einer Brackwasserflora sprechen kann. 4. Die Süßwasserflora besteht in den unteren Schichten vorwiegend aus Grundformen; und zwar machen die epiphytischen Bewohner flacher Sumpfgewässer einen großen Teil der Flora aus. 5. In einzelnen Bohrungen kommt in den untersten alluvialen Schichten eine Grundflora mit zahlreichen Mastogloien vor. Dies sind die ältesten diatomeenführenden Schichten, entstanden in isolierten Sumpfgewässern. 6. Die übrigen Schichten mit überwiegender Grundflora sind vermutlich Ablagerungen der Ancyluszeit. 7. Die oberen Schichten, in denen die Planktondiatomeen überwiegen, dürften größtenteils der Litorina-Transgressionszeit angehören, jedoch ist der Transgressions-Kontakt nicht klar zu erkennen. 8. Das Ende der Litorinazeit ist noch weniger erkennbar, da eine grundsätzliche Veränderung der Flora nach oben nicht zu beobachten ist. 9. Die ostbaltischen Charakterformen sind in allen Schichten vertreten.

Pollen and diatom analysis on varved sediments in Lake Jues (Harz Mountains, Germany)

Studies combining sedimentological and biological evidence to reconstruct Holocene climate beyond the major changes, and especially seasonality, are rare in Europe, and are nearly completely absent in Germany. The present study tries to reconstruct changes of seasonality from evidence of annual algal successions within the framework of well-established pollen zonation and 14C-AMS dates from terrestrial plants. Laminated Holocene sediments in Lake Jues (10°20.70' E, 51°39.30' N, 241 m a.s.l.), located at the SW margin of the Harz Mountains, central Germany, were studied for sediment characteristics, pollen, diatoms and coccal green algae. An age model is based on 21 calibrated AMS radiocarbon dates from terrestrial plants. The sedimentary record covers the entire Holocene period. Trophic status and circulation/stagnation patterns of the lake were inferred from algal assemblages, the subannual structure of varves and the physico-chemical properties of the sediment. During the Holocene, mixing conditions alternated between di-, oligo- and meromictic depending on length and variability of spring and fall periods, and the stability of winter and summer weather. The trophic state was controlled by nutrient input, circulation patterns and the temperature-dependent rates of organic production and mineralization. Climate shifts, mainly in phase with those recorded from other European regions, are inferred from changing limnological conditions and terrestrial vegetation. Significant changes occurred at 11,600 cal. yr. BP (Preboreal warming), between 10,600 and 10,100 cal. yr. BP (Boreal cooling), and between 8,400 and 4,550 cal. yr. BP (warm and dry interval of the Atlantic). Since 4,550 cal. yr. BP the climate became gradually cooler, wetter and more oceanic. This trend was interrupted by warmer and dryer phases between 3,440 and 2,850 cal. yr. BP and, likely, between 2,500 and 2,250 cal. yr. BP.

Sedimentology, biogeochemistry stable isotopes, pollen, plant macrofossils, and diatoms from two sediments cores from the northern Yukon permafrost peatlands (Canada)

Ice-wedge polygon (IWP) mires in the Arctic and Subarctic are extremely vulnerable to climatic and environmental change. We present the results of a multidisciplinary paleoenvironmental study on IWPs in the northern Yukon, Canada. High-resolution laboratory analyses were carried out on a permafrost core and the overlying seasonally thawed (active) layer, from a low-centered IWP located in a drained lake basin on Herschel Island. In relation to 14 Accelerator Mass Spectrometry (AMS) radiocarbon dates spanning the last 5000 years, we report sedimentary data including grain size distribution and biogeochemical parameters (organic carbon, nitrogen, C/N ratio, d13C), stable water isotopes (d18O, dD), as well as fossil pollen, plant macrofossil and diatom assemblages. Three sediment units (SUs) correspond to the main stages of deposition (1) in a thermokarst lake (SU1: 4950 to 3950 cal yrs BP), (2) during transition from lacustrine to palustrine conditions after lake drainage (SU2: 3950 to 3120 cal yrs BP), and (3) in palustrine conditions in the IWP field that developed after drainage (SU3: 3120 cal yrs BP to AD 2012). The lacustrine phase (pre 3950 cal yrs BP) is characterized by planktonic-benthic and pioneer diatoms species indicating circumneutral waters, and very few plant macrofossils. The pollen record has captured a regional signal of relatively stable vegetation composition and climate for the lacustrine stage of the record until 3950 cal yrs BP. Palustrine conditions with benthic and acidophilic species characterize the peaty shallow-water environments of the low-centered IWP. The transition from lacustrine to palustrine conditions was accompanied by acidification and rapid revegetation of the lake bottom within about 100 years. Since the palustrine phase we consider the pollen record as a local vegetation proxy dominated by the plant communities growing in the IWP. Ice-wedge cracking in water-saturated sediments started immediately after lake drainage at about 3950 cal yrs BP and led to the formation of an IWP mire. Permafrost aggradation through downward closed-system freezing of the lake talik is indicated by the stable water isotope record. The originally submerged IWP center underwent gradual drying during the past 2000 years. This study highlights the sensitivity of permafrost landscapes to climate and environmental change throughout the Holocene.

Radiocarbon ages and diatom abundance in samples obtained from Qarlikturvik Valley, Bylot Island

The formation of many arctic wetlands is associated with the occurrence of polygon-patterned permafrost. Existing scenarios to describe and explain surface landforms in arctic wetlands (low-center and high-center polygons and polygon ponds) invoke competing hypotheses: a cyclic succession (the thaw-lake hypothesis) or a linear succession (terrestrialization). Both hypotheses infer the predictable development of polygon-patterned wetlands over millennia. However, very few studies have applied paleoecological techniques to reconstruct long-term succession in tundra wetlands and thereby test the validity of existing hypotheses. This paper uses the paleoecological record of diatoms to investigate long-term development of individual polygons in a High Arctic wetland. Two landform processes were examined: (1) the millennial-scale development of a polygon-pond, and (2) the transition from low-center to erosive high-center polygons. Diatom assemblages were quantified from habitats associated with contrasting landforms in the present-day landscape, and used as an analog to reconstruct past transitions between polygon types. On the basis of this evidence, the paleoecological record does not support either of the existing models describing the predictable succession of polygon landforms in an arctic wetland. Our results indicate a need for greater paleoecological understanding, in combination with in situ observations in present-day geomorphology, in order to identify patterns of polygon wetland development and elucidate the long-term drivers of these landform transitions.

Water chemistry and diatom occurrences in sediments of Terrasovoje, Radok and Beaver Lake, Amery Oasis, East Antarctica

The diatom flora of three lakes in the ice-free Amery Oasis, East Antarctica, was studied. Two of the lakes are meltwater reservoirs, Terrasovoje Lake (31 m depth) and Radok Lake (362 m depth), while Beaver Lake (>435 m depth) is an epishelf lake. The lakes can be characterized as cold, ultra-oligotrophic and alkaline, displaying moderate (Radok and Terrasovoje lakes) to high (Beaver Lake) conductivities. There was no diatom phytoplankton present in any of the three lakes. While 34 benthic diatom taxa were identified from modern and Holocene sediments of Terrasovoje and Radok lakes, a 30-cm long sediment core recovered in Beaver Lake was barren. Five species (Luticola muticopsis, Muelleria peraustralis, Pinnularia cymatopleura, Psammothidium metakryophilum, P. stauroneioides) are endemic to the Antarctic region. All identified taxa are photographically documented and brief notes on their taxonomy, biogeography and ecology are provided. The most abundant diatom taxa are Amphora veneta, Craticula cf. molesta, Diadesmis spp, M. peraustralis and Stauroneis anceps. This is the first report on the diatom flora in lakes of the Amery Oasis.

Abundance of diatoms and foraminifers in the surface sediment layer of the southeastern Laptev Sea shelf

The study of diatoms and benthic foraminifers from the southeastern shelf of the Laptev Sea shows that their most diverse and abundant recent assemblages populate the peripheral underwater part of the Lena River delta representing the marginal filter of the sea. This area is characterized by intense interaction between fresh waters of Siberian rivers and basin seawater, Atlantic one included. Local Late Holocene (~last 2300 years) environments reflect the main regional and global paleoclimatic changes, the Medieval Warm Period (~600-1100 years B.P.) and the Little Ice Age (~100-600 years B.P.) inclusive. In addition, composition and distribution of planktonic foraminifers implies strong influence of Atlantic water during the Holocene optimum ~5100-6200 years B.P.