长期施肥对黄土旱塬区土壤—植物系统中氮、磷养分的影响

对1984年建立的长期试验田,分析了2005年小麦产量、养分吸收及土壤养分变化。结果表明,单施磷肥增产25.6%,单施氮肥增产48.1%,其吸氮、磷量也相应增加,但收获指数显著低于对照;氮磷配施增产幅度为101.3%3~02.8%,养分吸收量增加显著,最佳施肥量为N2P2(N 90 kg/hm2、P 56.4 kg/hm2)。施肥明显改变了耕层土壤养分的含量,也影响了养分在土壤剖面的分布。氮磷配施是培肥土壤的有效途径,耕层土壤全磷增加了8.3%~45.2%,速效磷增加54.8%9~17.8%。中等施氮(N 90 kg/hm2)水平下,随着磷的增加,耕层土壤全磷累积和施磷量的关系为y=0.002x-0.112。速效磷含量增加和磷肥用量的关系为y=9.6537Ln(x)-35.371,施肥对60 cm以下磷素影响较小。

黄土高原不同演替阶段草地植被细根垂直分布特征与土壤环境的关系

研究了黄土区不同演替阶段草地植被细根垂直分布特征与土壤环境的关系,结果表明不同演替阶段草地植被细根生物量、根长密度、表面积、直径和比根长均具有明显的垂直分布特征。细根生物量、根长密度和细根表面积一般随土层加深而逐渐减少,且集中分布于0~40cm土层;随着演替的进行,除20a弃耕地外,0~80 cm土层细根生物量、根长密度和细根表面积逐渐增加;除25a弃耕地外,细根直径随演替进行逐渐减小。0~100 cm土层土壤含水量随演替进行而增加,不同演替阶段深层土壤水分较表层稳定。土壤容重的变化趋势为9<4<15<20<25a弃耕地,根系对表层土壤水分和容重的影响较大,而对深层土壤水分与容重影响较少。不同演替阶段细根各参数和土壤水分、容重差异均达到显著水平。各弃耕地细根参数之间,细根参数和土壤环境因子之间存在不同程度的相关关系,土壤含水量在草本植被的不同演替阶段均是影响其细根垂直分布的关键因素。土壤容重在演替早期对草本植被根系的影响较小,随着演替进行其影响作用进一步增强。

Changes in individual plant traits and biomass allocation in alpine meadow with elevation variation on the Qinghai-Tibetan Plateau

Plant traits and individual plant biomass allocation of 57 perennial herbaceous species, belonging to three common functional groups (forbs, grasses and sedges) at subalpine (3700 m ASL), alpine (4300 m ASL) and subnival (>= 5000 m ASL) sites were examined to test the hypothesis that at high altitudes, plants reduce the proportion of aboveground parts and allocate more biomass to belowground parts, especially storage organs, as altitude increases, so as to geminate and resist environmental stress. However, results indicate that some divergence in biomass allocation exists among organs. With increasing altitude, the mean fractions of total biomass allocated to aboveground parts decreased. The mean fractions of total biomass allocation to storage organs at the subalpine site (7%+/- 2% S.E.) were distinct from those at the alpine (23%+/- 6%) and subnival (21%+/- 6%) sites, while the proportions of green leaves at all altitudes remained almost constant. At 4300 m and 5000 m, the mean fractions of flower stems decreased by 45% and 41%, respectively, while fine roots increased by 86% and 102%, respectively. Specific leaf areas and leaf areas of forbs and grasses deceased with rising elevation, while sedges showed opposite trends. For all three functional groups, leaf area ratio and leaf area root mass ratio decreased, while fine root biomass increased at higher altitudes. Biomass allocation patterns of alpine plants were characterized by a reduction in aboveground reproductive organs and enlargement of fine roots, while the proportion of leaves remained stable. It was beneficial for high altitude plants to compensate carbon gain and nutrient uptake under low temperature and limited nutrients by stabilizing biomass investment to photosynthetic structures and increasing the absorption surface area of fine roots. In contrast to forbs and grasses that had high mycorrhizal infection, sedges had higher single leaf area and more root fraction, especially fine roots.

Temperature and light tolerance of representative brown, green and red algae in tumble culture revealed by chlorophyll fluorescence measurements

Laminaria japonica, Undaria pinnatifida, Ulva lactuca, Grateloupia turuturu and Palmaria palmata are Suitable species that fit the requirements of a seaweed-animal integrated aquaculture system in terms of their viable biomass, rapid growth and promising nutrient uptake rates. fit this investigation, the responses of the optimal chlorophyll fluorescence yield of the five algal species in tumble Culture were assessed at a temperature range of 10 similar to 30 degrees C. The results revealed that Ulva lactuca was the most resistant species to high temperature, withstanding 30 degrees C for 4 h without apparent decline in the optimal chlorophyll fluorescence yield. While the arctic alga Palmaria palmata was the most vulnerable one, showing significant decline in the optimal chlorophyll fluorescence yield at 25 degrees C for 2 h. The cold-water species Laminaria japonica, however, demonstrated strong ability to cope with higher temperature (24 similar to 26 degrees C) for shorter time (within 24 h) without significant decline in the optimal chlorophyll fluorescence yield. Grateloupia turuturu showed a general decrease in the optimal chlorophyll fluorescence yield with the rising temperature from 23 to 30 degrees C, similar to the temperate kelp Undaria pinnatifida. Changes of chlorophyll fluorescence yields of these algae were characterized differently indicating the existence of species-unique strategy to cope with high light. Measurements of the optimal chlorophyll fluorescence yield after short exposure to direct solar irradiance revealed how long these exposures could be without significant photoinhibition or with promising recovery in photosynthetic activities. Seasonal pattern of alternation of algal species in tank culture in the Northern Hemisphere at the latitude of 36 degrees N was proposed according to these basic measurements.

尖刺菱形藻的营养吸收和增殖动力学研究

本文采用批次培养和半连续培养的方法，研究了中国近海的主要赤潮生物之一尖刺菱形藻的营养盐吸收动力学和营养盐限制下的生长进行了研究。1）中国近海的尖刺菱形藻为尖刺型，不能形成软骨藻酸；2）尖刺菱形藻是一种典型的广温广盐的近岸型海洋浮游硅藻，其适应不同环境的能力较强；3）尖刺菱形藻的营养盐吸收动力学符合米氏酶动力学方程V=V_mXS/(Ks+S)；4）在稳定状态下，米氏方程与Droop方程一起，与Mond方程一样，都可以很好地描述尖刺菱形藻的生长率与外界环境中限制性营养盐浓度之间的关系 ；5）与其他浮游植物相比较，尖刺菱形藻吸收无机氮的能力较强，而吸收无机磷的能力相对较弱。

Potential of the seaweed Gracilaria lemaneiformis for integrated multi-trophic aquaculture with scallop Chlamys farreri in North China

In this study the red alga, Gracilaria lemaneiformis, was cultivated with the scallop Chlamys farreri in an integrated multi-trophic aquaculture (IMTA) system for 3 weeks at the Marine Aquaculture Laboratory of the Institute of Oceanology, Chinese Academy of Sciences (IOCAS) in Qingdao, Shandong Province, North China. The nutrient uptake rate and nutrient reduction efficiency of ammonium and phosphorus from scallop excretion were determined. The experiment included four treatments each with three replicates, and three scallop monoculture systems served as the control. Scallop density (407.9 +/- 2.84 g m(-3)) remained the same in all treatments while seaweed density differed. The seaweed density was set at four levels (treatments 1, 2, 3, 4) with thallus wet weight of 69.3 +/- 3.21, 139.1 +/- 3.80, 263.5 +/- 6.83, and 347.6 +/- 6.30 g m(-3), respectively. There were no significant differences in the initial nitrogen and phosphorus concentration between each treatment and the control group (ANOVA, p > 0.05). The results showed that at the end of the experiment, the nitrogen concentration in the control group and treatment 1 was significantly higher than in the other treatments. There was also a significant difference in phosphorus concentration between the control group and the IMTA treatments (ANOVA, p < 0.05). Growth rate, C and N content of the thallus, and mortality of scallop was different between the IMTA treatments. The nutrient uptake rate and nutrient reduction efficiency of ammonium and phosphorus changed with different cultivation density and time. The maximum reduction efficiency of ammonium and phosphorus was 83.7% and 70.4%, respectively. The maximum uptake rate of ammonium and phosphorus was 6.3 and 3.3 A mu mol g(-1) DW h(-1). A bivalve/seaweed biomass ratio from 1:0.33 to 1:0.80 (treatments 2, 3, and 4) was preferable for efficient nutrient uptake and for maintaining lower nutrient levels. Results indicate that G. lemaneiformis can efficiently absorb the ammonium and phosphorus from scallop excretion and is a suitable candidate for IMTA.

Potential P limitation leads to excess N in the pearl river estuarine coastal plume

There is excess nitrate (NO3) in the Pearl River coastal plume in the southern waters of Hong Kong in summer. We hypothesize that phosphorus (P) limitation controls the utilization of excess NO3 due to the high N:P ratio in the Pearl River. To test this hypothesis, we conducted two 1-day cruises on July 13 and 19, 2000 to examine the response of the phytoplankton to P additions with respect to changes in biomass, uptake of nutrients and nutrient uptake ratios using a batch incubation of natural water samples collected from the Pearl River estuary and adjacent coastal waters. At a station (E1, salinity =5) in the Pearl River estuary, the N/P ratio at the surface was 46:1, (64 muM DIN: 1.3 muM PO4) and decreased to 24:1 (12 muM DIN: 0.5 muM PO4) downstream at a station (Stn 26, salinity =26) in the coastal plume south of Hong Kong. Without a P addition, NO3 in the water samples collected at E1 could not be depleted during a 9 day incubation (similar to20 muM NO3 remaining). With a P addition, NO3 disappeared completely on day 6 with the depletion of the added PO4 (2-3 muM). This was also true for a station, E4 (salinity= 15) further downstream, but within the estuary. At Stn 26, in the coastal plume south of Hong Kong, NO3 (similar to11.5 muM) was eventually depleted without the addition of PO4, but it took 8 days instead of 5 days for Stn E4. The uptake ratio of dissolved inorganic nitrogen (DIN) to PO4, without a P addition was 51:1, 43:1 and 46:1 for Stns E1, E4 and 26, respectively. With a P addition, the DIN/PO4 uptake ratio decreased to 20:1, 14:1 and 12:1, respectively, for the 3 stations. These results clearly indicate potential P limitation to utilization of NO3 in the Pearl River estuary, resulting in excess NO3 in waters of the coastal plume downstream of the estuary, some of which would eventually be transported offshore. High uptake ratios of N:P without a P addition (43N:1P) suggest that phytoplankton have a nitrogen uptake capacity in excess of the Redfield ratio of 16N: 1P by 2.5-3 times. The value of 2.5-3 times was likely a maximum that should have contained a contribution of P released from desorption of P from sediments or from regeneration by zooplankton grazing and bacterial activity during the incubation of natural water samples. Without a P addition, however, phytoplankton biomass did not increase. This means that P turnover rates or regeneration may allow phytoplankton to take up additional N in excess of the Redfield ratio and store it, but without increasing the algal biomass. Therefore, high ambient N:P ratios in excess of the Redfield ratio do indicate potential P limitation to phytoplankton biomass in this estuarine coastal ecosystem. (C) 2004 Elsevier Ltd. All rights reserved.

Nutritional Control of L1 Arrest and Recovery in Caenorhabditis elegans by Insulin-like Peptides and Signaling

Animals must coordinate development with fluctuating nutrient availability. Nutrient availability governs post-embryonic development in Caenorhabditis elegans: larvae that hatch in the absence of food do not initiate post-embryonic development but enter "L1 arrest" (or "L1 diapause") and can survive starvation for weeks, while rapidly resume normal development once get fed. Insulin-like signaling (IIS) has been shown to be a key regulator of L1 arrest and recovery. However, the C. elegans genome encodes 40 insulin-like peptides (ILPs), and it is unknown which peptides participate in nutritional control of L1 arrest and recovery. Work in other contexts has identified putative receptor agonists and antagonists, but the extent of specificity versus redundancy is unclear beyond this distinction.

We measured mRNA expression dynamics with high temporal resolution for all 40 insulin-like genes during entry into and recovery from L1 arrest. Nutrient availability influences expression of the majority of insulin-like genes, with variable dynamics suggesting complex regulation. We identified 13 candidate agonists and 8 candidate antagonists based on expression in response to nutrient availability. We selected ten candidate agonists (daf-28, ins-3, ins-4, ins-5, ins-6, ins-7, ins-9, ins-26, ins-33 and ins-35) for further characterization in L1 stage larvae. We used destabilized reporter genes to determine spatial expression patterns. Expression of candidate agonists was largely overlapping in L1 stage larvae, suggesting a role of the intestine, chemosensory neurons ASI and ASJ, and the interneuron PVT in systemic control of L1 development. Transcriptional regulation of candidate agonists was most significant in the intestine, as if nutrient uptake was a more important influence on transcription than sensory perception. Scanning in the 5' upstream promoter region of these 40 ILPs, We found that transcription factor PQM-1 and GATA putative binding sites are depleted in the promoter region of antagonists. A novel motif was also found to be over-represented in ILPs.

Phenotypic analysis of single and compound deletion mutants did not reveal effects on L1 recovery/developmental dynamics, though simultaneous disruption of ins-4 and daf-28 extended survival of L1 arrest without enhancing thermal tolerance, while overexpression of ins-4, ins-6 or daf-28 shortened L1 survival. Simultaneous disruption of several ILPs showed a temperature independent, transient dauer phenotype. These results revealed the relative redundancy and specificity among agonistic ILPs.

TGF- β and steroid hormone (SH) signaling have been reported to control the dauer formation along with IIS. Our preliminary results suggest they may also mediate the IIS control of L1 arrest and recovery, as the expression of several key components of TGF-β and SH signaling pathway genes are negatively regulated by DAF-16, and loss-of-function of these genes partially represses daf-16 null phenotype in L1 arrest, and causes a retardation in L1 development.

In summary, my dissertation study focused on the IIS, characterized the dynamics and sites of ILPs expression in response to nutrient availability, revealed the function of specific agonistic ILPs in L1 arrest, and suggested potential cross-regulation among IIS, TGF-β signaling and SH signaling in controlling L1 arrest and recovery. These findings provide insights into how post-embryonic development is governed by insulin-like signaling and nutrient availability.

Mechanisms shaping size structure and functional diversity of phytoplankton communities in the ocean

The factors regulating phytoplankton community composition play a crucial role in structuring aquatic food webs. However, consensus is still lacking about the mechanisms underlying the observed biogeographical differences in cell size composition of phytoplankton communities. Here we use a trait-based model to disentangle these mechanisms in two contrasting regions of the Atlantic Ocean. In our model, the phytoplankton community can self-assemble based on a trade-off emerging from relationships between cell size and (1) nutrient uptake, (2) zooplankton grazing, and (3) phytoplankton sinking. Grazing 'pushes' the community towards larger cell sizes, whereas nutrient uptake and sinking 'pull' the community towards smaller cell sizes. We find that the stable environmental conditions of the tropics strongly balance these forces leading to persistently small cell sizes and reduced size diversity. In contrast, the seasonality of the temperate region causes the community to regularly reorganize via shifts in species composition and to exhibit, on average, bigger cell sizes and higher size diversity than in the tropics. Our results raise the importance of environmental variability as a key structuring mechanism of plankton communities in the ocean and call for a reassessment of the current understanding of phytoplankton diversity patterns across latitudinal gradients.

Trait-based representation of diatom functional diversity in a plankton functional type model of the eutrophied southern North Sea

We introduce a trait-based description of diatom functional diversity to an existing plankton functional type (PFT) model, implemented for the eutrophied coastal ecosystem in the Southern Bight of the North Sea. The trait-based description represents a continuum of diatom species, each characterized by a distinct cell volume, and includes size dependence of four diatom traits: the maximum growth rate, the half-saturation constants for nutrient uptake, the photosynthetic efficiency, and the relative affinity of copepods for diatoms. Through competition under seasonally varying forcing, the fitness of each diatom varies throughout time, and the outcome of competition results in a changing community structure. The predicted seasonal change in mean cell volume of the community is supported by field observations: smaller diatoms, which are more competitive in terms of resource acquisition, prevail during the first spring bloom, whereas the summer bloom is dominated by larger species which better resist grazing. The size-based model is used to determine the ecological niche of diatoms in the area and identifies a range of viable sizes that matches observations. The general trade-off between small, competitive diatoms and large, grazing-resistant species is a convenient framework to study patterns in diatom functional diversity. PFT models and trait-based approaches constitute promising complementary tools to study community structure in marine ecosystems.

Farmer perception of suitable conditions for slurry application compared with decision support system recommendations

The application of slurry nutrients to land can be associated with unintended losses to the environment depending on soil and weather conditions. Correct timing of slurry application, however, can increase plant nutrient uptake and reduce losses. A decision support system (DSS), which predicts optimum conditions for slurry spreading based on the Hybrid Soil Moisture Deficit (HSMD) model, was investigated for use as a policy tool. The DSS recommendations were compared to farmer perception of suitable conditions for slurry spreading for three soil drainage classes (well, moderate and poorly drained) to better understand on farm slurry management practices and to identify potential conflict with farmer opinion. Six farmers participated in a survey over two and a half years, during which they completed a daily diary, and their responses were compared to Soil Moisture Deficit (SMD) calculations and weather data recorded by on farm meteorological stations. The perception of land drainage quality differed between farmers and was related to their local knowledge and experience. It was found that the allocation of grass fields to HSMD drainage classes using a visual assessment method aligned farmer perception of drainage at the national scale. Farmer opinion corresponded to the theoretical understanding that slurry should not be applied when the soil is wetter than field capacity, i.e. when drainage can occur. While weather and soil conditions (especially trafficability) were the principal reasons given by farmers not to spread slurry, farm management practices (grazing and silage) and current Nitrates Directive policies (closed winter period for spreading) combined with limited storage capacities were obstacles to utilisation of slurry nutrients. Despite the slightly more restrictive advice of the DSS regarding the number of suitable spreading opportunities, the system has potential to address an information deficit that would help farmers to reduce nutrient losses and optimise plant nutrient uptake by improved slurry management. The DSS advice was in general agreement with the farmers and, therefore, they should not be resistant to adopting the tool for day to day management.

The influence of water motion on the growth rate of the kelp Laminaria hyperborea

The kelp Laminaria hyperborea is a dominant component of the subtidal nearshore ecosystem and is subjected to a heterogeneous wave and current climate. Water motion is known to influence physiological processes in macroalgae such as photosynthesis and nutrient uptake attributed to mass-transfer limitation. The study attempts to establish the effect of water motion on the growth rates of blades and elongation rates of the stipes of L. hyperborea at adjacent wave-exposed and wave-sheltered locations over a 12month period from field observations. The observations were supported by detailed physical and chemical measurements (light, temperature, seawater nutrient concentrations and hydrodynamics) and of tissue carbon and nitrogen concentrations together with δ¹³carbon. Despite a 30% difference in the root mean square of the velocity (Vel_rms) between the two survey locations, there was no evidence to suggest that water motion had any direct influence on the growth rates of either the blades or elongation of stipes of L. hyperborea. No significant differences were observed between either environmental or plant physiological variables between the sheltered and exposed locations. Using an integral velocity parameter (Vel_rms) the present study also highlighted the importance of the tidally induced current component of water flow in the subtidal zone. 

Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi

Les champignons mycorhiziens arbusculaires (CMA) sont très répandus dans le sol où ils forment des associations symbiotiques avec la majorité des plantes appelées mycorhizes arbusculaires. Le développement des CMA dépend fortement de la plante hôte, de telle sorte qu'ils ne peuvent vivre à l'état saprotrophique, par conséquent ils sont considérés comme des biotrophes obligatoires. Les CMA forment une lignée évolutive basale des champignons et ils appartiennent au phylum Glomeromycota. Leurs mycélia sont formés d’un réseau d’hyphes cénocytiques dans lesquelles les noyaux et les organites cellulaires peuvent se déplacer librement d’un compartiment à l’autre. Les CMA permettent à la plante hôte de bénéficier d'une meilleure nutrition minérale, grâce au réseau d'hyphes extraradiculaires, qui s'étend au-delà de la zone du sol explorée par les racines. Ces hyphes possèdent une grande capacité d'absorption d’éléments nutritifs qui vont être transportés par ceux-ci jusqu’aux racines. De ce fait, les CMA améliorent la croissance des plantes tout en les protégeant des stresses biotiques et abiotiques. Malgré l’importance des CMA, leurs génétique et évolution demeurent peu connues. Leurs études sont ardues à cause de leur mode de vie qui empêche leur culture en absence des plantes hôtes. En plus leur diversité génétique intra-isolat des génomes nucléaires, complique d’avantage ces études, en particulier le développement des marqueurs moléculaires pour des études biologiques, écologiques ainsi que les fonctions des CMA. C’est pour ces raisons que les génomes mitochondriaux offrent des opportunités et alternatives intéressantes pour étudier les CMA. En effet, les génomes mitochondriaux (mt) publiés à date, ne montrent pas de polymorphismes génétique intra-isolats. Cependant, des exceptions peuvent exister. Pour aller de l’avant avec la génomique mitochondriale, nous avons besoin de générer beaucoup de données de séquençages de l’ADN mitochondrial (ADNmt) afin d’étudier les méchanismes évolutifs, la génétique des population, l’écologie des communautés et la fonction des CMA. Dans ce contexte, l’objectif de mon projet de doctorat consiste à: 1) étudier l’évolution des génomes mt en utilisant l’approche de la génomique comparative au niveau des espèces proches, des isolats ainsi que des espèces phylogénétiquement éloignées chez les CMA; 2) étudier l’hérédité génétique des génomes mt au sein des isolats de l’espèce modèle Rhizophagus irregularis par le biais des anastomoses ; 3) étudier l’organisation des ADNmt et les gènes mt pour le développement des marqueurs moléculaires pour des études phylogénétiques. Nous avons utilisé l’approche dite ‘whole genome shotgun’ en pyroséquençage 454 et Illumina HiSeq pour séquencer plusieurs taxons de CMA sélectionnés selon leur importance et leur disponibilité. Les assemblages de novo, le séquençage conventionnel Sanger, l’annotation et la génomique comparative ont été réalisés pour caractériser des ADNmt complets. Nous avons découvert plusieurs mécanismes évolutifs intéressant chez l’espèce Gigaspora rosea dans laquelle le génome mt est complètement remanié en comparaison avec Rhizophagus irregularis isolat DAOM 197198. En plus nous avons mis en évidence que deux gènes cox1 et rns sont fragmentés en deux morceaux. Nous avons démontré que les ARN transcrits les deux fragments de cox1 se relient entre eux par épissage en trans ‘Trans-splicing’ à l’aide de l’ARN du gene nad5 I3 qui met ensemble les deux ARN cox1.1 et cox1.2 en formant un ARN complet et fonctionnel. Nous avons aussi trouvé une organisation de l’ADNmt très particulière chez l’espèce Rhizophagus sp. Isolat DAOM 213198 dont le génome mt est constitué par deux chromosomes circulaires. En plus nous avons trouvé une quantité considérable des séquences apparentées aux plasmides ‘plasmid-related sequences’ chez les Glomeraceae par rapport aux Gigasporaceae, contribuant ainsi à une évolution rapide des ADNmt chez les Glomeromycota. Nous avons aussi séquencé plusieurs isolats de l’espèces R. irregularis et Rhizophagus sp. pour décortiquer leur position phylogénéque et inférer des relations évolutives entre celles-ci. La comparaison génomique mt nous montré l’existence de plusieurs éléments mobiles comme : des cadres de lecture ‘open reading frames (mORFs)’, des séquences courtes inversées ‘short inverted repeats (SIRs)’, et des séquences apparentées aux plasimdes ‘plasmid-related sequences (dpo)’ qui impactent l’ordre des gènes mt et permettent le remaniement chromosomiques des ADNmt. Tous ces divers mécanismes évolutifs observés au niveau des isolats, nous permettent de développer des marqueurs moléculaires spécifiques à chaque isolat ou espèce de CMA. Les données générées dans mon projet de doctorat ont permis d’avancer les connaissances fondamentales des génomes mitochondriaux non seulement chez les Glomeromycètes, mais aussi de chez le règne des Fungi et les eucaryotes en général. Les trousses moléculaires développées dans ce projet peuvent servir à des études de la génétique des populations, des échanges génétiques et l’écologie des CMA ce qui va contribuer à la compréhension du rôle primorial des CMA en agriculture et environnement.

La génomique évolutive mitochondriale révèle des échanges génétiques et la ségrégation chez les Gloméromycètes

Les champignons mycorhiziens à arbuscules (CMA) sont des organismes microscopiques du sol qui jouent un rôle crucial dans les écosystèmes naturels et que l’on retrouve dans tous les habitats de la planète. Ils vivent en relation symbiotique avec la vaste majorité des plantes terrestres. Ils sont des biotrophes obligatoires, c'est-à-dire qu'ils ne peuvent croître qu'en présence d'une plante hôte. Cette symbiose permet entre autres à la plante d'acquérir des nutriments supplémentaires, en particulier du phosphore et du nitrate. Malgré le fait que cette symbiose apporte des services importants aux écosystèmes, la richesse des espèces, la structure des communautés, ainsi que la diversité fonctionnelle des CMA sont mal connues et l'approfondissement des connaissances dans ces domaines dépend d’outils de diagnostic moléculaire. Cependant, la présence de polymorphisme nucléaire intra-isolat combiné à un manque de données génomiques dans différents groupes phylogénétique de ces champignons complique le développement de marqueurs moléculaires et la détermination de l'affiliation évolutive à hauts niveaux de résolution (c.a.d. entre espèces génétiquement similaires et/ou isolats de la même espèce). . Pour ces raisons, il semble une bonne alternative d’utiliser un système génétique différent en ciblant le génome mitochondrial, qui a été démontré homogène au sein d'un même isolat de CMA. Cependant, étant donné le mode de vie particulier de ces organismes, une meilleure compréhension des processus évolutifs mitochondriaux est nécessaire afin de valoriser l'utilisation de tels marqueurs dans des études de diversité et en génétique des populations. En ce sens, mon projet de doctorat consistait à investiguerétudier: i) les vecteurs de divergences inter-isolats et -espèces génétiquement rapprochéesphylogénétiquement apparentées, ii) la plasticité des génomes mitochondriaux, iii) l'héritabilité mitochondriale et les mécanismes potentiels de ségrégation, ainsi que iv) la diversité mitochondriale intra-isolat in situ. À l'aide de la génomique mitochondriale comparative, en utilisant le séquençage nouvelle génération, on a démontré la présence de variation génétique substantielle inter-isolats et -espèces, engendrées par l'invasion d'éléments mobiles dans les génomes mitochondriaux des CMA, donnant lieu à une évolution moléculaire rapide des régions intergéniques. Cette variation permettait de développer des marqueurs spécifiques à des isolats de la même espèce. Ensuite, à l'aide d'une approche analytique par réseaux de gènes sur des éléments mobiles, on a été en mesure de démontrer des évènements de recombinaisons homologues entre des haplotypes mitochondriaux distincts, menant à des réarrangements génomiques. Cela a permis d'ouvrir les perspectives sur la dynamique mitochondriale et l'hétéroplasmie dans un même isolatsuggère une coexistence de différents haplotypes mitochondriaux dans les populations naturelles et que les cultures monosporales pourraient induirent une sous-estimation de la diversité allélique mitochondriale. Cette apparente contradiction avec l'homogénéité mitochondriale intra-isolat généralement observée, a amené à investiguer étudier les échanges génétiques à l'aide de croisements d'isolats génétiquement distincts. Malgré l'observation de quelques spores filles hétéroplasmiques, l'homoplasmie était le statut par défaut dans toutes les cultures monosporales, avec un biais en faveur de l'un des haplotypes parentaux. Ces résultats suggèrent que la ségrégation opère durant la formation de la spore et/ou le développement de la coloniedu mycélium. De plus, ils supportent la présence d'une machinerie protéique de ségrégation mitochondriale chez les CMAAMF, où l'ensemble des gènes impliqués dans ce mécanisme ont été retrouvé et sont orthologues aux autres champignons. Finalement, on est revenue aux sources avecon a étudié le polymorphisme mitochondrial intra-isolat à l'aide d'une approche conventionnelle de PCR en utilisant une Taq polymérase de haute fidélité, suivie de clonage et de séquençage Sanger, sur deux isolats de R. irregularis. Cela a permis l'observation d'hétéroplasmie in situ, ainsi que la co-expression de variantes de variantes de protéines'ARNm dans une souche in vitro. Les résultats suggèrent que d'autres études basées sur le séquençage nouvelle génération aurait potentiellement ignorée cette variation, offrant ainsi plusieurs nouveaux arguments permettant de considérer les CMA comme des organismes possédant une population de génomes mitochondriaux et nucléaires distincts.

Genetic variation of and environmental effects on inducibility of resistance in tomatoes (Solanum lycopersicum L.) to Phytophthora infestans (Mont) de Bary

Many plant strengtheners are promoted for their supposed effects on nutrient uptake and/or resistance induction (IR). In addition, many organic fertilizers are supposed to enhance plant health and several studies have shown that tomatoes grown organically are more resistant to late blight, caused by Phytophthora infestans to tomatoes grown conventionally. Much is known about the mechanisms underlying IR. In contrast, there is no systematic knowledge about genetic variation for IR. Therefore, the following questions were addressed in the presented dissertation: (i) Is there genetic variation among tomato genotypes for inducibility of resistance to P. infestans? (ii) How do different PS compare with the chemical inducer BABA in their ability to IR? (iii) Does IR interact with the inducer used and different organic fertilizers? A varietal screening showed that contrary to the commonly held belief IR in tomatoes is genotype and isolate specific. These results indicate that it should be possible to select for inducibility of resistance in tomato breeding. However, isolate specificity also suggests that there could be pathogen adaptation. The three tested PS as well as two of the three tested organic fertilisers all induced resistance in the tomatoes. Depending on PS or BABA variety and isolate effects varied. In contrast, there were no variety and isolate specific effects of the fertilisers and no interactions with the PS and fertilisers. This suggests that the different PS should work independent of the soil substrate used. In contrast the results were markedly different when isolate mixtures were used for challenge inoculations. Plants were generally less susceptible to isolate mixtures than to single isolates. In addition, the effectiveness of the PS was greater and more similar to BABA when isolate mixtures were used. The fact that the different PS and BABA differed in their ability to induce resistance in different host genotype -pathogen isolate combinations puts the usefulness of IR as a breeding goal in question. This would result in varieties depending on specific inducers. The results with the isolate mixtures are highly relevant. On the one hand they increase the effectiveness of the resistance inducers. On the other hand, measures that increase the pathogen diversity such as the use of diversified host populations will also increase the overall resistance of the hosts. For organic tomato production the results indicate that it is possible to enhance the tomato growing system with respect to plant health management by using optimal fertilisers, plant strengtheners and any measures that increase system diversity.