Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways.

ABSTRACT: BACKGROUND: Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. RESULTS: Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. CONCLUSIONS: This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.

Buttress form of the central African rain forest tree Microberlinia bisulcata, and its possible role in nutrient acquisition

Buttressing is a trait special to tropical trees but explanations for its occurrence remain inconclusive. The two main hypotheses are that they provide structural support and/or promote nutrient acquisition. Studies of the first are common but the second has received much less attention. Architectural measurements were made on adult and juvenile trees of the ectomycorrhizal species Microberlinia bisulcata, in Korup (Cameroon). Buttressing on this species is highly distinctive with strong lateral extension of surface roots of the juveniles leading to a mature buttress system of a shallow spreading form on adults. This contrasts with more vertical buttresses, closer to the stem, found on many other tropical tree species. No clear relationship between main buttress and large branch distribution was found. Whilst this does not argue against the essential structural role of buttresses for these very large tropical trees, the form on M. bisulcata does suggest a likely second role, that of aiding nutrient acquisition. At the Korup site, with its deep sandy soils of very low phosphorus status, and where most nutrient cycling takes place in a thin surface layer of fine roots and mycorrhizas, it appears that buttress form could develop from soil-surface root exploration for nutrients by juvenile trees. It may accordingly allow M. bisulcata to attain the higher greater competitive ability, faster growth rate, and maximum tree size that it does compared with other co-occurring tree species. For sites across the tropics in general, the degree of shallowness and spatial extension of buttresses of the dominant species is hypothesized to increase with decreasing nutrient availability.

Mineral Nutrition Of Campos Rupestres Plant Species On Contrasting Nutrient-impoverished Soil Types.

In Brazil, the campos rupestres occur over the Brazilian shield, and are characterized by acidic nutrient-impoverished soils, which are particularly low in phosphorus (P). Despite recognition of the campos rupestres as a global biodiversity hotspot, little is known about the diversity of P-acquisition strategies and other aspects of plant mineral nutrition in this region. To explore nutrient-acquisition strategies and assess aspects of plant P nutrition, we measured leaf P and nitrogen (N) concentrations, characterized root morphology and determined the percentage arbuscular mycorrhizal (AM) colonization of 50 dominant species in six communities, representing a gradient of soil P availability. Leaf manganese (Mn) concentration was measured as a proxy for carboxylate-releasing strategies. Communities on the most P-impoverished soils had the highest proportion of nonmycorrhizal (NM) species, the lowest percentage of mycorrhizal colonization, and the greatest diversity of root specializations. The large spectrum of leaf P concentration and variation in root morphologies show high functional diversity for nutritional strategies. Higher leaf Mn concentrations were observed in NM compared with AM species, indicating that carboxylate-releasing P-mobilizing strategies are likely to be present in NM species. The soils of the campos rupestres are similar to the most P-impoverished soils in the world. The prevalence of NM strategies indicates a strong global functional convergence in plant mineral nutrition strategies among severely P-impoverished ecosystems.

Leaf Manganese Accumulation And Phosphorus-acquisition Efficiency.

Plants that deploy a phosphorus (P)-mobilising strategy based on the release of carboxylates tend to have high leaf manganese concentrations ([Mn]). This occurs because the carboxylates mobilise not only soil inorganic and organic P, but also a range of micronutrients, including Mn. Concentrations of most other micronutrients increase to a small extent, but Mn accumulates to significant levels, even when plants grow in soil with low concentrations of exchangeable Mn availability. Here, we propose that leaf [Mn] can be used to select for genotypes that are more efficient at acquiring P when soil P availability is low. Likewise, leaf [Mn] can be used to screen for belowground functional traits related to nutrient-acquisition strategies among species in low-P habitats.

Nutrient dynamics in Queensland savannas: Implications for the sustainability of land clearing for pasture production

Eucalyptus savannas on low nutrient soils are being extensively cleared in Queensland. In this paper we provide background information relevant to understanding nutrient (particularly nitrogen) dynamics in sub/tropical savanna, and review the available evidence relevant to understanding the potential impact of clearing Eucalyptus savanna on nutrient relations. The limited evidence presently available can be used to argue for the extreme positions that: (i) woody vegetation competes with grasses Cor resources. and tree/shrub clearing improves pasture production, (ii) woody vegetation benefits pasture production. At present, the lack of fundamental knowledge about Australian savanna nutrient relations makes accurate predictions about medium- and long-term effects of clearing on nutrient relations in low nutrient savannas difficult. The future of cleared savannas will differ if herbaceous species maintain all functions that woody vegetation has previously held, or if woody species have functions distinct from those of herbaceous vegetation. Research suggests that savanna soils are susceptible to nitrate leaching, and that trees improve the nutrient status of savanna soils in some situations. The nitrogen capital of cleared savanna is at risk if mobile ions are not captured efficiently by the vegetation. and nitrogen input via N-2 fixation from vegetation and microbiotic crusts is reduced. In order to predict clearing effects on savanna nutrient relations, research should be directed to answering (i) how open or closed nutrient cycles are in natural and cleared savanna, (ii) which functions are performed by savanna constituents such as woody and herbaceous vegetation, native and exotic plant species. termites, and microbiotic 7 crusts in relation to nutrient cycles. In the absence of detailed knowledge about savanna functioning, clearing carries the risk of promoting continuous nutrient depiction.

Rhizodeposition of organic carbon by plants with contrasting traits for resource acquisition: responses to different fertility regimes

Background and aims Rhizodeposition plays an important role in mediating soil nutrient availability in ecosystems. However, owing to methodological difficulties (i.e., narrow zone of soil around roots, rapid assimilation by soil microbes) fertility-induced changes in rhizodeposition remain mostly unknown. Methods We developed a novel long-term continuous 13C labelling method to address the effects of two levels of nitrogen (N) fertilization on rhizodeposited carbon (C) by species with different nutrient acquisition strategies. Results Fertility-induced changes in rhizodeposition were modulated by root responses to N availability rather than by changes in soil microbial biomass. Differences among species were mostly related to plant biomass: species with higher total leaf and root biomass also had higher total rhizodeposited C, whereas species with lower root biomass had higher specific rhizodeposited C (per gram root mass). Experimental controls demonstrated that most of the biases commonly associated with this type of experiment (i.e., long-term steady-state labelling) were avoided using our methodological approach. Conclusions These results suggest that the amount of rhizodeposited C from plants grown under different levels of N were driven mainly by plant biomass and root morphology rather than microbial biomass. They also underline the importance of plant characteristics (i.e., biomass allocation) as opposed to traits associated with plant resource acquisition strategies in predicting total C rhizodeposition.

Proteomic analysis of the shistosome tegument and its surface membranes

The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS), and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting the preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, including phosphohydrolases, esterases and carbonic anhydrase were located with their catalytic domains external to the plasma membrane, while five tetraspanins, annexin and dysferlin were implicated in membrane architecture. In contrast, few parasite proteins could be assigned to the membranocalyx but mouse immune response proteins, including three immunoglobulins and two complement factors, were detected, plus host membrane proteins such as CD44, integrin and a complement regulatory protein, testifying to the acquisitive properties of the secreted bilayer.

Disruption of the peritrophic matrix by exogenous chitinase feeding reduces fecundity in Lutzomyia longipalpis females

Lutzomyia longipalpis is the most important vector of visceral leishmaniasis in Brazil. When female sandflies feed on blood, a peritrophic matrix (PM) is formed around the blood bolus. The PM is secreted by midgut cells and composed of proteins, glycoproteins and chitin microfibrils. The PM functions as both a physical barrier against pathogens present in the food bolus and blood meal digestion regulator. Previous studies of mosquitoes and sandflies have shown that the absence of a PM, resulting from adding an exogenous chitinase to the blood meal, accelerates digestion. In the present study, we analysed biological factors associated with the presence of a PM in L. longipalpis females. Insects fed blood containing chitinase (BCC) accelerated egg-laying relative to a control group fed blood without chitinase. However, in the BCC-fed insects, the number of females that died without laying eggs was higher and the number of eggs laid per female was lower. The eggs in both groups were viable and generated adults. Based on these data, we suggest that the absence of a PM accelerates nutrient acquisition, which results in premature egg production and oviposition; however, the absence of a PM reduces the total number of eggs laid per female. Reduced fecundity in the absence of a PM may be due to inefficient nutrient conversion or the loss of the protective role of the PM.

Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices.

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.

Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.

Ecology and evolution of multigenomic arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) form extremely important mutualistic symbioses with most plants. Their role in nutrient acquisition, plant community structure, plant diversity, and ecosystem productivity and function has been demonstrated in recent years. New findings on the genetics and biology of AMF also give us a new picture of how these fungi exist in ecosystems. In this article, I bring together some recent findings that indicate that AMF have evolved to contain multiple genomes, that they connect plants together by a hyphal network, and that these different genomes may potentially move around in this network. These findings show the need for more intensive studies on AMF population biology and genetics in order to understand how they have evolved with plants, to better understand their ecological role, and for applying AMF in environmental management programs and in agriculture. A number of key features of AMF population biology have been identified for future studies and most of these concern the need to understand drift, selection, and genetic exchange in multigenomic organisms, a task that has not previously presented itself to evolutionary biologists.

Evolutionary forces affect multigenomic arbuscular mycorhizal fungi : an experimental approach using Glomus intraradices

Abstract Arbuscular Mycorhizal Fungi (AMF) are important plant symbionts that can improve floristic diversity and ecosystem productivity. These important fungi are obligate biotrophs and form symbioses with roots of the majority of plant species, improving plant nutrient acquisition in exchange of photosynthates. AM fungi are successful both ecologically as they occupy a very large spectrum of environments as well as host range and evolutionarily, as this symbiosis is over 400 million years old. These fungi grow and reproduce clonally by hyphae and multinucleate spores. AMF are coenocytic and recent work has shown that they harbor genetically different nuclei and that AMF populations are genetically diverse. How AMF species diversity is maintained has been addressed theoretically and experimentally at the community level. Much less attention has been drawn to understand how genetic diversity is maintained within populations although closely related individuals are more likely to compete for the same resources and occupy similar niches. How infra-individual genetic diversity is shaped and maintained has received even less attention. In Chapter 2, we show that individuals from a field population may differ in their symbiotic efficiency under reduced phosphate availability: We show there is genetic variation in an AMF field population for fitness-related growth traits in response to different phosphate availability acid host species. Furthermore, AFLP fingerprints of the same individuals growing in contrasting environments diverged suggesting that the composition in nuclei of AMF is dynamical and affected by environmental factors. Thus environmental heterogeneity is likely to play an important role for the maintenance of genetic diversity at the population level. In Chapter 3 we show that single spores do not inherit necessarily the same genetic material. We have found genetic divergences using two different types of molecular marker, as well as phenotypic divergences among single spore lines. Our results stress the importance of considering these organisms as a multilevel hierarchical system and of better knowing their life cycle. They have important consequences for the understanding of AMF genetics, ecology and the development of commercial AMF inocculum. Résumé Les champignons endomycorhiziens arbusculaires (CEA) sont d'importants symbiontes pour les plantes, car ils augmentent la diversité et la productivité des écosystèmes. Ces importants symbiontes sont des biotrophes obligatoires et forment une symbiose avec la plupart des plantes terrestres. Ils améliorent l'acquisition de substances nutritives de leurs hôtes en échange de sucres obtenus par photosynthèse. Ces champignons ont un grand succès écologique, ils colonisent une grande rangée d'environnements ainsi que d'hôtes. Ils ont aussi un succès évolutif certain de part le fait que cette symbiose existe depuis plus de 400 millions d'années. Les CEA sont asexués et croissent clonalement en formant des hyphes et des spores multinuclées. Les CEA sont des coenocytes et des travaux de recherche récents ont montré qu'ils possèdent des noyaux génétiquement différents. D'autres travaux ont aussi révélé que les populations de CEA sont génétiquement diversifiées. Comment la diversité des CEA est maintenue a seulement été adressée par des études théoriques et expérimentalement au niveau des communautés. Très peu d'attention a été portée sur le maintien de la diversité génétique infra et inter populationnelle, or ce sont les individus les plus proches génétiquement qui vont entrer en compétition pour des ressources et niches similaires. La formation et le maintien de la diversité intra-individu des CEA a reçu très peu d'attention. Dans le chapitre 2, nous montrons que des individus CEA d'un même champ différent dans leur efficacité symbiotique lorsque la concentration en phosphoré est réduite. Nous montrons qu'il existe de la variance génétique dans une population de CEA provenant d'un même champ en réponse à différentes concentrations de phosphore, ainsi qu'en réponse à différentes espèces d'hôtes, et ceci pour des traits de croissance vraisemblablement liés au succès reproducteur. De plus grâce à des AFLP nous avons pu montrer que le génome de ces individus subissent des changements lorsqu'ils croissent dans des environnements contrastés. Ceci suggère que les noyaux génétiquement différents des CEA sont des entités dynamiques. Il est fort probable que l'hétérogénéité environnementale joue un rôle dans le maintien de la diversité génétique des populations de CEA. Dans le chapitre 3, nous montrons que toutes les spores d'un même mycélium parental de CEA ne reçoivent pas exactement le même contenu génétique. Nous avons mis en évidence des divergences entre des Lignées monosporales en utilisant deux types de marqueur moléculaires, ainsi que des différences phénotypiques. Nos résutats soulignent l'importance de considézer ces organismes comme dés systëmes hiérarchiques mufti-niveaux, ainsi que de mieux connaître leur cycle de vie. Nos résultats ont d'importantes conséquences pour la compréhension du système génétique des CEA, ainsi que de leur évolution, leur écológie, mais également des conséquences pour la production d' inoccultim commercial.

The mycorrhizal contribution to plant productivity, plant nutrition and soil structure in experimental grassland.

Previous studies have shown that arbuscular mycorrhizal fungi (AMF) can influence plant diversity and ecosystem productivity. However, little is known about the effects of AMF and different AMF taxa on other important community properties such as nutrient acquisition, plant survival and soil structure. We established experimental grassland microcosms and tested the impact of AMF and of different AMF taxa on a number of grassland characteristics. We also tested whether plant species benefited from the same or different AMF taxa in subsequent growing seasons. AMF enhanced phosphorus acquisition, soil aggregation and survival of several plant species, but AMF did not increase total plant productivity. Moreover, AMF increased nitrogen acquisition by some plant species, but AMF had no effect on total N uptake by the plant community. Plant growth responses to AMF were temporally variable and some plant species obtained the highest biomass with different AMF in different years. Hence the results indicate that it may be beneficial for a plant to be colonized by different AMF taxa in different seasons. This study shows that AMF play a key role in grassland by improving plant nutrition and soil structure, and by regulating the make-up of the plant community.

The cooler side of mycorrhizas: their occurrence and functioning at low temperatures

Mycorrhizal associations occur in a range of habitats in which soils are subject to low temperature (≤15 °C) for a significant part of the year. Despite this, most of our understanding of mycorrhizal fungi and their interactions with their plant hosts is based on physiological investigations conducted in the range 20–37 °C using fungi of temperate origin. Comparatively little consideration has been given to the cold edaphic conditions in which many mycorrhizas survive and prosper, and the physiological and ecological consequences of their low temperature environments. In this review, we consider the distribution and persistence of arbuscular and ectomycorrhizal mycorrhizal associations in cold environments and highlight progress in understanding adaptations to freezing resistance and nutrient acquisition at low temperature in mycorrhizal fungi.

Temperature regulation of extracellular proteases in ectomycorrhizal fungi (Hebeloma spp.) grown in axenic culture

Strains of Hebeloma representative of different climatic zones were grown in axenic culture at either 2 °C and 22° or 6° and 22°. Culture filtrates were assayed for proteolytic activity using FITC labelled BSA as a substrate. Assays were run between 0–37°. Growth at low temperature induced greater proteolytic activity (g−1 D.W. mycelium). Many of the strains produced protease(s) which retained significant activity at temperatures as low as 0°, and a thermal optimum between 0–6° with a second optimum at higher temperature. The results are discussed in relation the nutrient acquisition potential of ectomycorrhizal fungi at low temperature and the contribution such cold active proteases might make to the soil enzyme pool.