Diversity arrays technology (DArT) markers in apple for genetic linkage maps

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.     

Can the negative plant–soil feedback of Jacobaea vulgaris be explained by autotoxicity?

Field and bioassay studies with Jacobaea vulgaris (ragwort) have shown that plants grow poorly in soil originating from the rhizosphere of this species and that this can influence the dynamics of ragwort populations during secondary succession. In the present study we examined whether the negative effect of ragwort on conspecifics may be due to autotoxicity. First, we experimentally established that ragwort exerts negative plant–soil feedback. We subsequently examined the inhibitory effects on germination and seedling performance of different strengths of aqueous extracts made from shoot and root tissues of ragwort, and from soil in which ragwort had been growing. The effects of the extracts were tested for seedlings growing in sterilised soil or in glass beads with water. Finally, the inhibitory effect of entire root fragments on seedling performance was tested. We observed that performance of seedlings growing in glass beads was significantly reduced by the high and medium strength root and shoot extracts. Extracts made from soil did not differ significantly from the control, and seedlings growing in sterilised soil were also not affected by ragwort extracts. Seed germination was significantly reduced by the high strength shoot extract only. The root length of seedlings growing in water with root fragments was reduced significantly. We conclude that under laboratory conditions ragwort can be autotoxic and discuss the role that autotoxicity may play in influencing the dynamics of ragwort populations during secondary succession.     

Reciprocal effects of litter from exotic and congeneric native plant species via soil nutrients

Invasive exotic plant species are often expected to benefit exclusively from legacy effects of their litter inputs on soil processes and nutrient availability. However, there are relatively few experimental tests determining how litter of exotic plants affects their own growth conditions compared to congeneric native plant species. Here, we test how the legacy of litter from three exotic plant species affects their own performance in comparison to their congeneric natives that co-occur in the invaded habitat. We also analyzed litter effects on soil processes. In all three comparisons, soil with litter from exotic plant species had the highest respiration rates. In two out of the three exotic-native species comparisons, soil with litter from exotic plant species had higher inorganic nitrogen concentrations than their native congener, which was likely due to higher initial litter quality of the exotics. When litter from an exotic plant species had a positive effect on itself, it also had a positive effect on its native congener. We conclude that exotic plant species develop a legacy effect in soil from the invaded range through their litter inputs. This litter legacy effect results in altered soil processes that can promote both the exotic plant species and their native congener.     

Mechanism of control of root-feeding nematodes by mycorrhizal fungi in the dune grass Ammophila arenaria

Root-feeding herbivores can affect plant performance and the composition of natural plant communities, but there is little information about the mechanisms that control root herbivores in natural systems. This study explores the interactions between the pioneer dune grass Ammophila arenaria, arbuscular mycorrhizal fungi (AMF) and the root-feeding nematode Pratylenchus penetrans. Our objectives were to determine whether AMF can suppress nematode infection and reproduction and to explore the mechanisms of nematode control by AMF. A sequential inoculation experiment and a split-root experiment were designed to analyse the importance of plant tolerance and resistance and of direct competition between AMF and P. penetrans for the root herbivore and the plant. Root infection and multiplication of P. penetrans were significantly reduced by the native inoculum of AMF. Plant preinoculation with AMF further decreased nematode colonization and reproduction. Nematode suppression by AMF did not occur through a systemic plant response but through local mechanisms. Our results suggest that AMF are crucial for the control of root-feeding nematodes in natural systems and illustrate that locally operating mechanisms are involved in this process.     

Consequences of variation in species diversity in a community of root-feeding herbivores for nematode dynamics and host plant biomass

To date, no study has explicitly addressed effects of variation in species diversity of root‐feeding herbivores on host plant biomass. Root‐feeding nematodes typically occur in multi‐species communities. In a three‐year field experiment, we investigated how variation in species diversity of root‐feeding nematodes affected nematode dynamics and response of the dune grass Ammophila arenaria to root‐feeder activity. This plant species needs regular burial by fresh beach sand to remain vigorous, suggesting that A. arenaria benefits from a temporary escape from root‐feeding soil organisms and that root‐feeders are involved in plant degeneration in stabilized dunes. We created series of ceased and continued sand burial and added the endoparasitic nematodes Meloidogyne maritima, Heterodera arenaria and Pratylenchus penetrans alone or in combination to A. arenaria. We included treatments with and without the whole soil community, measured plant biomass and quantified numbers of nematodes. Addition of H. arenaria and P. penetrans decreased numbers of M. maritima juveniles and delayed the first appearance in time of both juveniles and females, while numbers of males only decreased when plants had been buried. Burial with sand and addition of the other two endoparasites affected numbers of H. arenaria juveniles, while numbers of P. penetrans were low and not affected. Shoot biomass of A. arenaria was lower when M. maritima had been added alone than when the three species had been added together. Addition of root zone soil decreased biomass of all plant parts. Burial with sand decreased aboveground shoot biomass, whereas it increased belowground shoot and root biomass. Our results point at idiosyncratic effects of nematode diversity on A. arenaria biomass. Heterodera arenaria and P. penetrans protected their host by reducing numbers and delaying activity of M. maritima to a later stage in the growth season, when root‐feeding activity was less harmful for plant biomass development.     

Earthworms counterbalance the negative effect of microorganisms on plant diversity and enhance the tolerance of grasses to nematodes

Plant community composition is affected by a wide array of soil organisms with diverse feeding modes and functions. Former studies dealt with the high diversity and complexity of soil communities by focusing on particular functional groups in isolation, by grouping soil organisms into body size classes or by using whole communities from different origins. Our approach was to investigate both the individual and the interaction effects of highly abundant soil organisms (microorganisms, nematodes and earthworms) to evaluate their impacts on grassland plant communities. Earthworms increased total plant community biomass by stimulating root growth. Nematodes reduced the biomass of grasses, but this effect was alleviated by the presence of earthworms. Non-leguminous forb biomass increased in the presence of nematodes, probably due to an alleviation of the competitive strength of grasses by nematodes. Microorganisms reduced the diversity and evenness of the plant community, but only in the absence of earthworms. Legume biomass was not affected by soil organisms, but Lotus corniculatus flowered earlier in the presence of microorganisms and the number of flowers decreased in the presence of nematodes. The results indicate that earthworms have a profound impact on the structure of grassland plant communities by counterbalancing the negative effects of plant-feeding nematodes on grasses and by conserving the evenness of the plant community. We propose that interacting effects of functionally dissimilar soil organisms on plant community performance have to be taken into account in future studies, since individual effects of soil organism groups may cancel out each other in functionally diverse soil communities.     

Timing of simulated aboveground herbivory influences population dynamics of root-feeding nematodes

Aims

A soil-plant-atmosphere continuum (SPAC) model for simulating tree transpiration (Ep) with variable water stress and water distribution in the soil is presented. The model couples a sun/shade approach for the canopy with a discrete representation of the soil in different layers and compartments.

Methods

To test its performance, the outputs from the simulations are compared to those from an experiment using trees of olive ‘Picual’ and almond ‘Marinada’ with the root system split into two. Trees are subjected to different irrigation phases in which one side of the root system is dried out while the other is kept wet.

Results

The model is able to accurately predict Ep (R² and the efficiency factor (EF) around 0.9) in the two species studied. The use of a function that modulates the uptake capacity of a root according to the soil water content was necessary to track the fluxes observed from each split part. It was also appropriate to account for root clumping to match the measured and modelled leaf water potential.

Conclusions

Coupling the sun/shade approach with the soil multi-compartment solution provides a useful tool to explore tree Ep for different degrees of water availability and distribution.

     

Differential responses of soil bacteria,fungi, archaea and protists to plant species richness and plant functional group identity

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454‐pyrosequencing to analyse the soil microbial community composition in a long‐term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.     

Plant responses to variable timing of aboveground clipping and belowground herbivory depend on plant age

Aims Plants use different types of responses such as tolerance and induced defense to mitigate the effects of herbivores. The direction and magnitude of both these plant responses can vary with plant age. However, most studies have focused on aboveground herbivory, whereas important feeding occurs belowground. Here, we tested the hypothesis that plant tolerance and defense following shoot damage or root herbivory depends on plant age.     

Basolateral Invasion and Trafficking of Campylobacter jejuni in Polarized Epithelial Cells

Campylobacter jejuni is a major cause of bacterial diarrheal disease. Most enteropathogenic bacteria including C. jejuni can invade cultured eukaryotic cells via an actin- and/or microtubule-dependent and an energy-consuming uptake process. Recently, we identified a novel highly efficient C. jejuni invasion pathway that involves bacterial migration into the subcellular space of non-polarized epithelial cells (termed subvasion) followed by invasion from the cell basis. Here we report cellular requirements of this entry mechanism and the subsequent intracellular trafficking route of C. jejuni in polarized islands of Caco-2 intestinal epithelial cells. Advanced microscopy on infected cells revealed that C. jejuni invades the polarized intestinal cells via the subcellular invasion pathway. Remarkably, invasion was not blocked by the inhibitors of microtubule dynamics colchicine or paclitaxel, and was even enhanced after disruption of host cell actin filaments by cytochalasin D. Invasion also continued after dinitrophenol-induced cellular depletion of ATP, whereas this compound effectively inhibited the uptake of invasive Escherichia coli. Confocal microscopy demonstrated that intracellular C. jejuni resided in membrane-bound CD63-positive cellular compartments for up to 24 h. Establishment of a novel luciferase reporter-based bacterial viability assay, developed to overcome the limitations of the classical bacterial recovery assay, demonstrated that a subset of C. jejuni survived intracellularly for up to 48 h. Taken together, our results indicate that C. jejuni is able to actively invade polarized intestinal epithelial cells via a novel actin- and microtubule-independent mechanism and remains metabolically active in the intracellular niche for up to 48 hours.