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posted to medicago qtl symbiosis
by maren
on 2012-12-01 13:31:23
Abstract
Mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. To date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. In the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in the initiation of ...
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by Jordi Comadran, Benjamin Kilian, Joanne Russell, et al.Luke Ramsay, Nils Stein, Martin Ganal, Paul Shaw, Micha Bayer, William Thomas, David Marshall, Pete Hedley, Alessandro Tondelli, Nicola Pecchioni, Enrico Francia, Viktor Korzun, Alexander Walther, Robbie Waugh
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posted to aphid symbiosis virus
by maren
on 2012-11-29 18:51:57
Abstract
Terrestrial arthropods are often infected with heritable bacterial symbionts, which may themselves be infected by bacteriophages. However, what role, if any, bacteriophages play in the regulation and maintenance of insect–bacteria symbioses is largely unknown. Infection of the aphid Acyrthosiphon pisum by the bacterial symbiont Hamiltonella defensa confers protection against parasitoid wasps, but only when H. defensa is itself infected by the phage A. pisum secondary endosymbiont (APSE). Here, we use a controlled genetic background and correlation-based assays to show that loss ...
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posted to lichen phylogeography
by maren
on 2012-11-25 17:14:29
Abstract
In lichen symbiosis, fungal and algal partners form close associations, often codispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate symbiotic system in Europe, we genotyped the fungal and algal symbionts of the epiphytic lichen Lobaria pulmonaria at eight and seven microsatellite loci, respectively, and analysed about 4300 L. pulmonaria thalli from 142 ...
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Abstract
The human gut harbours a large and genetically diverse population of symbiotic microbes that both feed and protect the host. Evolutionary theory, however, predicts that such genetic diversity can destabilise mutualistic partnerships. How then can the mutualism of the human microbiota be explained? Here we develop an individual-based model of host-associated microbial communities. We first demonstrate the fundamental problem faced by a host: The presence of a genetically diverse microbiota leads to the dominance of the fastest growing microbes instead of ...
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posted to no-tag
by maren
on 2012-11-13 05:56:09
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by Noah Fierer, Scott Ferrenberg, Gilberto E. Flores, et al.Antonio González, Jordan Kueneman, Teresa Legg, Ryan C. Lynch, Daniel McDonald, Joseph R. Mihaljevic, Sean P. O'Neill, Matthew E. Rhodes, Se J. Song, William A. Walters
Abstract
The human body is inhabited by billions of microbial cells and these microbial symbionts play critical roles in human health. Human-associated microbial communities are diverse, and the structure of these communities is variable across body habitats, through time, and between individuals. We can apply concepts developed by plant and animal ecologists to better understand and predict the spatial and temporal patterns in these communities. Due to methodological limitations and the largely unknown natural history of most microbial taxa, this integration of ...
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Abstract
Environmental drivers of biodiversity can be identified by relating patterns of community similarity to ecological factors. Community variation has traditionally been assessed by considering changes in species composition and more recently by incorporating phylogenetic information to account for the relative similarity of taxa. Here, we describe how an important class of measures including Bray-Curtis, Canberra, and UniFrac can be extended to allow community variation to ...
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Abstract
Aims Low numbers of rhizobia in soil or inoculants delay nodulation and decrease symbiotic legume productivity. This study investigated the effect of co-inoculation with a helper bacterium, Pseudomonas fluorescens WSM3457 on the Medicago truncatula - Ensifer (Sinorhizobium) medicae WSM419 symbiosis challenged by a low inoculum dose. Methods In a glasshouse experiment the effect of co-inoculation with WSM3457 on the kinetics of nodule initiation and development was assessed 5, 7, 10, 14, 17, 21, and 42 days after inoculation of M. truncatula ...
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by Matthias Schleuning, Jochen Fründ, Alexandra-Maria Klein, et al.Stefan Abrahamczyk, Ruben Alarcón, Matthias Albrecht, Georg K. S. Andersson, Simone Bazarian, Katrin Böhning-Gaese, Riccardo Bommarco, Bo Dalsgaard, D. Matthias Dehling, Ariella Gotlieb, Melanie Hagen, Thomas Hickler, Andrea Holzschuh, Christopher N. Kaiser-Bunbury, Holger Kreft, Rebecca J. Morris, Brody Sandel, William J. Sutherland, Jens-Christian Svenning, Teja Tscharntke, Stella Watts, Christiane N. Weiner, Michael Werner, Neal M. Williams, Camilla Winqvist, Carsten F. Dormann, Nico Blüthgen
Abstract
Species-rich tropical communities are expected to be more specialized than their temperate counterparts [13]. Several studies have reported increasing biotic specialization toward the tropics [47], whereas others have not found latitudinal trends once accounting for sampling bias [8, 9] or differences in plant diversity [10, 11]. Thus, the direction of the latitudinal specialization gradient remains contentious. With an unprecedented global data set, we investigated how biotic specialization between plants and animal pollinators or seed dispersers is associated with latitude, past and ...
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Abstract
Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application ...
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posted to medicago myc_factor
by maren
on 2012-10-02 06:25:45
Abstract
The formation of root nodules and arbuscular mycorrhizal (AM) roots is controlled by a common signaling pathway including the calcium/calmodulin-dependent kinase Doesn't Make Infection3 (DMI3). While nodule initiation by lipochitooligosaccharide (LCO) Nod factors is well characterized, diffusible AM fungal signals were only recently identified as sulfated and nonsulfated LCOs. Irrespective of different outcomes, the perception of symbiotic LCOs in Medicago truncatula is mediated by the ...
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Abstract
The effect of inoculation of N 2 fixation by soybean plants, grown in sandy soil was studied in pot experiments. Bradyrhizobium japonicum (Rh) and/or mycorrhizæ, in the presence of basic application of a P fertilizer (super or rock P), and two levels of 15 N-labelled ammonium sulfate (20 and 100 mg N per kg soil), were used. Highest N 2 fixation was observed after a dual inoculation (Rh+VAM), followed by single inoculation (Rh) and by mycorrhizal infection. Higher doses of N ...
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posted to defoliation myc rhizobia soybean
by maren
on 2012-09-30 18:05:02
Abstract
Soybean [Glycine max (L.) Merr. cv. Wells] plants grown in a greenhouse were inoculated with Rhizobium japonicum strain 61A118 and the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus fasciculatum (Thaxt. sensu Gerd.) Gerd. & Trappe. Plants were defoliated (26, 48 and 66%) throughout the growth period and evaluated for VAM colonization, N2, fixation and photosynthesis at harvest (six weeks). Photosynthate stress as a result of defoliation affected nodulation and nodule activity most severely. Colonization of the roots by the VAM fungus was little ...
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Abstract
Soybean plants can form tripartite symbiotic associations with rhizobia and arbuscular mycorrhizal (AM) fungi, but little is known about effects of co-inoculation with rhizobia and AM fungi on plant growth, or their relationships to root architecture as well as nitrogen (N) and phosphorus (P) availability. In the present study, two soybean genotypes contrasting in root architecture were grown in a field experiment to evaluate relationships among soybean root architecture, AMF colonization, and nodulation under natural conditions. Additionally, a soil pot experiment ...
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Abstract
We introduce a theoretical framework that predicts the optimum planting density and maximal yield for an annual crop plant. Two critical parameters determine the trajectory of plant growth and the optimal density, , where canopies of growing plants just come into contact, and competition: (i) maximal size at maturity, , which differs among varieties due to artificial selection for different usable products; and (ii) intrinsic growth rate, g, which may vary with variety and environmental conditions. The model predicts (i) when ...
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posted to medicinal_plants
by maren
on 2012-09-26 23:52:56
Abstract
There is controversy about whether traditional medicine can guide drug discovery, and investment in bioprospecting informed by ethnobotanical data has fluctuated. One view is that traditionally used medicinal plants are not necessarily efficacious and there are no robust methods for distinguishing those which are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogenetic tree representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand, and the ...
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posted to genetic_diversity host-pathogen
by maren
on 2012-09-20 18:52:51
Abstract
It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,’ is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required ...
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posted to arabidopsis cost_resistance fba
by maren
on 2012-09-13 19:49:45
Abstract
* Here, we describe our updated mathematical model of Arabidopsis thaliana Columbia metabolism, which adds the glucosinolates, an important group of secondary metabolites, to the reactions of primary metabolism. In so doing, we also describe the evolutionary origins of the enzymes involved in glucosinolate synthesis. We use this model to address a long-standing question in plant evolutionary biology: whether or not apparently defensive compounds such as glucosinolates are metabolically costly to produce. * We use flux balance analysis to estimate the ...
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posted to host_control lotus mixed_nodule
by maren
on 2012-09-13 19:48:17
Abstract
* To sample the natural variation in genes controlling compatibility in the legume–rhizobium symbiosis, we isolated rhizobia from nodules of endemic Lotus species from 21 sites across Europe. * The majority of isolates were identified as Mesorhizobium- or Bradyrhizobium-related and formed nitrogen-fixing root nodules on Lotus corniculatus and L. pendunculatus, respectively, thus confirming previously defined cross-inoculation groups. * Rhizobium leguminosarum (Rl) strain Norway, isolated from L. corniculatus nodules, displayed an exceptional phenotypic variation on different Lotus genotypes. On L. burttii, Rl Norway formed infected ...
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Proceedings of the Royal Society B: Biological Sciences, Vol. 279, No. 1745. (22 October 2012), pp. 4156-4164, doi:10.1098/rspb.2012.1449
posted to epistasis
by maren
on 2012-09-13 19:46:41
Abstract
Epistasis between mutations in two genes is thought to reflect an interdependence of their functions. While sometimes epistasis is predictable using mechanistic models, its roots seem, in general, hidden in the complex architecture of biological networks. Here, we ask how epistasis can be quantified based on the mathematical dependence of a system-level trait (e.g. fitness) on lower-level traits (e.g. molecular or cellular properties). We first focus on a model in which fitness is the difference between a benefit and a cost ...
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Abstract
Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help ...
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Abstract
Natural variation has been observed for various traits in Arabidopsis thaliana. Here, we investigated natural variation in the context of physiological and transcriptional responses to the phytohormone auxin, a key regulator of plant development. A survey of the general extent of natural variation to auxin stimuli revealed significant physiological variation among 20 genetically diverse natural accessions. Moreover, we observed dramatic variation on the global transcriptome ...
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Abstract
This manuscript describes the NIH Human Microbiome Project, including a brief review of human microbiome research, a history of the project, and a comprehensive overview of the consortium's recent collection of publications analyzing the human microbiome. ...
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Abstract
Gut epithelial cells contact both commensal and pathogenic bacteria, and proper responses to these bacteria require a balance of positive and negative regulatory signals. In the Drosophila intestine, peptidoglycan-recognition proteins (PGRPs), including PGRP-LE, play central roles in bacterial recognition and activation of immune responses, including induction of the IMD-NF-κB pathway. We show that bacteria recognition is regionalized in the Drosophila gut with various functional regions ...
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Abstract
Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species’ traits (body size and trophic position). We find ...
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posted to gxe
by maren
on 2012-08-15 18:22:18
Abstract
Theory predicts that genetic variation in phenotypic plasticity (genotype × environment interaction or G × E) should be eroded by selection acting across environments. However, it appears that G × E is often maintained under selection, although not universally. This variation in the presence and strength of G × E requires explanation. Here I ask whether the explanation may lie in the grain of the environment at which G × E is expressed. The grain (or grain size) of the environment refers to the scale of environmental heterogeneity relative ...
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by Irene Stefanini, Leonardo Dapporto, Jean-Luc Legras, et al.Antonio Calabretta, Monica Di Paola, Carlotta De Filippo, Roberto Viola, Paolo Capretti, Mario Polsinelli, Stefano Turillazzi, Duccio Cavalieri
Abstract
Saccharomyces cerevisiae is one of the most important model organisms and has been a valuable asset to human civilization. However, despite its extensive use in the last 9,000 y, the existence of a seasonal cycle outside human-made environments has not yet been described. We demonstrate the role of social wasps as vector and natural reservoir of S. cerevisiae during all seasons. We provide experimental evidence that queens of social wasps overwintering as adults (Vespa crabro and Polistes spp.) can harbor yeast ...
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Abstract
A comprehensive understanding of host-pathogen interactions requires a knowledge of the associated gene expression changes in both the pathogen and the host. Traditional, probe-dependent approaches using microarrays or reverse transcription PCR typically require the pathogen and host cells to be physically separated before gene expression analysis. However, the development of the probe-independent RNA sequencing (RNA-seq) approach has begun to revolutionize transcriptomics. Here, we assess the ...
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Proceedings of the Royal Society B: Biological Sciences, Vol. 279, No. 1743. (22 September 2012), pp. 3742-3748, doi:10.1098/rspb.2012.0769
posted to coevolution host-parasite model
by maren
on 2012-08-14 01:05:21
Abstract
Antagonistic coevolution between hosts and parasites can have a major impact on host population structures, and hence on the evolution of social traits. Using stochastic modelling techniques in the context of bacteria–virus interactions, we investigate the impact of coevolution across a continuum of host–parasite genetic specificity (specifically, where genotypes have the same infectivity/resistance ranges (matching alleles, MA) to highly variable ranges (gene-for-gene, GFG)) on population genetic structure, and on the social behaviour of the host. We find that host cooperation is ...
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Abstract
Simulation models of the evolution of genes in a branched metabolic pathway subject to stabilizing selection on flux are described and analyzed. The models are based either on metabolic control theory (MCT), with the assumption that enzymes are far from saturation, or on Michaelis-Menten kinetics, which allows for saturation and near saturation. Several predictions emerge from the models: (1) flux control evolves to be concentrated at pathway branch points, including the first enzyme in the pathway. (2) When flux is far ...
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Abstract
* • Shoot architecture, including the number and location of branches, is a crucial aspect of plant function, morphological diversification, life history evolution and crop domestication. Genes controlling shoot architecture are well characterized in, and largely conserved across, model flowering plant species. The role of these genes in the evolution of morphological diversity in natural populations, however, has not been explored. We identify axillary meristem outgrowth as a primary driver of divergent branch number and life histories in two locally adapted ...
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by Franciska T. de Vries, Pete Manning, Jerry R. Tallowin, et al.Simon R. Mortimer, Emma S. Pilgrim, Kathryn A. Harrison, Phil J. Hobbs, Helen Quirk, Bill Shipley, Johannes H. Cornelissen, Jens Kattge, Richard D. Bardgett, Nancy Johnson
Abstract
The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape-scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. ...
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by Marcus J. Claesson, Ian B. Jeffery, Susana Conde, et al.Susan E. Power, Eibhlis M. O/'Connor, Siobhan Cusack, Hugh M. B. Harris, Mairead Coakley, Bhuvaneswari Lakshminarayanan, Orla O/'Sullivan, Gerald F. Fitzgerald, Jennifer Deane, Michael O/'Connor, Norma Harnedy, Kieran O/'Connor, Denis O/'Mahony, Douwe van Sinderen, Martina Wallace, Lorraine Brennan, Catherine Stanton, Julian R. Marchesi, Anthony P. Fitzgerald, Fergus Shanahan, Colin Hill, R. Paul Ross, Paul W. O/'Toole
Abstract
Alterations in intestinal microbiota composition are associated with several chronic conditions, including obesity and inflammatory diseases. The microbiota of older people displays greater inter-individual variation than that of younger adults. Here we show that the faecal microbiota composition from 178 elderly subjects formed groups, correlating with residence location in the community, day-hospital, rehabilitation or in long-term residential care. However, clustering of subjects by diet separated ...
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posted to microbial_community
by maren
on 2012-08-08 15:53:19
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posted to no-tag
by maren
on 2012-08-08 15:52:09
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posted to no-tag
by maren
on 2012-08-08 15:51:46
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posted to no-tag
by maren
on 2012-08-08 15:51:23
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Abstract
Plants simultaneously interact with a plethora of species both belowground and aboveground, which can result in indirect effects mediated by plants. Studies incorporating plant genetic variation indicate that indirect effects mediated by plants may be a significant factor influencing the ecology and evolution of species within a community. Here, we present findings of a Quantitative Trait Locus (QTL) mapping study, where we mapped a rhizobacteria-aphid indirect effect onto the barley genome. We measured the size of aphid populations on barley when ...
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Abstract
Third party species, which interact with one or both partners of a pairwise species interaction, can shift the ecological costs and the evolutionary trajectory of the focal interaction. Shared genes that mediate a host’s interactions with multiple partners have the potential to generate evolutionary constraints, making multi-player interactions critical to our understanding of the evolution of key interaction traits. Using a field quantitative genetics approach, we studied phenotypic and genetic correlations among legume traits for rhizobium and herbivore interactions in two ...
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The American Naturalist, Vol. 180, No. 3. (September 2012), pp. 394-402, doi:10.1086/667194
posted to trade-offs
by maren
on 2012-08-07 19:20:32
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Abstract
The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, we analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania. These samples, which were derived ...
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Abstract
Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks; however, examples of dynamic DNA methylation are largely limited to gene imprinting. Here we report an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system. Profiling the DNA methylomes of plants exposed to bacterial pathogen, ...
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posted to aba arabidopsis host-pathogen pgpr sa
by maren
on 2012-08-07 04:57:03
Abstract
Plants exist in a complex multitrophic environment where they interact with and compete for resources with other plants, microbes and animals. Plants have a complex array of defense mechanisms such as the cell wall covered with a waxy cuticle serving as a potent physical barrier. While some pathogenic fungi infect plants by penetrating through the cell wall, many bacterial pathogens invade plants primarily through stomata on the leaf surface. Entry of the foliar pathogen, Pseudomonas syringae pathovar tomato DC3000 (hereafter PstDC3000), ...
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Abstract
Rhizobia are soil bacteria able to develop a nitrogen-fixing symbiosis with legumes. They are taxonomically spread among the alpha and beta subclasses of the Proteobacteria. Mimosa pudica, a tropical invasive weed, has been found to have an affinity for beta-rhizobia, including species within the Burkholderia and Cupriavidus genera. In this study, we describe the diversity of M. pudica symbionts in the island of New Caledonia, which is characterized by soils with high heavy metal content, especially of Ni. By using a plant-trapping ...
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Abstract
* •Functional traits, their plasticity and their integration in a phenotype have profound impacts on plant performance. We developed structural equation models (SEMs) to evaluate their relative contribution to promote invasiveness in plants along resource gradients. * •We compared 20 invasive–native phylogenetically and ecologically related pairs. SEMs included one morphological (root-to-shoot ratio (R/S)) and one physiological (photosynthesis nitrogen-use efficiency (PNUE)) trait, their plasticities in response to nutrient and light variation, and phenotypic integration among 31 traits. Additionally, these components were related ...
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by Linlin Qi, Jiao Yan, Yanan Li, et al.Hongling Jiang, Jiaqiang Sun, Qian Chen, Haoxuan Li, Jinfang Chu, Cunyu Yan, Xiaohong Sun, Yuanjie Yu, Changbao Li, Chuanyou Li
posted to phytohormone plant-path
by maren
on 2012-08-05 21:45:00
Abstract
* •Although the role of auxin in biotrophic pathogenesis has been extensively studied, relatively little is known about its role in plant resistance to necrotrophs. * •Arabidopsis thaliana mutants defective in different aspects of the auxin pathway are generally more susceptible than wild-type plants to the necrotrophic pathogen Alternaria brassicicola. We show that A. brassicicola infection up-regulates auxin biosynthesis and down-regulates the auxin transport capacities of infected plants, these effects being partially dependent on JA signaling. We also show that these effects ...
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posted to drought gxgxe microbiome
by maren
on 2012-08-01 03:04:02
Abstract
The diversity changes in the rhizosphere microbial communities of four grass species submitted to a stress (drought) and/or a disturbance (defoliation) were examined in a full factorial common garden experiment. The diversity of bacterial and fungal communities was determined using Single Strand Conformation Polymorphism (SSCP) and multivariate analyses of variance were performed to test for the effect of experimental factors on microbial beta diversity, i.e. the variation of microbial community composition among pots. Plant species identity contributed the most to microbial ...
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