Plant-Microbe Symbiosis
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Do trees communicate?

Root networks, trees, forest, mycorrhizae, (Do trees communicate?
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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The Evolution of Calcium-Based Signalling in Plants

The Evolution of Calcium-Based Signalling in Plants | Plant-Microbe Symbiosis | Scoop.it
The calcium-based intracellular signalling system is used ubiquitously to couple extracellular stimuli to their characteristic intracellular responses. It is becoming clear from genomic and physiological investigations that while the basic elements in the toolkit are common between plants and animals, evolution has acted in such a way that, in plants, some components have diversified with respect to their animal counterparts, while others have either been lost or have never evolved in the plant lineages. In comparison with animals, in plants there appears to have been a loss of diversity in calcium-influx mechanisms at the plasma membrane. However, the evolution of the calcium-storing vacuole may provide plants with additional possibilities for regulating calcium influx into the cytosol. Among the proteins that are involved in sensing and responding to increases in calcium, plants possess specific decoder proteins that are absent from the animal lineage. In seeking to understand the selection pressures that shaped the plant calcium-signalling toolkit, we consider the evolution of fast electrical signalling. We also note that, in contrast to animals, plants apparently do not make extensive use of cyclic-nucleotide-based signalling. It is possible that reliance on a single intracellular second-messenger-based system, coupled with the requirement to adapt to changing environmental conditions, has helped to define the diversity of components found in the extant plant calcium-signalling toolkit.

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Rescooped by Jean-Michel Ané from Transport in plants and fungi
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Cell-specific expression of plant nutrient transporter genes in orchid mycorrhizae 

Cell-specific expression of plant nutrient transporter genes in orchid mycorrhizae  | Plant-Microbe Symbiosis | Scoop.it
Orchid mycorrhizal protocorms and roots are heterogeneous structures composed of different plant cell-types, where cells colonized by intracellular fungal coils (the pelotons) are close to non-colonized plant cells. Moreover, the fungal coils undergo rapid turnover inside the colonized cells, so that plant cells containing coils at different developmental stages can be observed in the same tissue section. Here, we have investigated by laser microdissection (LMD) the localization of specific plant gene transcripts in different cell-type populations collected from mycorrhizal protocorms and roots of the Mediterranean orchid Serapias vomeracea colonized by Tulasnella calospora. RNAs extracted from the different cell-type populations have been used to study plant gene expression, focusing on genes potentially involved in N uptake and transport and previously identified as up-regulated in symbiotic protocorms. Results clearly showed that some plant N transporters are differentially expressed in cells containing fungal coils at different developmental stages, as well as in non-colonized cells, and allowed the identification of new functional markers associated to coil-containing cells.

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Nitrate transporters: an overview in legumes

Nitrate transporters: an overview in legumes | Plant-Microbe Symbiosis | Scoop.it
Nitrate plays an essential role during plant development as nutrient and also as signal molecule, in both cases working via the activity of nitrate transporters. To date, few studies on NRT2 or NPF nitrate transporters in legumes have been reported, and most of those concern Lotus japonicus and Medicago truncatula. A molecular characterization led to the identification of 4 putative LjNRT2 and 37 putative LjNPF gene sequences in L. japonicus. In M. truncatula, the NRT2 family is composed of 3 putative members. Using the new genome annotation of M. truncatula (Mt4.0), we identified, for this review, 97 putative MtNPF sequences, including 32 new sequences relative to previous studies. Functional characterization has been published for only two MtNPF genes, encoding nitrate transporters of M. truncatula. Both transporters have a role in root system development via abscisic acid signaling: MtNPF6.8 acts as a nitrate sensor during the cell elongation of the primary root, while MtNPF1.7 contributes to the cellular organization of the root tip and nodule formation. An in silico expression study of MtNPF genes confirmed that NPF genes are expressed in nodules, as previously shown for L. japonicus, suggesting a role for the corresponding proteins in nitrate transport, or signal perception in nodules. This review summarizes our knowledge of legume nitrate transporters and discusses new roles for these proteins based on recent discoveries.
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Ditch the term pathogen

Ditch the term pathogen | Plant-Microbe Symbiosis | Scoop.it
Disease is as much about the host as it is the infectious agent — the focus on microbes is hindering research into treatments, say Arturo Casadevall and Liise-anne Pirofski.

Via nemopeeters
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Excellent... I totally agree. Even having "Plant Pathology" departments reflects a poor and old-fashioned understanding of the biological interactions. We should have "Plant-Microbe Interactions" (PMI) departments. 

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Laser‐ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia

Laser‐ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia | Plant-Microbe Symbiosis | Scoop.it
Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen-fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well characterized symbiosis between soybean (Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI–IMS–MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI–IMS–MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis.

Via Christophe Jacquet
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Very interesting paper!

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Composition of the root mycorrhizal community associated with Coffea arabica in Fifa Mountains (Jazan region, Saudi Arabia)

Arbuscular mycorrhizal fungi (AMF) constitute a key functional group of soil biota that can greatly contribute to crop productivity and ecosystem sustainability. They improve nutrient uptake and enhance the ability of plants to cope with abiotic stresses. The presence of AMF in coffee (Coffea arabica L.) plant roots have been reported in several locations but not in Saudi Arabia despite the fact that coffee has been in cultivation here since ancient times. The objective of the present study was to investigate the diversity of AMF communities colonizing the roots of coffee trees growing in two sites of Fifa Mountains (south-west Saudi Arabia): site 1 at 700 m altitude and site 2 at 1400 m. The AMF large subunit rDNA regions (LSU) were subjected to nested PCR, cloning, sequencing, and phylogenetic analysis. Microscopic observations indicated higher mycorrhizal intensity (24.3%) and spore density (256 spores/100 g of soil) in site 2 (higher altitude). Phylogenetic analysis revealed 10 phylotypes, six belonging to the family Glomeraceae, two to Claroideoglomercea, one to Acaulosporaceae and one to Gigasporaceae family. Glomus was the dominant genus at both sites and the genus Gigaspora was detected only at site 2. This is the first study reporting the presence of AMF in coffee roots and the composition of this particular mycorrhizal community in Saudi Arabia.
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Arbuscular mycorrhiza effects on plant performance under osmotic stress

At present, drought and soil salinity are among the most severe environmental stresses that affect the growth of plants through marked reduction of water uptake which lowers water potential, leading to osmotic stress. In general, osmotic stress causes a series of morphological, physiological, biochemical, and molecular changes that affect plant performance. Several studies have found that diverse types of soil microorganisms improve plant growth, especially when plants are under stressful conditions. Most important are the arbuscular mycorrhizal fungi (AMF) which form arbuscular mycorrhizas (AM) with approximately 80% of plant species and are present in almost all terrestrial ecosystems. Beyond the well-known role of AM in improving plant nutrient uptake, the contributions of AM to plants coping with osmotic stress merit analysis. With this review, we describe the principal direct and indirect mechanisms by which AM modify plant responses to osmotic stress, highlighting the role of AM in photosynthetic activity, water use efficiency, osmoprotectant production, antioxidant activities, and gene expression. We also discuss the potential for using AMF to improve plant performance under osmotic stress conditions and the lines of research needed to optimize AM use in plant production.

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Bob Reeves's curator insight, July 3, 5:06 PM
Indeed. The University of Guelph (Ontario, Canada) conducted 4 years of efficacy testing on our mycorrhizal inoculate (9 endo + 9 ecto species). The trial simultaneously used a bank of 32 wireless stem psychrometers which monitored the water status (osmotic stress levels) of 8 test/8 control trees 24/7 for several consecutive weeks. The data produced showed that extra soil water was provided to the host plants in comparison to the non-inoculated control group.  About a 30% advantage was enjoyed by the test trees. The results were published in 2015: http://www.rootrescue.com/site/university-of-guelph-data
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Aujourd’hui les microbes avec Marc-André Selosse et les microbes sur tous les tons ! avec la troupe New Science

Aujourd’hui les microbes avec Marc-André Selosse et les microbes sur tous les tons ! avec la troupe New Science | Plant-Microbe Symbiosis | Scoop.it
Avant de découvrir cet univers incroyable, je vais vous présenter une troupe, New Science, qui propose des comédies musicales improvisées, à partir d’un thème scientifique.

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Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion

Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion | Plant-Microbe Symbiosis | Scoop.it
Plants engineer the rhizosphere to their advantage by secreting various nutrients and secondary metabolites. Coupling transcriptomic and metabolomic analyses of the pea (Pisum sativum) rhizosphere, a suite of bioreporters has been developed in Rhizobium leguminosarum bv viciae strain 3841, and these detect metabolites secreted by roots in space and time. Fourteen bacterial lux fusion bioreporters, specific for sugars, polyols, amino acids, organic acids, or flavonoids, have been validated in vitro and in vivo. Using different bacterial mutants (nodC and nifH), the process of colonization and symbiosis has been analyzed, revealing compounds important in the different steps of the rhizobium-legume association. Dicarboxylates and sucrose are the main carbon sources within the nodules; in ineffective (nifH) nodules, particularly low levels of sucrose were observed, suggesting that plant sanctions affect carbon supply to nodules. In contrast, high myo-inositol levels were observed prior to nodule formation and also in nifH senescent nodules. Amino acid biosensors showed different patterns: a γ-aminobutyrate biosensor was active only inside nodules, whereas the phenylalanine bioreporter showed a high signal also in the rhizosphere. The bioreporters were further validated in vetch (Vicia hirsuta), producing similar results. In addition, vetch exhibited a local increase of nod gene-inducing flavonoids at sites where nodules developed subsequently. These bioreporters will be particularly helpful in understanding the dynamics of root exudation and the role of different molecules secreted into the rhizosphere.

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A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination | Plant-Microbe Symbiosis | Scoop.it
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.

Via Ryohei Thomas Nakano, Ronny Kellner
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Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum)

Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum) | Plant-Microbe Symbiosis | Scoop.it
Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown.
Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study.
Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed.
The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.

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Rescooped by Jean-Michel Ané from Plants & Evolution
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The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects

B vitamins play essential roles in central metabolism. These organic water-soluble molecules act as, or as part of, coenzymes within the cell. Unlike land plants, many eukaryotic algae are auxotrophic for certain B vitamins. Recent progress in algal genetic resources and environmental chemistry have promoted a renewal of interest in the role of vitamins in governing phytoplankton dynamics, and illuminated amazing versatility in phytoplankton vitamin metabolism. Accumulating evidence demonstrates metabolic complexity in the production and bioavailability of different vitamin forms, coupled with specialized acquisition strategies to salvage and remodel vitamin precursors. Here, I describe recent advances and discuss how they redefine our view of the way in which vitamins are cycled in aquatic ecosystems and their importance in structuring phytoplankton communities.


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Rescooped by Jean-Michel Ané from microbial pathogenesis and plant immunity
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Interplay Between Innate Immunity and the Plant Microbiota 

Interplay Between Innate Immunity and the Plant Microbiota  | Plant-Microbe Symbiosis | Scoop.it
The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Via Stéphane Hacquard, Jim Alfano
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Carbon flow from plant to arbuscular mycorrhizal fungi is reduced under phosphorus fertilization. Plant and Soil 

Background and aims

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts highly specialized upon phosphorus (P) supply to their hosts. We investigated plants’ ability to regulate carbon (C) flow to AMF depending on the soil P supply.

 

Methods

Leek (Allium porrum), medic (Medicago truncatula), and ryegrass (Lolium perenne) were subjected to AMF inoculation and/or P fertilization in a glasshouse experiment. The C flows were traced using 13C pulse labelling.

 

Results

Mycorrhizal P uptake responses were lowered by P fertilization in all tested plant species. Independently from the C flow to the roots, the C flow to AMF-signature fatty acid 16:1ω5 were reduced by P fertilization in leek and ryegrass (but not in medic). Calculated mycorrhizal C costs ranged between 0.9% and 10.5% of the plant C budget.

 

Conclusions

Suppression of the C flow from the plants to AMF resulted from both reduced abundance of AMF in the roots and lowered relative C income per unit of AMF biomass in P-fertilized pots. Although inconsistencies amongst different plant species demand caution in making generalizations, these results suggest an active role of host plants in regulating the C flow to AMF.

 

Keywords:  Arbuscular mycorrhiza Carbon allocation Mycorrhizal cost Symbiotic benefits Biological market theory Phosphorus fertilization


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Ronald Noë's curator insight, July 23, 3:02 AM
An interesting result in line with biological market theory. The mentioning of BMT in the keywords suggests a more elaborated theoretical treatment and/or reference to similar results than what is actually discussed in the text.

This is all there is (a citation from the Introduction): "Recently, a model based on biological market theory predicted that AMF lose fitness when the plant can acquire more P directly (i.e.via roots) because plants become less reliant on the AMF and that the trade between the plants and AMF may cease at sufficiently high levels of P availability to plants (Wyatt et al. 2014 ). Analogously to commodity prices’ dependence on the fluctuating balance between supply and demand, market models further predicted the decrease of P’s 'price' (i.e. the C allocated to the AMF per unit of P delivered) with increasing P supply (Werner and Kiers 2015 )"
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Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula

Arbuscular mycorrhizas (AM) are the most common symbiotic associations between plant's root compartment and fungi. They provide nutritional benefit (mostly inorganic phosphate, Pi) leading to improved growth, and non-nutritional benefits including defense responses to environmental cues throughout the host plant, which in return delivers carbohydrates to the symbiont. However, how transcriptional and metabolic changes occurring in leaves of AM plants differ from those induced by Pi fertilization is poorly understood. We investigated systemic changes in the leaves of mycorrhized Medicago truncatula in conditions with no improved Pi status, and compared them with those induced by high Pi treatment in non-mycorrhized plants. Microarray-based genome-wide profiling indicated upregulation by mycorrhization of genes involved in flavonoid, terpenoid, jasmonic acid (JA) and abscisic acid (ABA) biosynthesis as well as enhanced expression of MYC2, the master regulator of JA-dependent responses. Accordingly, total anthocyanins and flavonoids increased, and most flavonoid species were enriched in AM-leaves. Both the AM- and Pi treatment co-repressed iron homeostasis genes resulting in lower levels of available iron in leaves. In addition, higher levels of cytokinins were found in leaves of AM- and Pi-treated plants whereas the level of ABA was specifically increased in AM-leaves. Treatment of non-mycorrhized plants with either ABA or JA induced upregulation of MYC2, whereas JA also induced upregulation of flavonoid and terpenoid biosynthetic genes. Based on these results, we propose that mycorrhization and Pi fertilization share cytokinin-mediated improved shoot growth, whereas enhanced ABA biosynthesis and JA-regulated flavonoid and terpenoid biosynthesis in leaves is specific to mycorrhization.

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Organic fertilizers alter the composition of pathogens and arbuscular mycorrhizal fungi in maize roots

Roots of agricultural crops, including maize, are hosts of different microorganisms, many beneficial, like plant growth and health-promoting arbuscular mycorrhizal fungi (AMF), as well as pathogens including Pythium, Polymyxa and Microdochium. To improve crop nutrition and health, profound knowledge is required regarding how agricultural practices affect field populations of root-associated microorganisms. Hence, the objective of this work was to evaluate the effect of crop genotype and organic fertilizers on the plant growth performance of maize and their root-associated microorganisms. The experiment was conducted as a fully factorial greenhouse pot experiment with maize cultivars (two land races and two hybrids) and organic fertilizers (green manure, cow manure and compost) as the two main factors. Plants were harvested 8 weeks after sowing. In general, the different maize cultivars responded similarly to the applications of the organic fertilizers. Cow manure and compost increased plant growth, whereas green manure had limited effect on plant growth. Root colonization with AMF was reduced by green manure with rape. Infection with the root pathogens Pythium and Polymyxa was reduced by all organic fertilizers, whereas in contrast, infection with Microdochium increased with the majority of the organic fertilizers applied. In conclusion, both maize genotype and organic fertilizers affect the abundance of AMF and root pathogens in maize, which should be considered when developing management strategies of these root-inhabiting microorganisms.
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The evolution of host-symbiont dependence

The evolution of host-symbiont dependence | Plant-Microbe Symbiosis | Scoop.it

Organisms across the tree of life form symbiotic partnerships with microbes for metabolism, protection and resources. While some hosts evolve extreme dependence on their symbionts, others maintain facultative associations. Explaining this variation is fundamental to understanding when symbiosis can lead to new higher-level individuals, such as during the evolution of the eukaryotic cell. Here we perform phylogenetic comparative analyses on 106 unique host–bacterial symbioses to test for correlations between symbiont function, transmission mode, genome size and host dependence. We find that both transmission mode and symbiont function are correlated with host dependence, with reductions in host fitness being greatest when nutrient-provisioning, vertically transmitted symbionts are removed. We also find a negative correlation between host dependence and symbiont genome size in vertically, but not horizontally, transmitted symbionts. These results suggest that both function and population structure are important in driving irreversible dependence between hosts and symbionts.


Via Pierre-Marc Delaux
Jean-Michel Ané's insight:

Very interesting but I have serious concerns with this paper...

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Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: patterns, mechanisms, and open questions

Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: patterns, mechanisms, and open questions | Plant-Microbe Symbiosis | Scoop.it

In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research.

First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity-stability theory.

Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects often occurred mostly in addition to, but not instead of, effects of plant species richness.

Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances.

Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle.

Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity-ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions.

Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed with diversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of the belowground microbial community. Manipulation experiments where particular organisms, e.g. belowground invertebrates, were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and water fluxes.

Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. The effect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect of a more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production from high-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse ‘High Nature Value Grasslands’ are multifunctional and can deliver a range of ecosystem services including production-related services.

A final task was to assess the importance of potential artefacts in biodiversity–ecosystem functioning relationships, caused by the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed a plot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables. Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number of biological reasons, as shown in plant-soil feedback experiments.

To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in an ecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitude of biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, among the multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have received limited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targeted analyses. Thus, from the current results in the Jena Experiment it seems likely that the positive biodiversity effect results from several mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of more plant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resource uptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity research has matured such that predictive approaches testing particular mechanisms are now possible.
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The Nodule Microbiome: N2-Fixing Rhizobia Do Not Live Alone 

The Nodule Microbiome: N2-Fixing Rhizobia Do Not Live Alone  | Plant-Microbe Symbiosis | Scoop.it
For decades, rhizobia were thought to be the only nitrogen-fixing inhabitants of legume nodules, and biases in culture techniques prolonged this belief. However, other bacteria, which are not typical rhizobia, are often detected within nodules obtained from soil, thus revealing the existence of a phytomicrobiome where the interaction among the individuals is not only complex, but also likely to affect the behavior and fitness of the host plant. Many of these nonrhizobial bacteria are nitrogen fixers, and some also induce nitrogen-fixing nodules on legume roots. Even more striking is the incredibly diverse population of bacteria residing within nodules that elicit neither nodulation nor nitrogen fixation. Yet, this community exists within the nodule, albeit clearly out-numbered by nitrogen-fixing rhizobia. Few studies of the function of these nodule-associated bacteria in nodules have been performed, and to date, it is not known whether their presence in nodules is biologically important or not. Do they confer any benefits to the Rhizobium-legume nitrogen-fixing symbiosis, or are they parasites/saprophytes, contaminants, or commensals? In this review, we highlight the lesser-known bacteria that dwell within nitrogen-fixing nodules and discuss their possible role in this enclosed community as well as any likely benefits to the host plant or to the rhizobial inhabitants of the nodule. Although many of these nodule inhabitants are not capable of nitrogen fixation, they have the potential to enhance legume survival especially under conditions of environmental stress. This knowledge will be useful in defining strategies to employ these bacteria as bioinoculants by themselves or combined with rhizobia. Such an approach will enhance rhizobial performance or persistence as well as decrease the usage of chemical fertilizers and pesticides.

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Can stress response genes be used to improve the symbiotic performance of rhizobia?

Can stress response genes be used to improve the symbiotic performance of rhizobia? | Plant-Microbe Symbiosis | Scoop.it
Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.
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Rescooped by Jean-Michel Ané from The Plant Microbiome
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Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism | Plant-Microbe Symbiosis | Scoop.it
The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated. Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles. The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.

Via Stéphane Hacquard
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The microRNA390/TAS3 pathway mediates in symbiotic nodulation and lateral root growth

Legume roots form two types of post-embryonic organs, lateral roots and symbiotic nodules. Nodule formation is the result of the interaction of legumes with rhizobia, and requires the mitotic activation and differentiation of root cells, as well as an independent, but coordinated, program that allows infection by rhizobia. MicroRNA390 (miR390) is an evolutionarily conserved miRNA that targets the non-coding Trans Acting Short Interference RNA3 (TAS3). Cleavage of TAS3 by ARGONAUTE7 results in the production of tasiRNAs, which target mRNAs encoding the AUXIN RESPONSE FACTOR 2 (ARF2), ARF3 and ARF4. Here, we show that activation of the miR390/TAS3 regulatory module by overexpression of miR390 in Medicago truncatula promotes lateral root growth, but prevents nodule organogenesis, rhizobial infection and the induction of two key nodulation genes, the Nodulation signaling Pathway 1 (NSP1) and NSP2. Accordingly, inactivation of the miR390/TAS3 module, either by expression of a miR390 target mimicry construct or mutations in ARGONAUTE7, enhances nodulation and rhizobial infection, alters the spatial distribution of the nodules and increases the percentage of nodules with multiple meristems. Our results revealed a key role of the miR390/TAS3 pathway in legumes as a modulator of lateral root organs, playing opposite roles in lateral root and nodule development.

Jean-Michel Ané's insight:

Wow... fantastic paper.

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Rescooped by Jean-Michel Ané from Adaptive Evolution and Speciation
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UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties 

UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties  | Plant-Microbe Symbiosis | Scoop.it
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed.
Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties.
Availability: UpSetR is available at
https://github.com/hms-dbmi/UpSetR/
and released under the MIT License. A Shiny app is available at
https://gehlenborglab.shinyapps.io/upsetr/

Via Ronny Kellner
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The paleosymbiosis hypothesis: host plants can be colonised by root symbionts that have been inactive for centuries to millenia

Paleoecologists have speculated that post-glacial migration of tree species could have been facilitated by mycorrhizal symbionts surviving glaciation as resistant propagules belowground. The general premise of this idea, which we call the ‘paleosymbiosis hypothesis’, is that host plants can access and be colonised by fungal root symbionts that have been inactive for millennia. Here, we explore the plausibility of this hypothesis by synthesising relevant findings from a diverse literature. For example, the paleoecology literature provided evidence of modern roots penetrating paleosols containing ancient (>6000 years) fungal propagules, though these were of unknown condition. With respect to propagule longevity, the available evidence is of mixed quality, but includes convincing examples consistent with the paleosymbiosis hypothesis (i.e. >1000 years viable propagules). We describe symbiont traits and environmental conditions that should favour the development and preservation of an ancient propagule bank, and discuss the implications for our understanding of soil symbiont diversity and ecosystem functioning. We conclude that the paleosymbiosis hypothesis is plausible in locations where propagule deposition and preservation conditions are favourable (e.g. permafrost regions). We encourage future belowground research to consider and explore the potential temporal origins of root symbioses.
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Steve Marek's curator insight, June 29, 11:56 AM
Table 1 blows me away!  So what happens when we lose permafrost-preserved soils to warming?
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Evolution of Hormone Signaling Networks in Plant Defense

Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens. In this review, we explore the evolution of defense hormone signaling networks by combining the model plant-based knowledge about molecular components mediating phytohormone signaling and cross talk with available genome information of other plant species.Wehighlight conserved hubs in hormone cross talk and discuss evolutionary advantages of defense hormone cross talk. Finally, we examine possibilities of engineering hormone cross talk for improvement of plant fitness and crop production.

Jean-Michel Ané's insight:

I like Figure 2...

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