Origin of the molecular "toolkit" for plant – microbe symbioses
Pierre-Marc Delaux, University of Wisconsin Madison
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Symbiotic associations between plants and microbes
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Jean-Michel Ané
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Nodulation and arbuscular mycorrhization require the activation of plant host symbiotic programs by Nod factors, and Myc-LCOs and COs, respectively. The pathways involved in the perception and downstream signaling of these signals include common and distinct components. Among the distinct components, NSP1, a GRAS transcription factor, has been considered for years to be specifically involved in nodulation.Here, we analyzed the degree of conservation of the NSP1 sequence in arbuscular mycorrhizal (AM) host and non-AM host plants and carefully examined the ability of Medicago truncatula nsp1 mutants to respond to Myc-LCOs and to be colonized by an arbuscular mycorrhizal fungus.In AM-host plants, the selection pressure on NSP1 is stronger than in non-AM host ones. The response to Myc-LCOs and the frequency of mycorrhizal colonization are significantly reduced in the nsp1 mutants.Our results reveal that NSP1, previously described for its involvement in the Nod factor signaling pathway, is also involved in the Myc-LCO signaling pathway. They bring additional evidence on the evolutionary relatedness between nodulation and mycorrhization.
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A new study has demonstrated that plants can use an underground network of fungi to warn each other about incoming insect attacks. Delete the scoop?
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Introduction Agrobacterium is a well-known genus in bacteriology and molecular biology, but research has shown that it cannot easily be separated from the Rhizobium genus, thus all Agrobacterium species should be renamed as Rhizobium species (the earlier name). However there has been some opposition to renaming Agrobacterium, in this article I explain the research and taxonomy, and suggest a solution.
Weir, B.S. (2013) Agrobacterium or Rhizobium, which name to use?, NZ Rhizobia, 27 April 2013. Via IvanOresnik Delete the scoop?
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The second is the legume-rhizobia symbiotic relationship, which enables legumes to have a reliable source of usable nitrogen fixed by a bacteria living inside a root nodule. It's a huge evolutionary advantage for legumes, Frugoli says, adding ...
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Good job Julia! Delete the scoop?
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Coming to a club near you...I am cyanide protected in my leaves, leaves, leaves...SDSU students interpret Thamer et al. (2011). Dual benefit from a belowgrou...
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Sorry... It's totally nerd but I can't help sharing it! Delete the scoop?
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In recent years, mycorrhizal research has undergone rapid expansion. Breakthroughs in genomics and other modern techniques have allowed us to break new ground in multiple domains, such as evolution, physiology, function, community patterns and biogeography of mycorrhizal fungi. The International Conference on Mycorrhiza (ICOM) is the most important platform for mycorrhizal scientists to present and discuss their work in both theoretical and applied areas of mycorrhizal symbiosis. ICOM 7 was held in New Delhi (India), January 6–11, 2013, and attracted over 400 participants from 48 countries. The theme of the conference was ‘Mycorrhiza for All: An Under-Earth Revolution’, stressing the importance of addressing scientific findings within an applied context to strengthen field implementations and improve sustainable agriculture. It addressed the urgent need to apply mycorrhizal research to the environmental crises that threatens our planet. Delete the scoop?
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Explosions, algae blooms, global warming. Why do we need so much ammonium nitrate again? (RT @GreenCartoons: Or our nitrogen fixation fixation. Delete the scoop?
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Bradyrhizobium japonicum was described from soybean root-nodule bacterial isolates. Since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. Strains assigned to B. japonicum Group Ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. Here we summarize published studies indicating that Group Ia strains are different from B. japonicum type strain USDA 6T and its closely related strains, and present new morpho-physiological, genotypic and genomic evidences to support their reclassification into a novel species for which the name Bradyrhizobium diazoefficiens sp. nov. is proposed. The type strain of the novel species is the well-studied USDA 110T strain (=IAM 13628, =CCRC 13528, =NRRL B-4361, =IFO 14792, =TAL 102T, =BCRC 13528, =JCM 10833, =TISTR 339T, =SEMIA 5032T, =3I1B110, =ACCC 15034, =CCT 4249, =NBRC 14792, =NRRL B-4450, =R-12974, CNPSo 46T). Delete the scoop?
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A parallel world of pseudo-academia, with prestigiously titled conferences and journals that will print seemingly anything for a fee, has the scientific community alarmed. Delete the scoop?
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The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant–microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding. Via Jennifer Mach 
Jennifer Mach's curator insight,
April 8, 1:10 PM
Free pdf here, thank you Dangl lab! http://labs.bio.unc.edu/Dangl/pub/pdf/PNAS_2013_Peiffer_RLey_corn_microbiome.pdf Delete the scoop?
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Reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), play an important role in signalling in various cellular processes. The involvement of H2O2 in the Medicago truncatula–Sinorhizobium meliloti symbiotic interaction raises questions about its effect on gene expression. A transcriptome analysis was performed on inoculated roots of M. truncatula in which ROS production was inhibited with diphenylene iodonium (DPI). In total, 301 genes potentially regulated by ROS content were identified 2 d after inoculation. These genes includedMtSpk1, which encodes a putative protein kinase and is induced by exogenous H2O2 treatment. MtSpk1 gene expression was also induced by nodulation factor treatment. MtSpk1 transcription was observed in infected root hair cells, nodule primordia and the infection zone of mature nodules. Analysis with a fluorescent protein probe specific for H2O2 showed that MtSpk1 expression and H2O2 were similarly distributed in the nodule infection zone. Finally, the establishment of symbiosis was impaired by MtSpk1 downregulation with an artificial micro-RNA. Several genes regulated by H2O2 during the establishment of rhizobial symbiosis were identified. The involvement of MtSpk1 in the establishment of the symbiosis is proposed. Delete the scoop?
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Nitrogen is quantitatively the most important nutrient that plants acquire from the soil. It is well established that plant roots take up nitrogen compounds of low molecular mass, including ammonium, nitrate, and amino acids. However, in the soil of natural ecosystems, nitrogen occurs predominantly as proteins. This complex organic form of nitrogen is considered to be not directly available to plants. We examined the long-held view that plants depend on specialized symbioses with fungi (mycorrhizas) to access soil protein and studied the woody heathland plant Hakea actites and the herbaceous model plant Arabidopsis thaliana, which do not form mycorrhizas. We show that both species can use protein as a nitrogen source for growth without assistance from other organisms. We identified two mechanisms by which roots access protein. Roots exude proteolytic enzymes that digest protein at the root surface and possibly in the apoplast of the root cortex. Intact protein also was taken up into root cells most likely via endocytosis. These findings change our view of the spectrum of nitrogen sources that plants can access and challenge the current paradigm that plants rely on microbes and soil fauna for the breakdown of organic matter. Via Kamoun Lab @ TSL 
Kamoun Lab @ TSL's comment,
April 4, 1:34 PM
Highly relevant paper to the root uptake assay debunked by Wawra et al. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-08-12-0200-R
Brett Tyler's comment,
April 26, 7:19 PM
The specific RxLR-dependent uptake of effectors into root tips under discussion at MPMI was always examined using newly formed root tips that lack root hairs. To quote from the Paungfoo-Lonhienne paper scooped here: "Acquisition of intact protein as shown by GFP fluorescence was not observed in newly formed lateral roots that lacked root hairs (data not shown), suggesting that protein uptake depends largely on the presence of root hairs in Hakea and Arabidopsis." Thus this paper is largely irrelevant to the discussion of specific entry, except perhaps to emphasize the importance of the careful controls contained in all the Tyler group's papers published to date, including the latest one in MPMI.
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Symbiotic nitrogen fixation by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. While exchanged molecules imply nitrogen compounds, carbohydrates and also various minerals, knowledge of the molecular basis of plant transporters that mediate those metabolite exchanges is still limited. In this study, we have shown that a multidrug and toxic compound extrusion (MATE) protein, LjMATE1, is specifically induced during nodule formation, which nearly paralleled nodule maturation, in a model legume Lotus japonicus. Reporter gene experiments indicated that the expression of LjMATE1 was restricted to the infection zone of nodules. To characterize the transport function of LjMATE1, we conducted a biochemical analysis using a heterologous expression system, Xenopus oocytes, and found that LjMATE1 is a specific transporter for citrate. The physiological role of LjMATE1 was analyzed after generation of L. japonicus RNA interference (RNAi) lines. One RNAi knock-down line revealed limited growth under nitrogen-deficient conditions with inoculation of rhizobia compared with the controls (the wild type and an RNAi line in which LjMATE1 was not suppressed). It was noteworthy that Fe localization was clearly altered in nodule tissues of the knock-down line. These results strongly suggest that LjMATE1 is a nodule-specific transporter that assists the translocation of Fe from the root to nodules by providing citrate. Delete the scoop?
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The vast majority of vascular plants are capable of forming Delete the scoop?
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Symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti results in the formation on the host roots of new organs, nodules, in which biological nitrogen fixation takes place. In infected cells, rhizobia enclosed in a plant-derived membrane, the symbiosome membrane, differentiate to nitrogen-fixing bacteroids. The symbiosome membrane serves as an interface for metabolite and signal exchanges between the host cells and endosymbionts. At some point during symbiosis, symbiosomes and symbiotic cells are disintegrated, resulting in nodule senescence. The regulatory mechanisms that underlie nodule senescence are not fully understood. Using a forward genetics approach, we have uncovered early senescent nodule 1 (esn1) mutant from a Medicago truncatula fast neutron-induced mutant collection. Nodules on esn1 roots are spherically-shaped, ineffective in nitrogen fixation and senesce early. Atypical amongst fix- mutants isolated so far, bacteroid differentiation and expression of nifH,Leghemoglobin and DNF1 genes are not affected in esn1 nodules, supporting that a process downstream of bacteroid differentiation and nitrogenase gene expression is affected in the esn1 mutant. Expression analysis shows that marker genes involved in senescence, macronutrient degradation and remobilization are greatly upregulated during nodule development in the esn1 mutant, consistent with a role ofESN1 in nodule senescence and symbiotic nitrogen fixation.
Xi J, Chen Y, Nakashima J, Wang SM, Chen R. (2013). Mol Plant Microbe Interact. May 1. [Epub ahead of print] Via IvanOresnik Delete the scoop?
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Arbuscular mycorrhiza (AM) fungi form nutrient-acquiring symbioses with the majority of higher plants. Nutrient exchange occurs via arbuscules, highly branched hyphal structures that are formed within root cortical cells. With a view to identify host genes involved in AM development, we isolated Lotus japonicus AM-defective mutants via a microscopic screen of an EMS-mutagenized population. A standardized mapping procedure was developed that facilitated positioning the defective loci on the genetic map of L. japonicus and, in five cases, identification of mutants of known symbiotic genes. Two additional mutants representing independent loci did not form mature arbuscules during symbiosis with two divergent AM fungal species, but exhibited signs of premature arbuscule arrest or senescence. Marker gene expression patterns indicated that the two mutants are affected in distinct steps of arbuscule development. Both mutants formed wild type-like root nodules upon inoculation with Mesorhizobium loti, indicating that the mutated loci are essential during AM but not during root nodule symbiosis.
Martin Groth, Sonja Kosuta, Caroline Gutjahr, Kristina Haage, Simone Liesel Hardel, Miriam Schaub, Andreas Brachmann, Shusei Sato, Satoshi Tabata, Kim Findlay, Trevor L. Wang, Martin Parniske (2013). Plant Journal Ahead of print.
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Improved survival of peat-cultured rhizobia when compared to liquid-cultured cells has been attributed to cellular adaptations during solid-state fermentation in moist peat. We have observed improved desiccation tolerance of Rhizobium leguminosarum bv. trifolii TA1 and Bradyrhizobium japonicum CB1809 after aerobic growth in water extracts of peat. Survival of TA1 grown in crude peat extract was 18-fold greater than cells grown in a defined liquid medium but was diminished when cells were grown in different colloidal size fractions of filtered peat extract with. Survival of CB1809 was generally better when grown in crude peat extract compared to the control but was not statistically significant (p > 0.05) and was strongly dependent on peat extract concentration. Accumulation of intracellular trehalose by both TA1 and CB1809 was higher after growth in peat extract compared to the defined medium control. Cells grown in water extracts of peat exhibit similar morphological changes to those observed after growth in moist peat. Electron microscopy revealed thickened plasma membranes, with an electron dense material occupying the periplasmic space in both TA1 and CB1809. Growth in peat extract also resulted in changes to polypeptide expression in both strains and peptide analysis by liquid chromatography-mass spectrometry indicated increased expression of stress response proteins. Our results suggest that increased capacity for desiccation tolerance in rhizobia is multi-factorial involving the accumulation of trehalose together with increased expression of proteins involved in protection of the cell envelope, repair of DNA-damage, oxidative stress responses and maintenance of stability and integrity of proteins.
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... Clemmensen said other ecosystems might also push much of their carbon down into the soil. “In agricultural fields, arbuscular mycorrhizal fungi are normally the dominant mycorrhizal type,” Clemmensen said in an email.
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Biological N2 fixation, the assimilation of atmospheric N2 into NH3, is the province of highly specialized microorganisms, and a key entry point for atmospheric nitrogen (N) into terrestrial ecosystems (Vitousek et al., 2002). It is probably the most important biologically mediated process after photosynthesis, and is universally carried out by the enzyme nitrogenase. Collectively, N2 fixing organisms are termed diazotrophs, some of which can fix N2 in a ‘free-living’ state, while others fix N2 in loose association with plants, and a select few in highly evolved, complex symbioses on plant roots or stems. Despite its importance, physiological control of biological N2 fixation is only partially understood and quantification of N2 fixation at the field level is difficult (Unkovich et al., 2008). Further progress in quantifying N cycle fluxes in ecosystems will rely heavily on stable isotope (15N) investigations. These powerful techniques can be used at scales ranging from cell to globe (Vandover et al., 1992; Robinson, 2001; Werner & Schmidt, 2002), but require an understanding of the isotope discrimination associated with N transformations. Generally, compounds containing the lighter of two isotopes react more quickly, resulting in reaction products being isotopically lighter than the substrate, unless all of the substrate is converted to the product (Dawson & Brooks, 2001). In the case of biological N2 fixation this equates to differences in the relative abundance of the stable isotopes 15N and14N between atmospheric N2 and the fixed NH3 produced by the nitrogenase enzyme in the diazotroph. Natural N isotope abundances (δ15N) are expressed as a parts per thousand (‰) deviation from the 15N composition of atmospheric N2 (0‰) (Mariotti, 1983) and thus one might anticipate fixed NH3 to have a negative δ15N given that the N2 fixation substrate substrate (N2) would be in unlimited supply and one would anticipate preferential reduction of 14N14N (mass 28) over 14N15N (mass 29) or 15N15N (mass 30). The aim of the present paper is to highlight uncertainties surrounding the extent of isotope fractionation associated with N2 fixation, and to provide a possible working framework for interpretation of the available data. Delete the scoop?
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Medicago truncatula or barrel medic is native to the Mediterranean. It is a member of the legume family of flowering plants. More famous members of the family include pea, soybean, beans, peanuts a... Delete the scoop?
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If we don’t watch out, agriculture could destroy our planet. Here’s how to grow all the food we need with fewer chemicals.
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Very interesting interacctive map too: http://ngm.nationalgeographic.com/2013/05/fertilized-world/nitrogen-flow-graphic Delete the scoop?
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The 22th North American Conference on Symbiotic Nitrogen Fixation will commence on July 14, 2013 with an opening reception from 6:30-9:30 PM in the Cowles Auditorium at the Hubert Humphrey Conference Center at the University of Minnesota.
The conference consists of three days of plenary sessions and poster presentations. The topics for the conference sessions are in the following areas: Nodule Development PhysiologyEvolution of Symbioses Bacterial Endophytes Agricultural Applications Physiology and Genetics of BacteriaPhysiology Genetics of the Legume Host Genomic Approaches to Understanding Symbioses
Organizing Committee Mike Sadowsky, University of Minnesota Ford Denison, University of Minnesota Carroll Vance, University of Minnesota Via IvanOresnik
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Jason Affourtit writes, “The encircling equation represents biological nitrogen fixation, which was at the core of my undergrad/graduate … (RT @carlzimmer: Pulling life out of thin air: a tattoo of nitrogen fixation.
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That's what I call dedication to nitrogen-fixation... Delete the scoop?
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Symbiotic associations between leguminous plants and nitrogen-fixing rhizobia culminate in the formation of specialized organs called root nodules, in which the rhizobia fix atmospheric nitrogen and transfer it to the plant. Efficient biological nitrogen fixation depends on metabolites produced by and exchanged between both partners. The Medicago truncatula–Sinorhizobium meliloti association is an excellent model for dissecting this nitrogen-fixing symbiosis because of the availability of genetic information in both symbiotic partners. Here, we employed a powerful imaging technique, matrix-assisted laser desorption/ionization (MALDI)-mass spectrometric imaging (MSI), to study metabolite distribution in roots and root nodules of M. truncatula during nitrogen fixation. The combination of an efficient, novel MALDI matrix 1,8-bis(dimethyl-amino) naphthalene (DMAN) with a conventional matrix 2,5-dihydroxybenzoic acid (DHB) allowed the detection of a large array of organic acids, amino acids, sugars, lipids, flavonoids and their conjugates with improved coverage. Ion density maps of representative metabolites are presented and correlated with the nitrogen fixation process. We demonstrate differences in metabolite distribution between roots and nodules, and also between fixing and non-fixing nodules produced by plant and bacterial mutants. Our study highlights the benefits of using MSI for detecting differences in metabolite distributions in plant biology.
Ye VH, Gemperline E, Venkateshwaran M, Chen R, Delaux PM, Howes-Podoll M, Ané JM, Li L.(2013).Plant J. Mar 30. doi: 10.1111/tpj.12191. [Epub ahead of print] Via IvanOresnik
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The interaction of legumes with N2-fixing bacteria collectively called rhizobia results in root nodule development. The number of nodules formed is tightly restricted through the systemic negative feedback control by the host called autoregulation of nodulation (AON). Here, we report the characterization and gene identification of TOO MUCH LOVE (TML), a root factor that acts during AON in a model legume Lotus japonicus. In our genetic analyses using another root-regulated hypernodulation mutant,plenty, the tml-1 plenty double mutant showed additive effects on the nodule number, whereas the tml-1 har1-7 double mutant did not, suggesting that TML and PLENTY act in different genetic pathways and that TML and HAR1 act in the same genetic pathway. The systemic suppression of nodule formation by CLE-RS1/RS2 overexpression was not observed in the tml mutant background, indicating that TML acts downstream of CLE-RS1/RS2. The tml-1 Snf2 double mutant developed an excessive number of spontaneous nodules, indicating that TML inhibits nodule organogenesis. Together with the determination of the deleted regions in tml-1/-2/-3, the fine mapping of tml-4 and the next-generation sequencing analysis, we identified a nonsense mutation in the Kelch repeat-containing F-box protein. As the gene knockdown of the candidate drastically increased the number of nodules, we concluded that it should be the causative gene. An expression analysis revealed that TMLis a root-specific gene. In addition, the activity of ProTML-GUS was constitutively detected in the root tip and in the nodules/nodule primordia upon rhizobial infection. In conclusion, TML is a root factor acting at the final stage of AON. Delete the scoop?
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