Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital "in situ". This digital "in situ" offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies.
Limpens E, Moling S, Hooiveld G, Pereira PA, Bisseling T, Becker JD, Küster H (2013). PLoS One. 2013 May 29;8(5):e64377
Receptor(-like) kinases with Lysin Motif (LysM) domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. Arabidopsis thaliana CERK1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas Medicago truncatula NFP and LYK3 mediate signalling upon perception of bacterial lipo-chitooligosaccharides, termed Nod factors, during the establishment of mutualism with nitrogen-fixing rhizobia. However, little is still known about the exact activation and signalling mechanisms of MtNFP and MtLYK3. We aimed at investigating putative molecular interactions of MtNFP and MtLYK3 produced in Nicotiana benthamiana. Surprisingly, heterologous co-production of these proteins resulted in an induction of defence-like responses, which included defence-related gene expression, accumulation of phenolic compounds, and cell death. Similar defence-like responses were observed upon production of AtCERK1 in N. benthamiana leaves. Production of either MtNFP or MtLYK3 alone or their co-production with other unrelated receptor(-like) kinases did not induce cell death in N. benthamiana, indicating that a functional interaction between these LysM receptor-like kinases is required for triggering this response. Importantly, structure-function studies revealed that the MtNFP intracellular region, specific features of the MtLYK3 intracellular region (including several putative phosphorylation sites), and MtLYK3 and AtCERK1 kinase activity were indispensable for cell death induction, thereby mimicking the structural requirements of nodulation or chitin-induced signalling. The observed similarity of N. benthamiana response to MtNFP and MtLYK3 co-production and AtCERK1 production suggests the existence of parallels between Nod factor-induced and chitin-induced signalling mediated by the respective LysM receptor(-like) kinases. Notably, the conserved structural requirements for MtNFP and MtLYK3 biological activity in M. truncatula (nodulation) and in N. benthamiana (cell death induction) indicates the relevance of the latter system for studies on these, and potentially other symbiotic LysM receptor-like kinases.
Plants constantly engage in interactions with microbial organisms. These interactions can either be detrimental such as those with the economically relevant fungus-like oomycete Phytophthora infestans, the causal agent of the Irish Potato Famine or beneficial to supply phosphate such as in symbiotic interactions with mycorrhizal fungi that occur in most plant species.
Both, pathogenic and mutualistic symbioses follow structurally similar developmental processes to establish intracellular interfaces. It is generally accepted that both, plants and microorganisms contribute to the formation of dedicated accommodation structures. However, we know little about the underlying molecular mechanisms that drive differentiation of host cells and tissues to form intracellular interfaces.
The Schornack group aims to characterize the extent to which beneficial and detrimental microorganisms employ similar plant developmental processes for colonization. To this end we plan to assess the overlap between Mycorrhiza processes and root infection by the biotrophic pathogenPhytophthora palmivora and will characterize genetic elements with common functions. Furthermore, we will elucidate the role of microbial effectors for development of plant cells into intracellular accommodation structures. This work will reveal the boundaries between symbiosis and pathogenesis and will provide novel insights into plant development driven by biotic cues.
Jean-Michel Ané's insight:
Great system to study the relationships between symbbiotic and pathogenic pathways.
The vast majority of vascular plants are capable of forming an arbuscular mycorrhizal symbiosis, and only 18% cannot (Brundrett 2009). It is widely accepted that all ancestors of vascular plant species were arbuscular mycorrhizal (Pirozynski & Malloch 1975; Wang et al. 2010). Nonmycorrhizal species presumably lost or suppressed their ability to establish an arbuscular mycorrhizal symbiosis because its benefits did not outweigh its costs, but the mechanism explaining a high cost to benefit relationship may have been very different in distant plant lineages, as explored below.
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]
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.
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.
Andrea Casteriano, Meredith A. Wilkes and Rosalind Deaker (2013). Appl Environ Microbiol. Apr 19. [Epub ahead of print]
... 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.
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.
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...
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:
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.
Jean-Michel Ané's insight:
That's what I call dedication to nitrogen-fixation...
Interactions between species are important catalysts of the evolutionary processes that generate the remarkable diversity of life. Symbioses, conspicuous and inherently interesting forms of species interaction, are pervasive throughout the tree of life. However, nearly all studies of the impact of species interactions on diversification have concentrated on competition and predation leaving unclear the importance of symbiotic interaction. Here, I show that, as predicted by evolutionary theories of symbiosis and diversification, multiple origins of a key innovation, symbiosis between gall-inducing insects and fungi, catalysed both expansion in resource use (niche expansion) and diversification. Symbiotic lineages have undergone a more than sevenfold expansion in the range of host-plant taxa they use relative to lineages without such fungal symbionts, as defined by the genetic distance between host plants. Furthermore, symbiotic gall-inducing insects are more than 17 times as diverse as their non-symbiotic relatives. These results demonstrate that the evolution of symbiotic interaction leads to niche expansion, which in turn catalyses diversification.
Only species belonging to the Fabid clade, limited to four classes and ten families of Angiosperms, are able to form nitrogen-fixing root nodule symbioses (RNS) with soil bacteria. This concerns plants of the legume family (Fabaceae) and Parasponia (Cannabaceae)associated with the Gram-negative proteobacteria collectively called rhizobia and actinorhizal plants associated with the Gram-positive actinomycetes of the genus Frankia. Calcium and calmodulin-dependent protein kinase (CCaMK) is a key component of the common signaling pathway leading to both rhizobial and arbuscular mycorrhizal symbioses (AM) and plays a central role in cross-signaling between root nodule organogenesis and infection processes. Here, we show that CCaMK is also needed for successful actinorhiza formation and interaction with AM fungi in the actinorhizal tree Casuarina glauca and is also able to restore both nodulation and AM symbioses in a Medicago truncatula ccamk mutant. Besides, we expressed auto-active CgCCaMK lacking the auto-inhibitory/CaM domain in two actinorhizal species: C. glauca (Casuarinaceae), which develops an intracellular infection pathway, andDiscaria trinervis (Rhamnaceae) which is characterized by an ancestral intercellular infection mechanism. In both species, we found induction of nodulation independent of Frankia similar to response to the activation of CCaMK in the rhizobia-legume symbiosis and conclude that the regulation of actinorhiza organogenesis is conserved regardless of the infection mode. It has been suggested that rhizobial and actinorhizal symbioses originated from a common ancestor with several independent evolutionary origins. Our findings are consistent with the recruitment of a similar genetic pathway governing rhizobial and Frankia nodule organogenesis.
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.
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.
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 ...
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...
Jean-Michel Ané's insight:
Sorry... It's totally nerd but I can't help sharing it!
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.
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).
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.
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.
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