Most vascular plants interact with arbuscular mycorrhizal fungi (AMF) and are thereby provided significant advantages in nutrient acquisition, especially phosphate. The widespread retention of this symbiosis in vascular plants is testament to its importance and ancient origins. This highlight focuses on the reports of two of the first genes identified through forward genetic screens for AMF symbiotic mutants: Required for Abuscular Mycorrhization 1 (RAM1) and RAM2, which respectively encode a GRAS transcription factor and a glycerol-3-phosphate acyl-transferase (GPAT) that are required for the formation of fungal entry structures (hyphopodia) on the root surface. This provides the first insights into a mycorrhization specific signaling pathway and reveals cutin monomers as a critical component of signaling in the mycorrhizal symbiosis. We discuss the proposed links between these genes, and the role of cutin and its precursors in interactions with AMF, and oomycete and fungal pathogens.
Arbuscular mycorrhizal symbiosis (AMS) and root nodule symbiosis (RNS) are mutualistic plant-microbe interactions that confer nutritional benefits to both partners. Leguminous plants possess a common genetic system for ...
Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia (NH3), accounts for roughly half of the bioavailable nitrogen supporting extant life.
The Tree of Life: Worst science by press release of the year: nitrogen fixation in crops http://t.co/42GLoe2edD
Jean-Michel Ané's insight:
I totally agree... I am still waiting to see the scientific evidence supporting this press release. This kind of hoax really hurts our research field on nitrogen fixation and, more generally, discredits the scientific community.
Nitrogen fixation is essential for the synthesis of many important chemicals (e.g., fertilizers, explosives) and basic building blocks for all forms of life (e.g., nucleotides for DNA and RNA, amino acids for proteins). However, direct nitrogen fixation is challenging as nitrogen (N2) does not easily react with other chemicals. By dry ball-milling graphite with N2, we have discovered a simple, but versatile, scalable and eco-friendly, approach to direct fixation of N2 at the edges of graphene nanoplatelets (GnPs). The mechanochemical cracking of graphitic C−C bonds generated active carbon species that react directly with N2 to form five- and six-membered aromatic rings at the broken edges, leading to solution-processable edge-nitrogenated graphene nanoplatelets (NGnPs) with superb catalytic performance in both dye-sensitized solar cells and fuel cells to replace conventional Pt-based catalysts for energy conversion.
Homoserine represents a substantial component of pea root exudate that may be important for plant–microbe interactions in the rhizosphere. We identified a gene cluster on plasmid pRL8JI that is required for homoserine utilization by Rhizobium leguminosarum bv.viciae. The genes are arranged as two divergently expressed predicted operons that were induced by L-homoserine, pea root exudate, and were expressed on pea roots. A mutation in gene pRL80083 that prevented utilization of homoserine as a sole carbon and energy source affected the mutant's ability to nodulate peas and lentils competitively. The homoserine gene cluster was present in approximately 47% of natural R. leguminosarum isolates (n = 59) and was strongly correlated with homoserine utilization. Conjugation of pRL8JI to R. leguminosarum 4292 or Agrobacterium tumefaciens UBAPF2 was sufficient for homoserine utilization. The presence of L-homoserine increased conjugation efficiency of pRL8JI from R. leguminosarum to a pRL8JI-cured derivative of R. leguminosarum 1062 and to A. tumefaciens UBAPF2, and induced expression of the plasmid transfer gene trbB; however, there was no difference in conjugation efficiency or trbB expression with A. tumefaciens UBAPF2pRL8-Gm as the donor suggesting that other genes in R. leguminosarum may contribute to regulating conjugation of pRL8 in the presence of homoserine.
Vanderlinde EM, Hynes MF, Yost CK. (2013). Environ Microbiol. 2013Jun 21. . [Epub ahead of print]
Nice to see this work published! It has long been known that peas exude homoserine. To characterize the genes repsonsible for the catabolism and to show they affect competition for nodule occupancy strengthens the idea of a biased rhizosphere.
Here's how to create a new species. Put animals—say finches—from the same species on separate islands and let them do their thing for many, many generations. Over time, each group will adapt to its new environment, and the genomes of the two populations will become so different that if you reintroduce the animals to the same habitat, they can no longer breed successfully. Voilà, one species has become two. But a new study suggests that DNA isn't the only thing that separates species: Some populations diverge because of the microbes in their guts.
The paper is "important and potentially groundbreaking," says John Werren, a biologist at the University of Rochester in New York. "Scientists have studied speciation … for many years, and this opens up a whole new aspect to it."
The new work involves three different species of parasitic jewel wasps, tiny insects that drill into the pupas of flies and lay their eggs, letting the offspring feed on the host. Two of the species, Nasonia giraulti and N. longicornis, are closely related, whereas the third species, N. vitripennis, diverged from the other two about 1 million years ago. When N. giraultiand N. longicornis mate in the lab, most of their offspring survive, but when either mates with N. vitripennis, almost all male larvae in the second generation die.
Seth Bordenstein and Robert Brucker, biologists at Vanderbilt University in Nashville, wondered if the reason for this mortality went beyond incompatible DNA. They knew that the gut microbes in N. vitripennis differed from those in the other two species, and they suspected that these microbes could play a role in the offspring deaths. Indeed, when they raised all three species of Nasonia without gut microbes—by rearing them on sterile food—almost all the second generation offspring of matings between N. vitripennis and N. giraulti wasps survived. Andwhen the scientists reintroduced bacteria into the germ-free wasps, most of their second-generation offspring died, the duo report online today in Science.
Werren says that the work introduces a whole new way to look at what sets species apart. Instead of just thinking about genes of the parents not meshing in hybrids, he says, biologists could now think about how the parents' genes are incompatible with the offspring's microorganisms. Some parental genes could enable the immune system to keep certain gut bacteria in check, for instance, and without them the gut microbes might sicken the animal and kill it.
Bordenstein goes one step further. The genes of microbes harbored by an organism are just as important for evolution as the genes in its own cells, he says, calling both together a "hologenome." Werren disagrees. Microbes in the gut interact with the bigger organism, just like other organisms in nature interact, for instance predator and prey, Werren says. "They are not co-evolving as a single unit, so why would we call them a single genome?"
Axel Meyer, an evolutionary biologist at the University of Konstanz in Germany, is skeptical about whether gut microbes have a big effect on speciation. The paper is "exciting," he says, "but there might be huge biological differences between species in how the microbiome [the community of microbes in an organism] is established." As a result, he says, it is an open question whether there will be many more examples of gut microbes separating species. Werren thinks there will be. "No pun intended," he says, "but my gut tells me that this is going to be common."
Jean-Michel Ané's insight:
I know that it's not about plants and microbes... but it's so cool!
R. irregularis is an arbuscular mycorrhizal fungus which forms symbiotic relationship with plant roots in important crop plants (Soybean, Rice, Maize, Poplar trees). The genome was sequenced through the JGI Mycorrhizal ...
Plant plasma membrane-bound receptors with extracellular lysin motif (LysM) domains participate in interactions with microorganisms. In Medicago truncatula, the LysM receptor-like kinase gene nodulation (Nod) factor perception (NFP) is a key gene that controls the perception of rhizobial lipochitooligosaccharide (LCO) Nod factors for the establishment of the Rhizobium–legume symbiosis. In this article, we review recent data that have refined our understanding of this function and that have revealed a role for NFP in the perception of arbuscular mycorrhizal (AM) symbiotic signals and plant pathogenic microorganisms. The dual role of NFP in symbiosis and immunity suggests that this receptor protein controls the perception of different signals and the activation of different downstream signalling pathways. These advances provide new insights into the evolution and functioning of this versatile plant protein.
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, and Discaria 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.
Sergio Svistoonoff, Faiza Meriem Benabdoun, Mathish Nambiar-Veetil, Leandro Imanishi, Virginie Vaissayre, Stella Cesari, Nathalie Diagne, Valérie Hocher, Françoise de Billy, Jocelyne Bonneau, Luis Wall, Nadia Ykhlef, Charles Rosenberg, Didier Bogusz, Claudine Franche, and Hassen Gherbi (2013). PLoS One.; 8(5): e64515.
Understanding commonalities and differences of how symbiotic and parasitic microbes interact with plants will improve advantageous interactions and allow pathogen control strategies in crops. Recently established systems enable studies of root pathogenic and symbiotic interactions in the same plant species.
Plant NADPH oxidases (RBOHs) regulate the early stages of rhizobial infection in Phaseolus vulgaris and affect nodule function in Medicago truncatula. In contrast, the role of RBOHs in the plant-arbuscular mycorrhizal (AM) symbiosis and in the regulation of reactive oxygen species (ROS) production during the establishment of the AM interaction is largely unknown. In this study, we assessed the role of P. vulgaris Rboh (PvRbohB) during the symbiosis with the AM fungus,Rhizophagus irregularis. Our results indicate that PvRbohB transcript is significantly up-regulated in the mycorrhized roots of P. vulgaris. Further, the PvRbohB promoter was found to be active during the invasion of R. irregularis. Down-regulation of PvRbohB transcription by RNAi silencing resulted in diminished ROS levels in the transgenic mycorrhized roots and induced early hyphal root colonization. Interestingly, the size of appressoria increased in PvRbohB-RNAi roots (760±70.1 μm) relative to controls (251±73.2 μm). Finally, the overall level of mycorrhizal colonization significantly increased in PvRbohB-RNAi roots (48.1±3.3% root length colonization, RLC) compared to controls (29.4±1.9%RLC). We propose that PvRbohB negatively regulates AM colonization in P. vulgaris.
In this real-life model of forest resilience and regeneration, Professor Suzanne Simard shows that all trees in a forest ecosystem are interconnected, with t...
Last week I attended a PhD student symposium. It was a very interesting day filled with student research talks and poster sessions and networking. One of the talks was given by Matt Cooper (Alison ...
Mutualisms are common in nature, though these symbioses can be quite permeable to cheaters in situations where one individual parasitizes the other by discontinuing cooperation yet still exploits the benefits of the partnership. In the Rhizobium-legume system, there are two separate contexts, namely nodulation and nitrogen fixation processes, by which residentRhizobium individuals can benefit by cheating. Here, we constructed reversible and irreversible mutations in key nodulation and nitrogen-fixation pathways of Rhizobium etli and compared their interaction with plant hosts Phaseolus vulgaris to that of wild type. We show that R. etli reversible mutants deficient in nodulation factor production are capable of intra-specific cheating, wherein mutants exploit other Rhizobium individuals capable of producing these factors. Similarly, we show that R. etli mutants are also capable of cheating inter-specifically, colonizing the host legume yet contributing nothing to the partnership in terms of nitrogen fixation. Our findings indicate that cheating is possible in both of these frameworks, seemingly without damaging the stability of the mutualism itself. These results may potentially help explain observations suggesting that legume plants are commonly infected by multiple bacterial lineages during the nodulation process.
ing J, Zheng H, Katzianer DS, Wang H, Zhong Z, et al. (2013) PLoS ONE 8(7): e70138.
Socrates Logos's insight: byXia Wang, Jian-Guo Yang, Li Chen, Ji-Long Wang, Qi Cheng, Ray Dixon Yi-Ping Wang "Biological nitrogen fixation is a complex process requiring multiple genes working in concert.
While chitooligosaccharides (COs) derived from fungal chitin are potent elicitors of defense reactions, structurally related signals produced by certain bacteria and fungi, called lipo-chitooligosaccharides (LCOs), play important roles in the establishment of symbioses with plants. Understanding how plants distinguish between friend and foe through the perception of these signals is a major challenge. We report the synthesis of a range of COs and LCOs, including photoactivatable probes, to characterize a membrane protein from the legumeMedicago truncatula. By coupling photoaffinity labeling experiments with proteomics and transcriptomics, we identified the likely LCO-binding protein as LYR3, a lysin motif receptor-like kinase (LysM-RLK). LYR3, expressed heterologously, exhibits high-affinity binding to LCOs but not COs. Homology modeling, based on the Arabidopsis CO-binding LysM-RLK AtCERK1, suggests that LYR3 could accommodate the LCO in a conserved binding site. The identification of LYR3 opens up ways for the molecular characterization of LCO/CO discrimination.
33rd New Phytologist Symposium.Networks of Power and Influence: A symposium on the ecology and evolution of symbiotic associations between plants and mycorrhizal fungi (33rd NewPhyt Symposium Networks of Power & Influence May'14
Soil bacteria known as rhizobia are able to establish an endosymbiosis with legumes that takes place in neoformed nodules in which intracellularly hosted bacteria fix nitrogen. Intracellular accommodation that facilitates nutrient exchange between the two partners and protects bacteria from plant defense reactions has been a major evolutionary step towards mutualism. Yet the forces that drove the selection of the late event of intracellular infection during rhizobium evolution are unknown. To address this question, we took advantage of the previous conversion of the plant pathogen Ralstonia solanacearum into a legume-nodulating bacterium that infected nodules only extracellularly. We experimentally evolved this draft rhizobium into intracellular endosymbionts using serial cycles of legume-bacterium cocultures. The three derived lineages rapidly gained intracellular infection capacity, revealing that the legume is a highly selective environment for the evolution of this trait. From genome resequencing, we identified in each lineage a mutation responsible for the extracellular–intracellular transition. All three mutations target virulence regulators, strongly suggesting that several virulence-associated functions interfere with intracellular infection. We provide evidence that the adaptive mutations were selected for their positive effect on nodulation. Moreover, we showed that inactivation of the type three secretion system of R. solanacearum that initially allowed the ancestral draft rhizobium to nodulate, was also required to permit intracellular infection, suggesting a similar checkpoint for bacterial invasion at the early nodulation/root infection and late nodule cell entry levels. We discuss our findings with respect to the spread and maintenance of intracellular infection in rhizobial lineages during evolutionary times.
Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.
The Arbuscular Mycorrhizal (AM) symbiosis is a ubiquitous relationship established in terrestrial ecosystems between the roots of most plants and fungi of the Glomeromycota. AM fungi occur amongst many other inhabitants of the soil, and successful development of AM symbioses relies on a pre-symbiotic signal exchange that allows mutual recognition and reprogramming for the anticipated physical interaction. The nature of some of the signals has been discovered in recent years, providing a first insight into the type of chemical language spoken between the two symbiotic partners. Importantly, these discoveries suggest that the dialogue is complex and that additional factors and corresponding receptors remain to be unveiled. Here, we explore the latest advances in this pre-symbiotic plant–fungal signal exchange and present the resulting current understanding of rhizosphere communication in AM symbioses.
Plant communications The Economist The researchers who conducted this study knew that soil fungi whose hyphae are symbiotic with tomatoes (providing them with minerals in exchange for food) also form a network connecting one plant to another.
Symbiotic root nodules in leguminous plants result from interaction between the plant and nitrogen-fixing rhizobia bacteria. There are two major types of legume nodules, determinate and indeterminate. Determinate nodules do not have a persistent meristem while indeterminate nodules have a persistent meristem. Auxin is thought to play a role in the development of both these types of nodules. However, inhibition of rootward auxin transport at the site of nodule initiation is crucial for the development of indeterminate nodules, but not determinate nodules. Using the synthetic auxin-responsive DR5 promoter in soybean, we show that there is relatively low auxin activity during determinate nodule initiation and that it is restricted to the nodule periphery subsequently during development. To examine if and what role auxin plays in determinate nodule development, we generated soybean composite plants with altered sensitivity to auxin. We over-expressed microRNA393 to silence the auxin receptor gene family and these roots were hyposensitive to auxin. These roots nodulated normally suggesting that only minimal/reduced auxin signaling is required for determinate nodule development. We over-expressed microRNA160 to silence a set of repressor ARF transcription factors and these roots were hypersensitive to auxin. These roots were not impaired in epidermal responses to rhizobia, but had significantly reduced nodule primordium formation suggesting that auxin hypersensitivity inhibits nodule development. These roots were also hyposensitive to cytokinin, and had attenuated expression of key nodulation-associated transcription factors known to be regulated by cytokinin. We propose a regulatory feedback loop involving auxin and cytokinin during nodulation.
Turner M, Nizampatnam NR, Baron M, Coppin S, Damodaran S, Adhikari S, Arunachalam S, Yu O, Subramanian S. (2013). Plant Physiol. Jun 24. [Epub ahead of print]
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