Food demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.
BACKGROUND: High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to generate experimental data in the last few years, few computational methods are available to analyze this huge amount of transcription data. The computational methods for constructing gene regulatory networks from RNA-Seq expression data of hundreds or even thousands of genes are particularly lacking and urgently needed.
RESULTS: We developed an automated bioinformatics method to predict gene regulatory networks from the quantitative expression values of differentially expressed genes based on RNA-Seq transcriptome data of a cell in different stages and conditions, integrating transcriptional, genomic and gene function data. We applied the method to the RNA-Seq transcriptome data generated for soybean root hair cells in three different development stages of nodulation after rhizobium infection. The method predicted a soybean nodulation-related gene regulatory network consisting of 10 regulatory modules common for all three stages, and 24, 49 and 70 modules separately for the first, second and third stage, each containing both a group of co-expressed genes and several transcription factors collaboratively controlling their expression under different conditions. 8 of 10 common regulatory modules were validated by at least two kinds of validations, such as independent DNA binding motif analysis, gene function enrichment test, and previous experimental data in the literature.
CONCLUSIONS: We developed a computational method to reliably reconstruct gene regulatory networks from RNA-Seq transcriptome data. The method can generate valuable hypotheses for interpreting biological data and designing biological experiments such as ChIP-Seq, RNA interference, and yeast two hybrid experiments.
Zhu M, Dahmen JL, Stacey G, Cheng J. (2013). BMC Bioinformatics. Sep 22;14(1):278. [Epub ahead of print]
Most plants interact with both arbuscular mycorrhizal (AM) fungi, which increase nutrient acquisition, and herbivores such as aphids, which drain nutrients from plants. Both AM fungi and aphids can affect plant metabolic pathways and may influence each other by altering the condition of the shared host plant.
This study tests simultaneously the effects of AM fungi on interactions with aphids (bottom-up effects), and the effects of aphids on interactions with AM fungi (top-down effects). We hypothesised that: (i) attractiveness of plants to aphids is regulated by induced changes in production of plant volatile organic compounds (VOCs) triggered by AM fungi or aphids; (ii) aphids reduce AM fungal colonisation; and (iii) AM fungal colonisation affects aphid development.
Broad beans were exposed to AM fungi, aphids, and a combination of both. To test for the strength of bottom-up and top-down effects, separate treatments enabled establishment of mycorrhizas either before or after aphids were added to plants. VOCs produced by plants were used to (i) test their attractiveness to aphids, and (ii) identify the semiochemicals causing attraction. We also measured plant growth and nutrition, AM fungal colonisation and aphid reproduction.
AM fungi increased the attractiveness of plants to aphids, and this effect tended to prevail even for aphid-infested plants. However, both attractiveness and aphid population growth depended on the timing of AM fungal inoculation. AM fungi suppressed emission of the sesquiterpenes (E)- caryophyllene and (E)-β-farnesene, and aphid attractiveness to VOCs was negatively associated with the proportion of sesquiterpenes in the sample. Emission of (Z)-3-hexenyl acetate, naphthalene, and (R)-germacrene D was regulated by an interaction between aphids and AM fungi. Aphids had a negative effect on mycorrhizal colonisation, plant biomass and nutrition.
Our data show that below- and above-ground organisms can interact by altering the quality of their shared host plant even though there is no direct contact between them. Plant interactions with herbivores and AM fungi operate in both directions: AM fungi have a key bottom-up role in insect host location by increasing the attractiveness of plant VOCs to aphids, whereas aphids inhibit formation of AM symbioses.
A new synthesis of the fungal lipo-chitooligosaccharide Myc-IV (C16:0, S), which was recently reported to be a major symbiotic signalling molecule in arbuscular mycorrhiza, is described. Key steps include the oxidative cleavage of a 4,6-O-benzylidene acetal to prepare a disaccharidic glycosyl acceptor, and stereoselective glycosylations with 2-methyl-5-tert-butylphenyl thioglycosyl donors.
Rhizobia, the nitrogen-fixing bacterial symbionts of legumes, represent an agricultural application of primary relevance and a model of plant–microbe molecular dialogues. We recently described rhizobium proteome alterations induced by plant flavonoids using iTRAQ. Herein, we further extend that experimentation, proving that the transient elevation in cytosolic calcium is a key signaling event necessary for the expression of the nodulation (nod) genes. Ca2+ involvement in nodulation is a novel issue that we recently flagged with genetic and physiological approaches and that hereby we demonstrate also by proteomics. Exploiting the multiple combinations of 4-plex iTRAQ, we analyzed Rhizobium leguminosarum cultures grown with or without the nod gene-inducing plant flavonoid naringenin and in the presence or absence of the extracellular Ca2+ chelator EGTA. We quantified over a thousand proteins, 189 of which significantly altered upon naringenin and/or EGTA stimulation. The expression of NodA, highly induced by naringenin, is strongly reduced when calcium availability is limited by EGTA. This confirms, from a proteomic perspective, that a Ca2+ influx is a necessary early step in flavonoid-mediated legume nodulation by rhizobia. We also observed other proteins affected by the different treatments, whose identities and roles in nodulation and rhizobium physiology are likewise discussed.
J. Proteome Res., (2013). Publication Date (Web): September 16,
Legumes have the unique capacity to undergo two important root endosymbioses: the root nodule symbiosis and the arbuscular mycorrhizal symbiosis. Medicago truncatula is widely used to unravel the functions of genes during these root symbioses. Here we describe the development of an artificial microRNA (amiR)-mediated gene silencing system for M. truncatula roots.
Results
The endogenous microRNA (miR) mtr-miR159b was selected as a backbone molecule for driving amiR expression. Heterologous expression of mtr-miR159b-amiR constructs in tobacco showed that the backbone is functional and mediates an efficient gene silencing. amiR-mediated silencing of a visible marker was also effective after root transformation of M. truncatula constitutively expressing the visible marker. Most importantly, we applied the novel amiR system to shed light on the function of a putative transcription factor, MtErf1, which was strongly induced in arbuscule-containing cells during mycorrhizal symbiosis. MtPt4 promoter driven amiR-silencing led to strongly decreased transcript levels and deformed, non-fully truncated arbuscules indicating that MtErf1 is required for arbuscule development.
Conclusions
The endogenous amiR system demonstrated here presents a novel and highly efficient tool to unravel gene functions during root endosymbioses.
The availability of nitrogen is one of the major limiting factors to crop growth. In the developed world, farmers use unsustainable levels of inorganic fertilisers to promote crop production. In contrast, in the developing world inorganic fertilisers are often not available and small-holder farmers suffer the resultant poor yields. Finding alternatives to inorganic fertilisers is critical for sustainable and secure food production. Bacteria and Archaea have evolved the capability to fix atmospheric nitrogen to ammonia, a form readily usable in biological processes. This capability presents an opportunity to improve the nutrition of crop plants, through the introduction into cereal crops of either the nitrogen fixing bacteria or the nitrogenase enzyme responsible for nitrogen fixation. While both approaches are challenging, recent advances have laid the groundwork to initiate these biotechnological solutions to the nitrogen problem.
Find out the rare symbiotic relationship that soy has with soil bacteria that allows it to convert atmospheric nitrogen into forms it can use as natural fert... (We love George Washington Carver. This is a great video about GWC and Nitrogen Fixation.
Photo: Dr. David Midgley. Students will explore one example of a symbiosis (mycorrhizae) and examine whether it is a mutualism or a parasitism. They will review the life requirements of producers (plants) and consumers ...
Rhizobial nodulation (Nod) factors activate both nodule morphogenesis and infection thread development during legume nodulation. Nod factors induce two different calcium responses: intra-nuclear calcium oscillations and a calcium influx at the root hair tip. Calcium oscillations activate nodule development; we wanted to test if the calcium influx is associated with infection.Sinorhizobium meliloti nodL and nodF mutations additively reduce infection of Medicago truncatula. Nod-factors made by the nodLmutant lack an acetyl group; mutation of nodF causes the nitrogen (N)-linked C16:2 acyl chain to be replaced by C18:1. We tested whether these Nod-factors differentially induced calcium influx and calcium spiking.The absence of the NodL-determined acetyl group greatly reduced the induction of calcium influx without affecting calcium spiking. The calcium influx was even further reduced if the N-linked C16:2 acyl group was replaced by C18:1. These additive effects on calcium influx correlate with the additive effects of mutations in nodF and nodL on legume infection. Infection thread development is inhibited by ethylene, which also inhibited Nod-factor-induced calcium influx.We conclude that Nod-factor perception differentially activates the two developmental pathways required for nodulation and that activation of the pathway involving the calcium influx is important for efficient infection.
Great scientific advance that will probably make nitrogen fertilizers cheaper but I am woried about the ecological consequences of an even more intensive use of such fertilizers. I may preach to the choir but I don't think that this is a viable option for sustainable agriculture.
Arbuscular mycorrhizal (AM) symbiosis is stimulated by phosphorus (P) limitation and contributes to P and nitrogen (N) acquisition. However, the effects of combined P and N limitation on AM formation are largely unknown.Medicago truncatula plants were cultivated in the presence or absence of Rhizophagus irregularis (formerly Glomus intraradices) in P-limited (LP), N-limited (LN) or combined P- and N-limited (LPN) conditions, and compared with plants grown in sufficient P and N.The highest AM formation was observed in LPN, linked to systemic signaling by the plant nutrient status. Plant free phosphate concentrations were higher in LPN than in LP, as a result of cross-talk between P and N. Transcriptome analyses suggest that LPN induces the activation of NADPH oxidases in roots, concomitant with an altered profile of plant defense genes and a coordinate increase in the expression of genes involved in the methylerythritol phosphate and isoprenoid-derived pathways, including strigolactone synthesis genes.Taken together, these results suggest that low P and N fertilization systemically induces a physiological state of plants favorable for AM symbiosis despite their higher P status. Our findings highlight the importance of the plant nutrient status in controlling plant–fungus interaction.
Via Nico Pauly
During the last decades the importance of the genus Populus increased because the poplar genome has been sequenced and molecular tools for basic research have become available. Poplar species occur in different habitats and harbor large genetic variation, which can be exploited for economic applications and for increasing our knowledge on the basic molecular mechanisms of the woody life style. Poplars are, therefore, employed to unravel the molecular mechanisms of wood formation, stress tolerance, tree nutrition and interaction with other organisms such as pathogens or mycorrhiza. The basis of these investigations is the reproducible production of homogeneous plant material. In this method paper we describe techniques and growth conditions for the in vitro propagation of different poplar species (Populus × canescens, P. trichocarpa, P. tremula, and P. euphratica) and ectomycorrhizal fungi (Laccaria bicolor, Paxillus involutus) as well as for their co-cultivation for ectomycorrhizal synthesis. Maintenance and plant preparation require different multiplication and rooting media. Growth systems to cultivate poplars under axenic conditions in agar and sand cultures with and without mycorrhizal fungi are described. Transfer of the plants from in vitro to in situ conditions is critical and hardening is important to prevent high mortality. Growth and vitality of the trees in vitro and outdoors with and without ectomycorrhizas are reported.
The symbiotic bacterium Buchnera aphidicola lacks key genes in the biosynthesis of five essential amino acids (EAAs), and yet its animal hosts (aphids) depend on the symbiosis for the synthesis of these EAAs (isoleucine, leucine, methionine, phenylalanine, and valine). We tested the hypothesis, derived from genome annotation, that the missing Buchnera reactions are mediated by host enzymes, with the exchange of metabolic intermediates between the partners. The specialized host cells bearing Buchnera were separated into a Buchnera fraction and a Buchnera-free host cell fraction (HF). Addition of HF to isolated Buchnerapreparations significantly increased the production of leucine and phenylalanine, and recombinant enzymes mediating the final reactions in branched-chain amino acid and phenylalanine synthesis rescued the production of these EAAs byBuchnera preparations without HF. The likely precursors for the missing proximal reactions in isoleucine and methionine synthesis were identified, and they differed from predictions based on genome annotations: synthesis of 2-oxobutanoate, the aphid-derived precursor of isoleucine synthesis, was stimulated by homoserine and not threonine via threonine dehydratase, and production of the homocysteine precursor of methionine was driven by cystathionine, not cysteine, via reversal of the transsulfuration pathway. The evolution of shared metabolic pathways in this symbiosis can be attributed to host compensation for genomic deterioration in the symbiont, involving changes in host gene expression networks to recruit specific enzymes to the host cell.
N-acetylglucosamine-based saccharides (chitosaccharides) are components of microbial cell walls and act as molecular signals during host-microbe interactions. In the legume plant Medicago truncatula, the perception of lipochitooligosaccharide signals produced by symbiotic rhizobia and arbuscular mycorrhizal fungi involves the Nod Factor Perception (NFP) lysin motif receptor-like protein and leads to the activation of the so-called common symbiotic pathway. In rice and Arabidopsis, lysin motif receptors are involved in the perception of chitooligosaccharides released by pathogenic fungi, resulting in the activation of plant immunity. Here we report the structural characterization of atypical chitosaccharides from the oomycete pathogen Aphanomyces euteiches, and their biological activity on the host Medicago truncatula. Using a combination of biochemical and biophysical approaches, we show that these chitosaccharides are linked to β-1,6-glucans, and contain a β-(1,3;1,4)-glucan backbone whose β-1,3-linked glucose units are substituted on their C-6 carbon by either glucose or N-acetylglucosamine residues. This is the first description of this type of structural motif in eukaryotic cell walls. Glucan-chitosaccharide fractions of A. euteiches induced the expression of defense marker genes in Medicago truncatula seedlings independently from the presence of a functional Nod Factor Perception protein. Furthermore, one of the glucan-chitosaccharide fractions elicited calcium oscillations in the nucleus of root cells. In contrast to the asymmetric oscillatory calcium spiking induced by symbiotic lipochitooligosaccharides, this response depends neither on the Nod Factor Perception protein nor on the common symbiotic pathway. These findings open new perspectives in oomycete cell wall biology and elicitor recognition and signaling in legumes.
The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
The root microbiome is composed of an incredibly diverse microbial community that provides services to the plant. A major question in rhizosphere research is how species in root microbiome communities interact with each other and their host. In the nutrient mutualism between host plants and arbuscular mycorrhizal fungi (AMF), competition often leads to certain species dominating host colonization, with the outcome being dependent on environmental conditions. In the past, it has been difficult to quantify the abundance of closely related species and track competitive interactions in different regions of the rhizosphere, specifically within and outside the host. Here, we used an artificial root system (in vitro root organ cultures) to investigate intraradical (within the root) and extraradical (outside the root) competitive interactions between two closely related AMF species, Rhizophagus irregularis and Glomus aggregatum, under different phosphorus availabilities. We found that competitive interactions between AMF species reduced overall fungal abundance. R. irregularis was consistently the most abundant symbiont for both intraradical and extraradical colonization. Competition was the most intense for resources within the host, where both species negatively affected each other's abundance. We found the investment ratio (i.e. extraradical abundance/intraradical abundance) shifted for both species depending on whether competitors were present or not. Phosphorus availability did not change the outcome of these interactions. Our results suggest that studies on competitive interactions should focus on intraradical colonization dynamics and consider how changes in investment ratio are mediated by fungal species interactions.
Forests contribute a significant portion of the land carbon sink, but their ability to sequester CO2may be constrained by nitrogen1, 2, 3, 4, 5, 6, a major plant-limiting nutrient. Many tropical forests possess tree species capable of fixing atmospheric dinitrogen (N2)7, but it is unclear whether this functional group can supply the nitrogen needed as forests recover from disturbance or previous land use1, or expand in response to rising CO2 (refs 6, 8). Here we identify a powerful feedback mechanism in which N2 fixation can overcome ecosystem-scale deficiencies in nitrogen that emerge during periods of rapid biomass accumulation in tropical forests. Over a 300-year chronosequence in Panama, N2-fixing tree species accumulated carbon up to nine times faster per individual than their non-fixing neighbours (greatest difference in youngest forests), and showed species-specific differences in the amount and timing of fixation. As a result of fast growth and high fixation, fixers provided a large fraction of the nitrogen needed to support net forest growth (50,000 kg carbon per hectare) in the first 12 years. A key element of ecosystem functional diversity was ensured by the presence of different N2-fixing tree species across the entire forest age sequence. These findings show that symbiotic N2 fixation can have a central role in nitrogen cycling during tropical forest stand development, with potentially important implications for the ability of tropical forests to sequester CO2.
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 fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of biological N2fixation. One key question is whether the limited availability of fixed nitrogen was a factor in life's origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth's biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained through phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex life sustaining process
Symbiosis between Rhizobium bacteria and legumes leads to the formation of the root nodule. The endosymbiotic bacteria reside in polyploid host cells as membrane-surrounded vesicles where they reduce atmospheric nitrogen to support plant growth by supplying ammonia in exchange for carbon sources and energy. The morphology and physiology of endosymbionts, despite their common function, are highly divergent in different hosts. In galegoid plants, the endosymbionts are terminally differentiated, uncultivable polyploid cells, with remarkably elongated and even branched Y-shaped cells. Bacteroid differentiation is controlled by host peptides, many of which have antibacterial activity and require the bacterial function of BacA. Although the precise and combined action of several hundred host peptides and BacA has yet to be discovered, similarities, especially to certain insect-bacterium symbioses involving likewise host peptides for manipulation of endosymbionts, suggest convergent evolution. Rhizobium-legume symbiosis provides a rich source of information for understanding host-controlled endosymbiotic life in eukaryotic cells.
Eva Kondorosi, Peter Mergaert,and Attila Kereszt (2013) Annual Review Microniology 67: 611-628 (Volume publication date September 2013)DOI: 10.1146/annurev-micro-092412-155630
Quick, which is the biggest symbiotic association on Earth? Did you guess the mycorrhizae? They are the huge symbioses between fungi and the roots of most terrestrial plants. Their total size is not easy to measure because ...
Smarter use of the microbes that live in and around crops could pay huge dividends for farmers in the near future, according to an Iowa State University microbiologist.
Virtually since the discovery of nitrogen fixing Rhizobium-legume symbioses, researchers have dreamed of transferring this capability into nonlegume crop species (e.g., corn). It has been generally assumed that nonlegumes lack the ability to respond to the rhizobial lipo-chitin Nod factors, which are the essential signal molecules that trigger legume nodulation. However, our data indicate that Arabidopsis thaliana, as well as other nonlegume plants, do indeed recognize the rhizobial Nod factor via a mechanism that results in strong suppression of microbe-associated molecular pattern (MAMP)–triggered immunity. The mechanism of action leads to reduced levels of pattern recognition receptors on the plasma membrane involved in MAMP recognition.
In other words... non-legumes can perceive LCOs and this down-regulates defense reactions. Given that mycorrhizal fungi and probably pathogens produce LCOs that totally makes sense. However, in the case of Arabidopsis, there is strong evidence that a large part of the symbiotic signaling pathway found in many other plants has been lost. Anyway, this is a very interesting paper.
A large population of Medicago truncatula insertion lines has been generated using the Tnt1retrotransposon. More than 21,000 insertion lines have been generated, representing more than 500,000 insertion events. This mutant population is being used by the legume research community to screen for various different mutants using a forward genetics approach. Some of the phenotypes that have been screened using this population include developmentally abnormal phenotypes in leaves, stem, flowers, and roots. In addition to these, mutants with defects in symbiosis withRhizobium and mycorrhiza, mutants with altered nonhost resistance against Asian Soybean Rust and switch grass rust pathogens, mutants with altered lignin content, mutants with altered cell wall structure, etc. have been identified. Here, we describe the high throughput methodology that is being used to identify these M. truncatula mutants.
Juan Carlos Serrani Yarce, Hee-Kyung Lee, Million Tadege, Pascal Ratet, Kirankumar S. Mysore (2013). Methods Mol Biol. 1069:93-100.
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I totally agree!