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Scooped by
Jean-Michel Ané
February 5, 6:02 PM
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In Mexico, the center of maize origin (Zea mays ssp. mays), there are landraces from the highlands that develop extensive aerial root systems which secrete a carbohydrate-rich mucilage. This mucilage produces a favorable environment for nitrogenase activity by diazotrophs. This plant-microbial interaction enables the fixation of nitrogen (N) from the atmosphere, reducing the required N that otherwise must come from the soil and/or fertilizers. The objective of this research was to investigate the degree to which other landraces of maize and nutrient management affect aerial root growth and the ability of maize to perform and benefit from N2 fixation. In two replicated field experiments in Columbus, Ohio, USA in 2019 and 2020, we planted 21 maize landraces and three improved varieties with and without fertilizer to measure their growth, production of aerial roots, and rate of atmospheric N2 fixation using the 15N natural abundance method. Maize accessions varied in the growth rate and number of nodes with aerial roots. Up to 36% of plant N was derived from the atmosphere, with values varying by accession, the reference plant used, and the fertilizer level. Moreover, there was a positive relationship between early growth parameters and numbers of nodes with aerial roots, which, in turn, predicted the amount of N derived from the atmosphere. Thus, larger seedlings may experience enhanced root growth and thereby benefit more from N fixation. By phenotyping a diverse set of maize accessions with and without fertilizer, this study explores both environmental and quantitative genetic variation in the traits involved in N fixation capacity, clarifying that N fixation found in the Sierra Mixe landrace is more broadly distributed than previously thought. In sum, farmers stewarding genetic diversity in a crop center of origin have preserved traits essential for biological symbioses that contribute to maize's nutrient requirements. These traits may enable maize crops grown by Mexican farmers, and farmers globally, to benefit from N fixation from the atmosphere.
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Scooped by
Jean-Michel Ané
February 3, 7:56 PM
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Legumes form root nodules with symbiotic nitrogen-fixing rhizobacteria, which require ample iron to ensure symbiosis establishment and efficient nitrogen fixation. The functions and mechanisms of iron in nitrogen-fixing nodules are well established. However, the role of iron and the mechanisms by which legumes sense iron and incorporate this cue into nodulation signalling pathways remain unclear. Here we show that iron is a key driver of nodulation because symbiotic nodules cannot form without iron, even under conditions of sufficient light and low nitrogen. We further identify an iron optimum for soybean nodulation and the iron sensor BRUTUS A (BTSa) which acts as a hub for integrating iron and nodulation cues. BTSa is induced by rhizobia, binds to and is stabilized by iron. In turn, BTSa stabilizes and enhances the transcriptional activation activity of pro-nodulation transcription factor NSP1a by monoubiquitination from its RING domain and consequently activates nodulation signalling. Monoubiquitination of NSP1 by BTS is conserved in legumes to trigger nodulation under iron sufficiency. Thus, iron status is an essential cue to trigger nodulation and BTSa integrates cues from rhizobial infection and iron status to orchestrate host responses towards establishing symbiotic nitrogen fixation.
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Scooped by
Jean-Michel Ané
January 21, 5:17 PM
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Arbuscular mycorrhizal (AM) fungi engage in symbiotic relationships with plants, influencing their phosphate (Pi) uptake pathways, metabolism, and root cell physiology. Despite the significant role of Pi, its distribution and response dynamics in mycorrhizal roots remain largely unexplored. While traditional techniques for Pi measurement have shed some light on this, real-time cellular-level monitoring has been a challenge. With the evolution of quantitative imaging with confocal microscopy, particularly the use of genetically encoded fluorescent sensors, live imaging of intracellular Pi concentrations is now achievable. Among these sensors, fluorescence resonance energy transfer (FRET)-based biosensors stand out for their accuracy. In this study, we employ the Pi-specific biosensor (cpFLIPPi-5.3m) targeted to the cytosol or plastids of Brachypodium distachyon plants, enabling us to monitor intracellular Pi dynamics during AM symbiosis. A complementary control sensor, cpFLIPPi-Null, is introduced to monitor non-Pi-specific changes. Leveraging a semi-automated ImageJ macro for sensitized FRET analysis, this method provides a precise and efficient way to determine relative intracellular Pi levels at the level of individual cells or organelles.
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Scooped by
Jean-Michel Ané
January 20, 8:37 AM
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While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Scooped by
Jean-Michel Ané
January 13, 11:05 AM
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The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens–infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.
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Scooped by
Jean-Michel Ané
December 23, 2024 6:21 PM
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The soil environment affected by plant roots and their exudates, termed the rhizosphere, significantly impacts crop health and is an attractive target for engineering desirable agricultural traits. Engineering microbes in the rhizosphere is one approach to improving crop yields that directly minimizes the number of genetic modifications made to plants. Soil microbes have the potential to assist with nutrient acquisition, heat tolerance, and drought response if they can persist in the rhizosphere in the correct numbers. Unfortunately, the mechanisms by which microbes adhere and persist on plant roots are poorly understood, limiting their application. This study examined the membrane proteome shift upon adherence to roots in two bacteria of interest, Klebsiella variicola and Pseudomonas putida. From this surface proteome data, we identified a novel membrane protein from a nonlaboratory isolate of P. putida that increases binding to maize roots using unlabeled proteomics. When this protein was moved from the environmental isolate to a common lab strain (P. putida KT2440), we observed increased binding capabilities of P. putida KT2440 to both abiotic mimic surfaces and maize roots. We observed a similar increased binding capability to maize roots when the protein was heterologously expressed in K. variicola and Stutzerimonas stutzeri. With the discovery of this novel binding protein, we outline a strategy for harnessing natural selection and wild isolates to build more persistent strains of bacteria for field applications and plant growth promotion.
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Scooped by
Jean-Michel Ané
December 19, 2024 5:53 PM
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The advent of genome editing technologies, particularly CRISPR/Cas9, has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis. The legume–rhizobia symbiosis is crucial for sustainable agriculture, enhancing nitrogen fixation and improving soil fertility. Numerous genes with a symbiosis-specific expression have been identified, sometimes exclusively expressed in cells forming infection threads or in nitrogen-fixing nodule cells. Typically, mutations in these genes do not affect plant growth. However, in some instances, germline homozygous mutations can be lethal or result in complex pleiotropic phenotypes that are challenging to interpret. To address this issue, a rhizobia-inducible and cell-type-specific CRISPR/Cas9 strategy was developed to knock-out genes in specific legume transgenic root tissues. In this review, we discuss recent advancements in legume genome editing, highlighting the cell-type-specific CRISPR system and its crucial applications in symbiotic nitrogen fixation and beyond.
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Scooped by
Jean-Michel Ané
December 19, 2024 4:50 PM
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Microbial co-cultures have been used in several biotechnological applications. Within these co-cultures, the micro-organisms tend to interact with each other and perform complex actions vis-à-vis a single organism. Investigating metabolic interactions in microbial co-cultures is crucial in designing microbial consortia tailored for specific applications. In this study, we present a pipeline integrating modelling and experimental approaches to understand metabolic interactions between organisms in a community. We define a new index named Metabolic Support Index (MSI), which quantifies the benefits derived by each organism in the presence of the other when grown as a co-culture. We computed MSI for several experimentally demonstrated co-culture systems and showed that MSI, as a metric, accurately identifies the organism that derives the maximum benefit. We also computed MSI for a commonly used yeast co-culture consisting of Saccharomyces cerevisiae and Pichia stipitis and observed that the latter derives higher benefit from the interaction. Further, we designed two-stage experiments to study mutual interactions and showed that P. stipitis indeed derives the maximum benefit from the interaction, as shown from our computational predictions. Also, using our previously developed computational tool MetQuest, we identified all the metabolic exchanges happening between these organisms by analysing the pathways spanning the two organisms. By analysing the HPLC profiles and studying the isotope labelling, we show that P. stipitis consumes the ethanol produced by S. cerevisiae when grown on glucose-rich medium under aerobic conditions, as also indicated by our in silico pathway analyses. Our approach represents an important step in understanding metabolic interactions in microbial communities through an integrating framework of modelling and experiments.
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Scooped by
Jean-Michel Ané
December 18, 2024 11:47 AM
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The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.
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Scooped by
Jean-Michel Ané
December 12, 2024 11:43 AM
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The symbiotic association of legumes with rhizobia results in the formation of new root organs called nodules. However, the lifespan of nodules is limited by the senescence process. Increased proteolytic activity is one of the hallmarks of nodule senescence. In Medicago truncatula, a papain cysteine protease encoding gene, MtCP6, is a marker for the onset of nodule senescence under both developmental and stress-induced pathways.
To identify promoter regions conferring MtCP6 senescence-related expression, progressive MtCP6 promoter deletions were generated and the resulting sequences were fused with a reporter gene for promoter::GUS fusion analysis in transgenic M. truncatula roots.
In planta, a minimal promoter sequence of 67 bp was identified as sufficient for specific spatiotemporal transcriptional activation of MtCP6 in nodules. The functionality of this cis-regulatory sequence, thereafter named Nodule Senescence (NS), was validated by both gain- and loss-of-function approaches.
ERF091, an AP2/ERF family transcription factor, was identified in a yeast one-hybrid (Y1H) screen as an NS-box interacting factor, and shown to mediate transcription activation of a NS-box:GUS reporter in transactivation assays in Nicotiana benthamiana.
This work uncovered a new senescence-related nodule specific cis-regulatory region (NS-box) and provided evidence for the likely involvement of a stress-related ERF family member in the regulation of MtCP6, at the onset of nodule senescence.
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Scooped by
Jean-Michel Ané
November 13, 2024 2:55 PM
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The maturation and installation of the active site metal cluster (FeMo-co, Fe7S9CMo-R-homocitrate) in Mo-dependent nitrogenase requires the protein product of the nifB gene for production of the FeS cluster precursor (NifB-co, [Fe8S9C]) and the action of the maturase complex composed of the protein products from the nifE and nifN genes. However, some putative diazotrophic bacteria, like Roseiflexus sp. RS-1, lack the nifEN genes, suggesting an alternative pathway for maturation of FeMo-co that does not require NifEN. In this study, the Roseiflexus NifH, NifB, and apo-NifDK proteins produced in Escherichia coli are shown to be sufficient for FeMo-co maturation and insertion into the NifDK protein to achieve active nitrogenase. The E. coli expressed NifDKRS contained P-clusters but was devoid of FeMo-co (referred to as apo-NifDKRS). Apo-NifDKRS could be activated for N2 reduction by addition of preformed FeMo-co. Further, it was found that apo-NifDKRS plus E. coli produced NifBRS and NifHRS were sufficient to yield active NifDKRS when incubated with the necessary substrates (homocitrate, molybdate, and S-adenosylmethionine [SAM]), demonstrating that these proteins can replace the need for NifEN in maturation of Mo-nitrogenase. The E. coli produced NifHRS and NifBRS proteins were independently shown to be functional. The reconstituted NifDKRS demonstrated reduction of N2, protons, and acetylene in ratios observed for Azotobacter vinelandii NifDK. These findings reveal a distinct NifEN-independent pathway for nitrogenase activation involving NifHRS, NifBRS, and apo-NifDKRS.
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Scooped by
Jean-Michel Ané
November 7, 2024 5:18 PM
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Transposable elements (TEs) are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi (AMF) are beneficial plant symbionts with large, TE-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model AMF strains. Here, we aimed to obtain a more comprehensive understanding of TE function and evolution in AMF by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing TE activity contributing to the diversification of AMF lineages. We also found that TEs are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of TEs in promoting the diversity in proteins involved in molecular dialogues with hosts and, more generally, in driving gene regulation. The mechanisms of TEs evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.
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Scooped by
Jean-Michel Ané
October 9, 2024 2:47 PM
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Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.
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Scooped by
Jean-Michel Ané
February 4, 2:35 PM
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Root exudation, the export of low-molecular weight organic carbon (C) from living plant roots to soil, influences microbial activity, nutrient availability, and ecosystem feedbacks to climate change, but the magnitude of this C flux at ecosystem and global scales is largely unknown. Here, we synthesize in situ measurements of root exudation rates and couple those to estimates of fine root biomass to estimate global and biome-level root exudate C fluxes. We estimate a global root exudate flux of 13.4 (10.1–20.2) Pg C y−1, or about 9% (7–14%) of global annual gross primary productivity. We did not find differences in root mass-specific exudation rates among biomes, though total exudate fluxes are estimated to be greatest in grasslands owing to their high density of absorptive root biomass. Our synthesis highlights the global importance of root exudates in the terrestrial C cycle and identifies regions where more in situ measurements are needed to improve future estimates of root exudate C fluxes.
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Scooped by
Jean-Michel Ané
January 24, 7:05 AM
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Soil carbon (C) and nitrogen (N) mineralization rates are critical indicators of ecosystem functioning in agricultural land. However, the effects of agricultural land use on the interactions between soil C and N mineralization at different soil depths, especially in tropical regions, are poorly understood. Here, a longan orchard (LO) was converted to a conventional tea plantation (CTP) and an organic tea plantation (OTP) in the tropical region of China, and the responses of fungal and bacterial communities to these changes were assessed. The characteristics of the microbial communities, enzyme activities, and N and C mineralization rates were evaluated in response to the changes in land use. It was found that LO and OTP had faster N and C mineralization rates than CTP in surface soil. However, in subsurface soil, LO and OTP showed a faster C mineralization rate and a slower N mineralization rate than CTP. Structural equation modeling revealed that pH and C/N were the most crucial factors affecting N and C mineralization rates in surface soil. In contrast,soil bacterial and fungal community structures were the principal drivers of both the C and N mineralization in subsurface soil. Although soil C and net N mineralization were positively correlated in surface soil, this was not seen in subsurface soil. Collectively, this study demonstrated that differential drivers and their effects on the interactions between soil C and N mineralization at different soil depths should be considered for more accurate prediction of soil C and N dynamics under land-use changes.
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Scooped by
Jean-Michel Ané
January 20, 8:42 AM
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Endosymbioses have profoundly impacted the evolution of life and continue to shape the ecology of a wide range of species. They give rise to new combinations of biochemical capabilities that promote innovation and diversification1,2. Despite the many examples of known endosymbioses across the tree of life, their de novo emergence is rare and challenging to uncover in retrospect3,4,5. Here we implant bacteria into the filamentous fungus Rhizopus microsporus to follow the fate of artificially induced endosymbioses. Whereas Escherichia coli implanted into the cytosol induced septum formation, effectively halting endosymbiogenesis, Mycetohabitans rhizoxinica was transmitted vertically to the progeny at a low frequency. Continuous positive selection on endosymbiosis mitigated initial fitness constraints by several orders of magnitude upon adaptive evolution. Phenotypic changes were underscored by the accumulation of mutations in the host as the system stabilized. The bacterium produced rhizoxin congeners in its new host, demonstrating the transfer of a metabolic function through induced endosymbiosis. Single-cell implantation thus provides a powerful experimental approach to study critical events at the onset of endosymbiogenesis and opens opportunities for synthetic approaches towards designing endosymbioses with desired traits.
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Scooped by
Jean-Michel Ané
January 20, 8:35 AM
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Nutrient acquisition is crucial for sustaining life. Plants develop beneficial intracellular partnerships with arbuscular mycorrhiza (AM) and nitrogen-fixing bacteria to surmount the scarcity of soil nutrients and tap into atmospheric dinitrogen, respectively1,2. Initiation of these root endosymbioses requires symbiont-induced oscillations in nuclear calcium (Ca2+) concentrations in root cells3. How the nuclear-localized ion channels, cyclic nucleotide-gated channel (CNGC) 15 and DOESN’T MAKE INFECTIONS1 (DMI1)4 are coordinated to specify symbiotic-induced nuclear Ca2+ oscillations remains unknown. Here we discovered an autoactive CNGC15 mutant that generates spontaneous low-frequency Ca2+ oscillations. While CNGC15 produces nuclear Ca2+ oscillations via a gating mechanism involving its helix 1, DMI1 acts as a pacemaker to specify the frequency of the oscillations. We demonstrate that the specificity of symbiotic-induced nuclear Ca2+ oscillations is encoded in its frequency. A high frequency activates endosymbiosis programmes, whereas a low frequency modulates phenylpropanoid pathways. Consequently, the autoactive cngc15 mutant, which is capable of generating both frequencies, has increased flavonoids that enhance AM, root nodule symbiosis and nutrient acquisition. We transferred this trait to wheat, resulting in field-grown wheat with increased AM colonization and nutrient acquisition. Our findings reveal a new strategy to boost endosymbiosis in the field and reduce inorganic fertilizer use while sustaining plant growth.
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Scooped by
Jean-Michel Ané
January 6, 5:46 PM
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Brace roots are the primary organs for water and nutrient absorption, and play an important role in lodging resistance. Dissecting the genetic basis of brace root traits will facilitate breeding new varieties with lodging resistance and high yield. In present study, genome-wide association study (GWAS) and genomic selection (GS) for brace root penetrometer resistance (PR), root number (RN), and tier number (TN) were conducted in a multi-parent doubled haploid (DH) population. Although the three brace root traits were significantly influenced by genotype-by-environment interactions, relatively high heritabilities were observed for RN (79.25%), TN (81.00%), and PR (74.28%). At the threshold of P-value < 7.42 × 10− 6, 22 SNPs distributed on all 10 chromosomes, except for chromosome 7, and 50 candidate genes were identified using the FarmCPU model. Zm00001d028733, Zm00001d002350, Zm00001d002349, and Zm00001d043694 may be involved in brace root growth. The prediction accuracies of RN, TN, and PR estimated by five-fold cross-validation method with genome-wide SNPs were 0.39, 0.36, and 0.51, respectively, which can be greatly improved by using 100–300 significant SNPs. This study provides new insights into the genetic architecture of brace root traits and genomic selection for breeding lodging resistance maize varieties.
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Scooped by
Jean-Michel Ané
December 19, 2024 6:04 PM
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Background and aims Given increasing climate variability, understanding how rhizosphere microbial communities respond to drying–rewetting cycles and how these cycles impact crop growth under different tillage practices is crucial for improving crop resilience and productivity.
Methods We conducted an experiment with 16 pots at the Institute of Soil Science, Chinese Academy of Sciences, using soils from Lishu, China that had undergone long-term (15-year) traditional (CK) and conservation (CT) tillage practices. We investigated the effects of drying–rewetting cycles on the assembly, diversity, and network of rhizosphere soil microbial communities and their relationships with plant growth.
Results Compared with consistently moist (W) conditions, the plant growth index (PGI, a comprehensive measure of plant health and growth) under drying–rewetting (D) conditions decreased significantly by 74.7–74.9%. Moreover, the PGI under CT was 46.6–48% greater than that under CK. The D conditions significantly increased the stochasticity of the protistan community assembly. Both D and CT conditions are conducive to the formation of complex associations in multitrophic networks. Soil moisture indirectly impacts potential cross-trophic associations and, ultimately, the PGI by influencing protistan community stochasticity and the β-diversity of bacterial communities.
Conclusion The results highlight the crucial roles of soil microbial community assembly and coexistence patterns in plant growth during drying–rewetting cycles. Such novel insights provide a basis for developing tillage strategies to increase crop resilience under moisture fluctuations. These findings are crucial for future research on synergistic drought resistance in rhizosphere soil micro-food webs and plants under global change.
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Scooped by
Jean-Michel Ané
December 19, 2024 5:51 PM
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While establishing symbiotic relationships with nitrogen-fixing soil bacteria certain legumes produce nodule-specific cysteine rich peptides. These peptides turn the bacteria into terminally differentiated non-replicative bacteroids. Here, we discuss the properties, essentiality, emerging clinical and agricultural applications, and the need to study the detailed mechanism of action of these peptides.
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Scooped by
Jean-Michel Ané
December 19, 2024 12:48 PM
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The domestication of agriculture is widely recognized as one of the most crucial technological adaptations for the transition of humanity from hunter-and-gatherer groups into early city-states and ultimately, complex civilizations. As humankind sets forth to permanently establish itself on the Moon and use it as a testing ground to colonize other worlds, like Mars, agriculture will again play a pivotal role. In this case, the development of sustainable crop production systems capable of succeeding in these harsh environments becomes vital to the success of our star-faring journey. Over decades, studies varying in species and approaches have been conducted in microgravity, testing the limits of plants and various growth systems, to better understand how Earth-based agriculture could be translated into environmental conditions and therefore evolutionary pressures beyond what life on our planet has known. While we have passed several significant milestones, we are still far from the goal of a sustainable agricultural system beyond our planet Regolith-based agriculture (RBA) should be a component of sustainable agriculture solutions beyond Earth, one which can also provide insight into plant growth in poor soils across our own world. However, RBA studies are in their infancy and, like any other new field, need an established set of parameters to be followed by the RBA community so the generated data can be standardized and validated. Here, we provide an extensive multi-disciplinary review of the state of RBA, outline important knowledge gaps, and propose a set of standardized methods and benchmarks for regolith simulant development and selection as well as plant, microbe, and plant-microbe interaction studies conducted in lunar and Martian regolith. Our goal is to spur dialog within the RBA community on proper regolith simulant selection, experimental design, and reporting. Our methods are divided into complexity tiers, providing a clear path for even the simplest experiments to contribute to the bulk of the knowledge that will shape the future of RBA science and see it mature as an integrated part of sustainable off-world agriculture.
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Scooped by
Jean-Michel Ané
December 18, 2024 11:37 AM
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The rhizosphere, where plant roots meet soil, is a hub of biogeochemical activity with ecosystem impacts on carbon stocks. Root derived carbon has been found to contribute more to soil carbon stocks than aboveground litter. Nonetheless, the molecular chemodiversity of root exudates remains poorly understood due to limited characterization and annotation. Here our goal was to discover the molecular chemodiversity of metabolites and lipids in root exudates to advance our understanding of plant root inputs belowground. We worked with mature, field-grown tall wheatgrass (Thinopyrum ponticum) and optimized exudate collection protocols to enable the capture of non-polar lipids in addition to polar and semi-polar metabolites. Rates of carbon input via hydrophobic exudates were approximately double that of aqueous exudates and carbon/nitrogen ratios were markedly higher in hydrophobic compared to aqueous exudates, emphasizing the importance of lipids, due to their high carbon content. To maximize molecular coverage of exudate chemodiversity, we used liquid chromatography coupled tandem mass-spectrometry for paired untargeted metabolomics and lipidomics or ‘metabo-lipidomics’. We substantially increased the characterization of exudate chemodiversity by employing both tandem mass spectral library searching and deep learning-based chemical class assignment. Notably, in this unprecedented characterization of intact lipids in root exudates, we discovered a diverse variety of lipids, including substantial levels of triacylglycerols (∼19 μg/g fresh root per min), fatty acyls, sphingolipids, sterol lipids, and glycerophospholipids. Comparison of the root exudate and tissue lipidomes revealed minimum glycerophospholipids in exudates, suggesting the exudate protocol did not extract lipids from root cell membranes.
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Scooped by
Jean-Michel Ané
December 10, 2024 11:15 AM
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Soil microbiota can confer fitness advantages to plants and increase crop resilience to drought and other abiotic stressors. However, there is little evidence on the mechanisms correlating a microbial trait with plant abiotic stress tolerance. Here, we report that Streptomyces effectively alleviate drought and salinity stress by producing spiroketal polyketide pteridic acid H (1) and its isomer F (2), both of which promote root growth in Arabidopsis at a concentration of 1.3 nM under abiotic stress. Transcriptomics profiles show increased expression of multiple stress responsive genes in Arabidopsis seedlings after pteridic acids treatment. We confirm in vivo a bifunctional biosynthetic gene cluster for pteridic acids and antimicrobial elaiophylin production. We propose it is mainly disseminated by vertical transmission and is geographically distributed in various environments. This discovery reveals a perspective for understanding plant-Streptomyces interactions and provides a promising approach for utilising beneficial Streptomyces and their secondary metabolites in agriculture to mitigate the detrimental effects of climate change.
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Scooped by
Jean-Michel Ané
November 12, 2024 3:05 PM
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Increasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. The aim of this research was to elucidate the mechanism of action of these strains. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha-1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.
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Scooped by
Jean-Michel Ané
October 9, 2024 2:52 PM
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The symbiosis between Mesorhizobium japonicum R7A and Lotus japonicus Gifu is an important model system for investigating the role of bacterial exopolysaccharides (EPS) in plant-microbe interactions. Previously, we showed that R7A exoB mutants that are affected at an early stage of EPS synthesis and in lipopolysaccharide (LPS) synthesis induce effective nodules on L. japonicus Gifu after a delay, whereas exoU mutants affected in the biosynthesis of the EPS side chain induce small uninfected nodule primordia and are impaired in infection. The presence of a halo around the exoU mutant when grown on Calcofluor-containing media suggested the mutant secreted a truncated version of R7A EPS. A nonpolar ΔexoA mutant defective in the addition of the first glucose residue to the EPS backbone was also severely impaired symbiotically. Here, we used a suppressor screen to show that the severe symbiotic phenotype of the exoU mutant was due to the secretion of an acetylated pentasaccharide, as both monomers and oligomers, by the same Wzx/Wzy system that transports wild-type exopolysaccharide. We also present evidence that the ΔexoA mutant secretes an oligosaccharide by the same transport system, contributing to its symbiotic phenotype. In contrast, ΔexoYF and polar exoA and exoL mutants have a similar phenotype to exoB mutants, forming effective nodules after a delay. These studies provide substantial evidence that secreted incompatible EPS is perceived by the plant, leading to abrogation of the infection process.
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Don't be too excited... Normalizing the data to sunflower is irrelevant, There is no evidence for significant biological nitrogen fixation here.