Plant-Microbe Symbiosis
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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Hyphosphere microbiome of arbuscular mycorrhizal fungi: a realm of unknowns

Hyphosphere microbiome of arbuscular mycorrhizal fungi: a realm of unknowns | Plant-Microbe Symbiosis | Scoop.it
The extraradical hyphae-associated microbiome of arbuscular mycorrhizal fungi (AMF), the “hyphosphere microbiome,” harbors a diverse reservoir of microbes. The biological interactions in the AMF hyphosphere have major implications for soil carbon and nutrient cycling, soil food web dynamics, and plant nutrition and health. Hyphosphere microbial communities are thought to assist AMF in accessing organic nutrients by degrading complex organic compounds that AMF are unable to do by themselves. The AMF, in return, provide an energy-rich microhabitat supplied with hyphal exudates that facilitates microbial growth and mobility in the hyphosphere. However, our current knowledge of hyphosphere entities, their trophic interactions and functional roles, and the underlying mechanisms facilitating microbial co-occurrence and co-operation is largely incomplete. Here, we review the current state of knowledge on the identity and putative roles of AMF hyphae-associated microbes, with a specific focus on prokaryotes, and potential drivers of such microbial communities in the hyphosphere. Moreover, we discuss the knowledge gaps and open challenges that should be addressed and prioritized in future studies on the AMF microbiomes. We also provide an appraisal of available and emerging tools and technologies and highlight the need for innovative approaches to disentangle AMF hyphosphere processes and answer the many unresolved questions.

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Mycorrhiza governs plant-plant interactions through preferential allocation of shared nutritional resources: A triple (13C, 15N and 33P) labeling study

Mycorrhiza governs plant-plant interactions through preferential allocation of shared nutritional resources: A triple (13C, 15N and 33P) labeling study | Plant-Microbe Symbiosis | Scoop.it
Plant-plant interactions and coexistence can be directly mediated by symbiotic arbuscular mycorrhizal (AM) fungi through asymmetric resource exchange between the plant and fungal partners. However, little is known about the effects of AM fungal presence on resource allocation in mixed plant stands. Here, we examined how phosphorus (P), nitrogen (N) and carbon (C) resources were distributed between coexisting con- and heterospecific plant individuals in the presence or absence of AM fungus, using radio- and stable isotopes. Congeneric plant species, Panicum bisulcatum and P. maximum, inoculated or not with Rhizophagus irregularis, were grown in two different culture systems, mono- and mixed-species stands. Pots were subjected to different shading regimes to manipulate C sink-source strengths. In monocultures, P. maximum gained more mycorrhizal phosphorus uptake benefits than P.bisulcatum. However, in the mixed culture, the AM fungus appeared to preferentially transfer nutrients (33P and 15N) to P.bisulcatum compared to P. maximum. Further, we observed higher 13C allocation to mycorrhiza by P.bisulcatum in mixed- compared to the mono-systems, which likely contributed to improved competitiveness in the mixed cultures of P.bisulcatum vs. P. maximum regardless of the shading regime. Our results suggest that the presence of mycorrhiza influenced competitiveness of the two Panicum species in mixed stands in favor of those with high quality partner, P. bisulcatum, which provided more C to the mycorrhizal networks. However, in mono-species systems where the AM fungus had no partner choice, even the lower quality partner (i.e., P.maximum) could also have benefitted from the symbiosis. Future research should separate the various contributors (roots vs. common mycorrhizal network) and mechanisms of resource exchange in such a multifaceted interaction.

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Great paper from @JanJansa8 and coll. 

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Putrescine acts as a signaling metabolite in the transition from nodulation to nitrogen fixation in Rhizobium phaseoli

Growth of the common bean plant Phaseolus vulgaris is tightly linked to its symbiotic relationship with diverse rhizobial species, particularly Rhizobium phaseoli, an alphaproteobacteria that forms root nodules and provides high levels of nitrogen to the plant. Molecular cross-talk is known to happen via plant-derived metabolites, but only flavonoids have been identified as signals. Flavonoids are transported inside the bacteria, where they signal the NodD regulator to elicit nodulation. Although seven other regulators are known to be involved, our knowledge of the regulatory mechanisms underlying the nodulation, and nitrogen fixation processes is limited, and the signals recognized by regulators are mostly unknown. Here, we identified 75 transcription factors in R. phaseoli genome through sequence conservation from Escherichia coli, and assembled a transcriptional regulatory network comprising 24 regulators, and 652 target genes. We identified the interactions relevant to nodulation via gene expression, and signaled out putrescine as a signaling metabolite. We propose a model where putrescine acts as a switch on the transition from nodulation to nitrogen fixation via the dual transcription factor PuuR, and its regulation of the nodI and nifU2 genes.

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Symbiosis for rhizobia is not an easy ride | Nature Microbiology

Symbiosis for rhizobia is not an easy ride | Nature Microbiology | Plant-Microbe Symbiosis | Scoop.it
Dear reader, let me tell you a story. A true story, mind you, as all the best ones are. It begins in Australia where the continental crust is among the lightest and oldest, with rocks up to 4.5 billion years old. This means that the crust is highly weathered with soils typically lacking minerals, particularly phosphorous and nitrogen. As a result, there is a strong selection pressure for the evolution of legumes — plants that can house rhizobia that fix atmospheric N2 in root nodules. However, this is Australia, and, of course, the native legumes often contain fluoroacetate, a poison to prevent grazing by animals. Now a bit of fluoroacetate doesn’t deter the average possum, wombat or kangaroo. The native marsupials are resistant but sheep and cattle are most definitely not. To prevent poisoning of livestock, Australians imported legumes, such as clovers, vetches and alfalfa, from the rest of the world as well their rhizobial microsymbionts. In the 1960s, the expression was that Australia rode on the sheep’s back, but I would argue it rode on the root nodules of legumes and their mighty rhizobia.

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Great read from @PooleLabOxford as always!

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Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography–mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.
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Phytophagy impacts the quality and quantity of plant carbon resources acquired by mutualistic arbuscular mycorrhizal fungi

Phytophagy impacts the quality and quantity of plant carbon resources acquired by mutualistic arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it

Really cool work from @KatieField4, @Chris_Bell6, @EmilyMagk, @UrwinLab and coll. on how plants deal with arbuscular mycorrhizal associations and nematodes at the same time. 

Arbuscular mycorrhizal (AM) fungi associate with the roots of many plant species, enhancing their hosts access to soil nutrients whilst obtaining their carbon supply directly as photosynthates. AM fungi often face competition for plant carbon from other organisms. The mechanisms by which plants prioritise carbon allocation to mutualistic AM fungi over parasitic symbionts remain poorly understood. Here, we show that host potato plants (Solanum tuberosum cv. Désirée) selectively allocate carbon resources to tissues interacting with AM fungi rather than those interacting with phytophagous parasites (the nematode Globodera pallida). We found that plants reduce the supply of hexoses but maintain the flow of plant-derived fatty acids to AM fungi when concurrently interacting with parasites. Transcriptomic analysis suggest that plants prioritise carbon transfer to AM fungi by maintaining expression of fatty acid biosynthesis and transportation pathways, whilst decreasing the expression of mycorrhizal-induced hexose transporters. We also report similar findings from a different plant host species (Medicago truncatula) and phytophagous pest (the aphid Myzus persicae). These findings suggest a general mechanism of plant-driven resource allocation in scenarios involving multiple symbionts.

Jean-Michel Ané's insight:

Really cool work from @KatieField4, @Chris_Bell6, @EmilyMagk, @UrwinLab and coll. on how plants deal with arbuscular mycorrhizal associations and nematodes at the same time. 

 

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Receptor-associated kinases control the lipid provisioning program in plant–fungal symbiosis

Receptor-associated kinases control the lipid provisioning program in plant–fungal symbiosis | Plant-Microbe Symbiosis | Scoop.it
The mutualistic association between plants and arbuscular mycorrhizal (AM) fungi requires intracellular accommodation of the fungal symbiont and maintenance by means of lipid provisioning. Symbiosis signaling through lysin motif (LysM) receptor-like kinases and a leucine-rich repeat receptor-like kinase DOES NOT MAKE INFECTIONS 2 (DMI2) activates transcriptional programs that underlie fungal passage through the epidermis and accommodation in cortical cells. We show that two Medicago truncatula cortical cell–specific, membrane-bound proteins of a CYCLIN-DEPENDENT KINASE-LIKE (CKL) family associate with, and are phosphorylation substrates of, DMI2 and a subset of the LysM receptor kinases. CKL1 and CKL2 are required for AM symbiosis and control expression of transcription factors that regulate part of the lipid provisioning program. Onset of lipid provisioning is coupled with arbuscule branching and with the REDUCED ARBUSCULAR MYCORRHIZA 1 (RAM1) regulon for complete endosymbiont accommodation.
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Outstanding work from Maria Harrison and Sergey Ivanov. A must read.

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NPF and NRT2 from Pisum sativum Potentially Involved in Nodule Functioning: Lessons from Medicago truncatula and Lotus japonicus

NPF and NRT2 from Pisum sativum Potentially Involved in Nodule Functioning: Lessons from Medicago truncatula and Lotus japonicus | Plant-Microbe Symbiosis | Scoop.it
In addition to absorbing nitrogen from the soil, legumes have the ability to use atmospheric N2 through symbiotic nitrogen fixation. Therefore, legumes have developed mechanisms regulating nodulation in response to the amount of nitrate in the soil; in the presence of high nitrate concentrations, nodulation is inhibited, while low nitrate concentrations stimulate nodulation and nitrogen fixation. This allows the legumes to switch from soil nitrogen acquisition to symbiotic nitrogen fixation. Recently, particular interest has been given to the nitrate transporters, such as Nitrate Transporter1/Peptide transporter Family (NPF) and Nitrate Transporter 2 (NRT2), having a role in the functioning of nodules. Nitrate transporters of the two model plants, Lotus japonicus and Medicago truncatula, shown to have a positive and/or a negative role in nodule functioning depending on nitrate concentration, are presented in this article. In particular, the following transporters were thoroughly studied: (i) members of NPF transporters family, such as LjNPF8.6 and LjNPF3.1 in L. japonicus and MtNPF1.7 and MtNPF7.6 in M. truncatula, and (ii) members of NRT2 transporters family, such as LjNRT2.4 and LjNRT2.1 in L. japonicus and MtNRT2.1 in M. truncatula. Also, by exploiting available genomic and transcriptomic data in the literature, we have identified the complete PsNPF family in Pisum sativum (69 sequences previously described and 21 new that we have annotated) and putative nitrate transporters candidate for playing a role in nodule functioning in P. sativum.
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A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot

A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot | Plant-Microbe Symbiosis | Scoop.it
While arbuscular mycorrhizal (AM) fungi are known for providing host plants with improved drought tolerance, we know very little about the fungal response to drought in the context of the fungal–plant relationship. In this study, we evaluated the drought responses of the host and symbiont, using the fungus Rhizophagus irregularis with carrot (Daucus carota) as a plant model. Carrots inoculated with spores of R. irregularis DAOM 197198 were grown in a greenhouse. During taproot development, carrots were exposed to a 10-day water restriction. Compared with well-watered conditions, drought caused diminished photosynthetic activity and reduced plant growth in carrot with and without AM fungi. Droughted carrots had lower root colonization. For R. irregularis, 93% of 826 differentially expressed genes (DEGs) were upregulated during drought, including phosphate transporters, several predicted transport proteins of potassium, and the aquaporin RiAQPF2. In contrast, 78% of 2,486 DEGs in AM carrot were downregulated during drought, including the symbiosis-specific genes FatM, RAM2, and STR, which are implicated in lipid transfer from the host to the fungus and were upregulated exclusively in AM carrot during well-watered conditions. Overall, this study provides insight into the drought response of an AM fungus in relation to its host; the expression of genes related to symbiosis and nutrient exchange were downregulated in carrot but upregulated in the fungus. This study reveals that carrot and R. irregularis exhibit contrast in their regulation of gene expression during drought, with carrot reducing its apparent investment in symbiosis and the fungus increasing its apparent symbiotic efforts.

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Latest paper from our lab on the interactions between arbuscular mycorrhizal associations and drought with @Emsilva624 and collaborators.

 
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The role of arbuscular mycorrhizal symbiosis in plant abiotic stress

The role of arbuscular mycorrhizal symbiosis in plant abiotic stress | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal fungi (AMF) can penetrate plant root cortical cells, establish a symbiosis with most land plant species, and form branched structures (known as arbuscules) for nutrient exchange. Plants have evolved a complete plant–AMF symbiosis system to sustain their growth and development under various types of abiotic stress. Here, we highlight recent studies of AM symbiosis and the regulation of symbiosis process. The roles of mycorrhizal symbiosis and host plant interactions in enhancing drought resistance, increasing mineral nutrient uptake, regulating hormone synthesis, improving salt resistance, and alleviating heavy metal stress were also discussed. Overall, studies of AM symbiosis and a variety of abiotic stresses will aid applications of AMF in sustainable agriculture and can improve plant production and environmental safety.

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Review for teaching purposes

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Nodulation Signaling Pathway 1 and 2 Modulate Vanadium Accumulation and Tolerance of Legumes

Vanadium (V) pollution potentially threatens human health. Here, it is found that nsp1 and nsp2, Rhizobium symbiosis defective mutants of Medicago truncatula, are sensitive to V. Concentrations of phosphorus (P), iron (Fe), and sulfur (S) with V are negatively correlated in the shoots of wild-type R108, but not in mutant nsp1 and nsp2 shoots. Mutations in the P transporter PHT1, PHO1, and VPT families, Fe transporter IRT1, and S transporter SULTR1/3/4 family confer varying degrees of V tolerance on plants. Among these gene families, MtPT1, MtZIP6, MtZIP9, and MtSULTR1;1 in R108 roots are significantly inhibited by V stress, while MtPHO1;2, MtVPT2, and MtVPT3 are significantly induced. Overexpression of Arabidopsis thaliana VPT1 or M. truncatula MtVPT3 increases plant V tolerance. However, the response of these genes to V is weakened in nsp1 or nsp2 and influenced by soil microorganisms. Mutations in NSPs reduce rhizobacterial diversity under V stress and simplify the V-responsive operational taxonomic unit modules in co-occurrence networks. Furthermore, R108 recruits more beneficial rhizobacteria related to V, P, Fe, and S than does nsp1 or nsp2. Thus, NSPs can modulate the accumulation and tolerance of legumes to V through P, Fe, and S transporters, ion homeostasis, and rhizobacterial community responses.

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14th International Conference of the French Society of Plant Biology, 2024 June 12-14 @ Bordeaux, save the date

14th International Conference of the French Society of Plant Biology, 2024 June 12-14 @ Bordeaux, save the date | Plant-Microbe Symbiosis | Scoop.it

The primary objective of the 14th International Conference organized by the French Society of Plant Biology (SFBV) is to unite individuals with a keen interest in the biological characteristics of photosynthetic organisms, with a particular focus on plants. The conference will explore the practical applications of this knowledge in agriculture and bioenergy, addressing crucial issues such as global climate change and environmental preservation. At its core, the event aims to champion the comprehensive field of plant biology, encompassing both fundamental and applied aspects, while celebrating its diverse facets.
Throughout the conference, there will be a deliberate examination of plants within their environments and their intricate interactions with the surroundings. Recent advancements in:

•    Session introduction: Olivier Hamant « The 1972 Meadows report: A wake-up call for plant science » Round table animated by Olivier le Gall

•    Session 1 : Plant Imaging – Martine Pastuglia (IJPB, Versailles)

•    Session 2 : Genome structure & expression – Frédy Barnèche (IBENS, Paris)

•    Session 3 : Agricultural systems in the agroecological transition – To Be Announced

•    Session 4 : Intra- and inter-cellular communications in plants – Fahrah Assaad (TUM, München)

 •    Session 5:  Plant and pathogen interactions – Christine Faulkner (JIC, Norwich)

•    Session 6 : Plant and beneficial microorganism interactions, microbiome – Sofie Goormachtig (VIB, Ghent)

•    Session 7 : Plant development and nutrition – Bruno Guillotin (NYU, New York)

•    Session 8 : Environmental stresses – Petra Marhava (UPSC, Umeå)

•    Session 9 : Genomics, genetics and breeding – Alain Charcosset (GQE Le Moulon, Saclay)

•    Session 10 : Plant and algae metabolism – Mark Stitt (MPI, Golm)

Importantly, this gathering also seeks to initiate or uphold scientific collaborations, facilitate interactions among diverse stakeholders in the realm of plant biology research, and forge connections between public research institutions and private enterprises. Prioritizing the involvement of emerging scientists in such events is a key focus of the SFBV. In line with this commitment, scholarships will be extended to students for their participation in the 14th International Conference of the French Society of Plant Biology, with recognition through awards for outstanding oral presentations and posters.

Opening subscription end of January 2024


Via Saclay Plant Sciences
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Global responses of soil bacteria and fungi to inoculation with arbuscular mycorrhizal fungi

Global responses of soil bacteria and fungi to inoculation with arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) fungi exist naturally in most ecosystems and have significant effects on other soil microbes, but how these effects vary across ecosystem types and experimental conditions remains unclear. We compiled a global dataset to identify the responses of soil bacteria and fungi to AM fungal inoculation, and whether these responses vary or are consistent across ecosystem types (cropland, grassland, and forest) and experimental conditions (sterilized vs. non-sterilized soils; mixed vs. single AM fungal inoculation; and field studies vs. greenhouse experiments). Our analysis of the global data showed that AM fungal inoculation increased almost all soil bacterial and fungal parameters examined (1.4–45.0 %), except for fungal abundance which decreased significantly (−13.6 %). Plant, shoot, and root biomass were also increased by 23.3 %, 15.7 %, and 30.1 % after AM fungal inoculation, respectively. Additionally, the effects of AM fungi on most soil bacterial and fungal metrics did not differ significantly among ecosystem types and experimental conditions applied. Changes in pH and soil organic carbon were key factors contributing to the responses of bacteria and fungi. These findings highlight the consistent positive effects of AM fungal inoculation on soil bacteria and fungi across various ecosystem types, which may simplify the prediction of AM fungal functionality and related important ecological processes at large spatial scales. Moreover, the roles of bacteria and fungi in supporting ecosystem functionality may be overestimated without considering the effects of AM fungi. Therefore, the effects of AM fungi on soil bacteria and fungi should be explicitly disentangled when evaluating the roles that bacteria and fungi play in terrestrial ecosystems.

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A CRISPR interference system for engineering biological nitrogen fixation

A CRISPR interference system for engineering biological nitrogen fixation | Plant-Microbe Symbiosis | Scoop.it
A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, the globally consequential, nitrogenase-catalyzed reduction of atmospheric nitrogen to bioavailable ammonia, is a vital area of focus. Nitrogen fixation engineering relies upon extensive understanding of underlying genetics in microbial models, including the broadly utilized gammaproteobacterium, Azotobacter vinelandii (A. vinelandii). Here, we report the first CRISPR interference (CRISPRi) system for targeted gene silencing in A. vinelandii that integrates genomically via site-specific transposon insertion. We demonstrate that CRISPRi can repress transcription of an essential nitrogen fixation gene by ~60%. Further, we show that nitrogenase genes are suitably expressed from the transposon insertion site, indicating that CRISPRi and engineered nitrogen fixation genes can be co-integrated for combinatorial studies of gene expression and engineering. Our established CRISPRi system fills an important gap for engineering microbial nitrogen fixation for desired purposes.
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Great paper from @betulland @UWBact on CRISPRi in Azotobacter. Super useful tool!

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The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

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Fantastic review from @fmartin1954 and @vandeHeijdenLab. I highly recommend it.

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Diazotrophs/Lettuce Symbiosis Platform Established upon Carbon Dots/Microalgae Hybrid System

Diazotrophs/plant symbiosis model system has been developed but the nitrogen fixation efficiency of engineering systems was suboptimal compared to the wild-type system. In this study, CDs with benzoquinone structure and phenazine structure that prepared from O-phenylenediamine (o-PD) and catechol (CAT) were selected as electron-donor and electron relay for constructing CDs/microalgae nitrogen fixation hybrid system. the X-ray photoelectron spectroscope (XPS) and Fourier transform infrared spectrometer (FTIR) results demonstrated the presence of C=O bond from benzoquinone on CDs. 1H-Nuclear magnetic resonance (NMR) spectra reveal the fluorescent molecules linking on the CDs’ surface. The photocurrent response demonstrates the photoelectron donor ability of CDs. Nostoc commune Vauch microalgae were selected as a diazotroph. The hybrid system exhibited 1.32 times ethylene-produced content compared to pure microalgae. Linking this hybrid system with the lettuce hydroponics platform, the lettuce successfully utilized the nitrogen in the atmosphere as ammonia fertilizer. The net photosynthetic rate, total fresh weight, total chlorophyll content, and total soluble protein content of lettuce growth in the established platform increased by 1.20, 1.12, 1.14, and 1.32 times, respectively.
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Medicago truncatula ABCG40 is a cytokinin importer that negatively regulates lateral root density and nodule number

Numerous studies suggest that cytokinin (CK) distribution plays a relevant role in shaping plant morphology in changing environments. Nonetheless, our knowledge about the involvement of short-distance CK translocation in root mineral nutrition remains scarce, and the specific role of CK transporters in root morphology has yet to be established. Therefore, the molecular identity of CK transporters should be determined to increase knowledge on root plasticity during soil fertility, as well as more frequently encountered plant nutrient deficiencies. In this work, we identified and characterized the Medicago truncatula full-size ATP-binding cassette (ABC) transporter of the G subfamily MtABCG40 as a plasma membrane CK importer. Its expression is root-specific and is induced by nitrogen deprivation and CKs. Our analyses indicate that MtABCG40 exerts a negative impact on lateral root density by decreasing lateral root initiation and enhancing primary root elongation. Moreover, we also observed that this transporter negatively influenced the nodule number. Our results suggest that MtABCG40 action affects CK signalling, which impacts the cellular response to auxin. In summary, we identified a novel ABCG-type CK transporter that regulates lateral root density and nodule number.

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Masters of Manipulation: How Our Molecular Understanding of Model Symbiotic Fungi and Their Hosts Is Changing the Face of “Mutualism”

Masters of Manipulation: How Our Molecular Understanding of Model Symbiotic Fungi and Their Hosts Is Changing the Face of “Mutualism” | Plant-Microbe Symbiosis | Scoop.it
Ectomycorrhizal (ECM) fungi are soil-borne organisms found predominantly in forest environments where they colonize the roots of trees and shrubs to gain nutrients that support growth. Classed as mutualistic fungi, this group of organisms also supports their host plants through a variety of mechanisms. However, to gain a foothold in these competitive environments, ECM fungi have evolved the ability to manipulate both their host plants and other organisms to carve a significant niche. In this chapter, using well-established and developing models, we will consider the role of ECM fungal signals involved in the structuring of their environment during the colonization of soil and plant tissues. We will also give an overview of the different signaling network hubs that ECM fungi must overcome or control to establish a nutrient exchange between both partners. We will conclude with the outlook in this area of research and future directions that are necessary to further our understanding of how fungal mutualism evolved and how to manage these symbioses under variable climate scenarios.

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The underground network: Decoding the dynamics of plant-fungal symbiosis

The underground network: Decoding the dynamics of plant-fungal symbiosis | Plant-Microbe Symbiosis | Scoop.it
New research, published in the journal Science, delves into this partnership, revealing key insights that deepen our understanding of plant-AM fungi interactions and could lead to advances in sustainable agriculture.

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Nice press release about @arb_myc's recent paper in @sciencemagazine

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Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

All living organisms contain genes that are expressed to fulfill all the functions an organism needs to survive. Understanding when and how genes are expressed is a major scientific goal. Circular RNAs are a type of RNA involved in plant gene expression, but we don't know much about what circular RNAs do in plants, how they work, or which ones are important. We used two different methods to find circRNAs in the plant Lotus japonicus because this plant is used by many research groups to understand gene expression in legumes, which are plants that can form symbioses with microbes. We found that both methods worked well, but neither method found all circular RNAs. We were able to identify almost 6000 circular RNAs. Now that we know some of the circRNAs in Lotus japonicus the research community can come up with hypotheses and design experiments to learn more about how circRNAs are involved in plant gene expression.

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Synthetic microbiology in sustainability applications

Synthetic microbiology in sustainability applications | Plant-Microbe Symbiosis | Scoop.it
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains — factory, farm and field — that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

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Great review from @jpmarken and coll. on the promise of synthetic biology for sustainability, including agricultural sustainability

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Time to support Indigenous science

There is a global groundswell of Indigenous-led research on stewardship of lands and waters, providing opportunities for Indigenous and Western knowledges to flourish together. A major step in this direction was announced last September by the US National Science Foundation, in its establishment of the Center for Braiding Indigenous Knowledges and Science (CBIKS). Led by a team of 54 predominantly Indigenous scholars and headquartered at the University of Massachusetts, Amherst, CBIKS aims to focus on complex issues at the nexus of nature and culture. The research teams, which span the globe, will address climate disruption, food insecurity, and cultural survival through learning from Indigenous community-based approaches. The goal is to identify and advance models of ethical and effective integration of Indigenous and Western sciences by creating mutually respectful and reciprocal relationships between them. CBIKS will develop generalizable approaches for a diversity of scientific communities.
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Really good editorial. A must read.

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Dynamic nitrogen fixation in an aerobic endophyte of Populus 

Biological nitrogen fixation (BNF) by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to BNF, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only approximately 11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single molecule fluorescence in-situ hybridization (smFISH). Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We co-cultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both BNF and beneficial plant-endophyte interactions.

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scPlant: A versatile framework for single-cell transcriptomic data analysis in plants

scPlant: A versatile framework for single-cell transcriptomic data analysis in plants | Plant-Microbe Symbiosis | Scoop.it
Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth, development, and responses to external stimuli. However, single-cell transcriptomic data analysis in plants is not trivial, given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies. Here, we present scPlant, a versatile framework for exploring plant single-cell atlases with minimum input data provided by users. The scPlant pipeline is implemented with numerous functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution, trajectory inference, cross-species data integration, and cell-type-specific gene regulatory network construction. In addition, a variety of visualization tools are bundled in a built-in Shiny application, enabling exploration of single-cell transcriptomic data on the fly.

Jean-Michel Ané's insight:

Nice package!

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Unraveling the Drought-Responsive Transcriptomes in Nodules of Two Common Bean Genotypes during Biological Nitrogen Fixation

Common bean (Phaseolus vulgaris) can efficiently fix atmospheric nitrogen when associated with Rhizobia. However, drought stress impairs plant metabolic processes, especially the biological nitrogen fixation (BNF). Here, we assessed transcriptional responses in nodules of two common bean genotypes to drought stress under BNF reliance. The RNA-Seq analysis yielded a total of 81,489,262 and 72,497,478 high quality reads for Negro Argel and BAT 477 genotypes, respectively. The reads were mapped to the Phaseolus vulgaris reference genome and expression analysis identified 145 and 1451 differentially expressed genes (DEGs) for Negro Argel and BAT 477 genotypes, respectively. Although BAT 477 had more DEGs, both genotypes shared certain drought-responsive genes, including an up-regulated heat shock protein (HSP) and a down-regulated peroxidase, indicating shared pathways activated during drought in nodule tissue. Functional analysis using MapMan software highlighted the up-regulation of genes involved in abiotic stress responses, such as HSPs and specific transcription factors (TFs), in both genotypes. There was a significant down-regulation in metabolic pathways related to antioxidant protection, hormone signaling, metabolism, and transcriptional regulation. To validate these findings, we conducted RT-qPCR experiments for ten DEGs in nodules from both genotypes, for which the expression profile was confirmed, thus reinforcing their functional relevance in the nodule responses to drought stress during BNF. BAT 477 genotype exhibited more pronounced response to drought, characterized by a high number of DEGs. The strong down-regulation of DEGs leads to transcriptional disturbances in several pathways related to stress acclimation such as hormone and antioxidant metabolism. Additionally, we identified several genes that are known to play key roles in enhancing drought tolerance, such as HSPs and crucial TFs. Our results provide new insights into the transcriptional responses in root-nodules, an underexplored tissue of plants mainly under drought conditions. This research paves the way for potential improvements in plant-bacteria interactions, contributing to common bean adaptations in the face of challenging environmental conditions.

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