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Stéphane Declerck - One of the best experts on this subject based on the ideXlab platform.

  • In vitro colonization of date palm plants by Rhizophagus irregularis during the rooting stage
    Symbiosis, 2021
    Co-Authors: Rania Hilali, Rachid Bouamri, Patrice Crozilhac, Maryline Calonne, Sarah Symanczik, Lahcen Ouahmane, Stéphane Declerck
    Abstract:

    The use of in vitro culture of date palm plants Phoenix dactylifera , associated with arbuscular mycorrhizal (AM) fungi is a novel approach for the production of bio-fortified plants that are free of pathogens. Here, we report, for the first time, the in vitro mycorrhization of in vitro date palm plants using the AM fungus Rhizophagus irregularis MUCL 41833. Date Plants were used in an in vitro cultured system that consisted of a root compartment (RC) containing germinated seeds of Barrel Clover, Medicago truncatula, and spores of Rhizophagus irregularis as a mycorrhizal donor, and a hyphal compartment (HC) with a barrier separating the RC from the HC. In vitro cultured date palm plants, at the two-leaf stage, were placed in the HC section of the culture plate that after 6 weeks contained an active growing extraradical mycelium network of the fungus. Roots of the date palm became colonized after 10 weeks and hyphae, vesicles, spores and arbuscules, were detected. No differences were noticed in above-ground parameters between mycorrhized and non-mycorrhized plants, in which there was no fungus in the HC. However, the total root length was significantly higher and secondary and tertiary roots were significantly more numerous, in the mycorrhized plants. It is hypothesized that these differences are related to stimulating molecules released by the profuse extraradical mycelium of the fungus growing in close contact with the palm root system. Root colonization percentages were of the same order as those reported in pots cultures of the date palm plants. This work opens the door for the large-scale in vitro mycorrhization of date palm plants, potentially better adapted to acclimatization phase and possibly to the field.

  • Fungicides With Contrasting Mode of Action Differentially Affect Hyphal Healing Mechanism in Gigaspora sp. and Rhizophagus irregularis
    Frontiers in plant science, 2021
    Co-Authors: Victor Hugo Rodriguez-morelos, Maryline Calonne-salmon, Vincent Bremhorst, Mónica Garcés-ruiz, Stéphane Declerck
    Abstract:

    Fungicides are widely used in conventional agriculture to control fungal diseases, but may also affect non-target microorganisms such as arbuscular mycorrhizal (AM) fungi. These root symbionts develop extended mycelial networks within the soil via mechanisms such as anastomosis that indistinctly concerns intact and damaged hyphae, the latter being named hyphal healing mechanism (HHM). The HHM differs between Glomeraceae and Gigasporaceae. However, the effects of fungicides on this mechanism in unknown. Here, the impact of azoxystrobin, pencycuron, flutolanil and fenpropimorph at 0.02 and 2 mg L−1 were tested in vitro on the HHM of Gigaspora sp. MUCL 52331 and Rhizophagus irregularis MUCL 41833, and repair events visualized carefully under a dissecting bright-field light microscope. Azoxystrobin was the more detrimental for both AM fungi at 2 mg L−1, while fenpropimorph impacted only R. irregularis (stimulating at low and inhibiting at high concentration). Conversely, flutolanil and pencycuron did not impact any of the two AMF fungi. The mechanisms involved remains to be elucidated, but perturbation in the still-to-be firmly demonstrated spitzenkorper or in sterols content as well as a process of hormesis are possible avenues that deserve to be explored in view of a rationale management of chemicals to control fungal pathogens without harming the beneficial AM fungi.

  • Diesel fuel differentially affects hyphal healing in Gigaspora sp. and Rhizophagus irregularis
    Mycorrhiza, 2021
    Co-Authors: Mónica Garcés-ruiz, Vincent Bremhorst, Maryline Calonne-salmon, Stéphane Declerck
    Abstract:

    Hydrocarbon pollution is an increasing problem affecting soil ecosystems. However, some microorganisms can cope with these pollutants and even facilitate plant establishment and thus phytoremediation. Within soil, arbuscular mycorrhizal fungi (AMF) have developed several strategies to survive and flourish under adverse conditions. Among these is the hyphal healing mechanism (HHM), a process allowing hyphae to re-establish integrity after physical injury. This mechanism differs among species and genera of AMF. However, whether and to what extent hydrocarbon pollution impacts the HHM is unknown. Here, the HHM was monitored in vitro on two AMF strains, Rhizophagus irregularis MUCL 41833 and Gigaspora sp. MUCL 52331, under increasing concentrations of diesel (1, 2, and 5% v:v). The addition of diesel slowed-down the HHM in both fungi. On Gigaspora sp., this effect was limited and most hyphae were able to heal after injury. Conversely, all steps of healing were severely impaired in R. irregularis . That fungus reconnected the injured hyphae at a much lower frequency than the Gigaspora sp., instead investing its energy to link neighboring hyphae or roots, or developing new branches from uninjured hyphae.

  • Impact of Rhizophagus irregularis MUCL 41833 on disease symptoms caused by Phytophthora infestans in potato grown under field conditions
    Crop Protection, 2018
    Co-Authors: Pierre-louis Alaux, Sylvie Cranenbrouck, Vincent César, Françoise Naveau, Stéphane Declerck
    Abstract:

    Abstract In organic potato production in Europe, only copper-based fungicides allow to directly control Phytophthora infestans (the causal agent of late blight). Due to environmental concerns caused by the repeated and excessive use of Cu before the nineties, the EU legislation has promoted alternatives approaches such as the use of biocontrol agents (e.g. arbuscular mycorrhizal fungi – AMF). Here, two field trials were conducted over two climatic-contrasting growing seasons. Trial 1 was characterized by a dry and hot cultural season with low pressure of P. infestans, while trial 2 was conducted under high humidity and relatively low temperatures with high pressure of the pathogen. In both trials, sprouted potato tubers were inoculated with AMF in the greenhouse before transplanting to the field. A Real-Time quantitative PCR assay was designed to target the inoculant strain Rhizophagus irregularis MUCL 41833 as well as the native Rhizophagus irregularis strains. In both trials, the inoculated AMF was detected in the roots at harvest, demonstrating the capacity of the inoculated strain to incorporate the microbiome of the potato plants. In the first trial, disease severity in AMF pre-colonized potato plants was markedly decreased and the onset of late blight symptoms was delayed by 10 days. In contrast, in the second trial no differences were noticed between AMF pre-colonized and control plants. In both trials, no mycorrhizal effect was noticed on tuber yield. As a conclusion, disease severity of P. infestans, measured by symptoms development on leaves, was decreased in AMF pre-colonized plants under conditions of low pressure of late blight and over a short period of time, while under conditions more adequate to the pathogen, no reduction in symptoms was noticed.

  • Potato field-inoculation in Ecuador with Rhizophagus irregularis: no impact on growth performance and associated arbuscular mycorrhizal fungal communities
    Symbiosis, 2017
    Co-Authors: Paul Loján, Arthur Schüßler, Carolina Senés-guerrero, Juan Pablo Suárez, Peter Kromann, Stéphane Declerck
    Abstract:

    A field trial was conducted in two localities of the Ecuadorian Andes to evaluate potato ( Solanum tuberosum c.v. INIAP - Fripapa) response to inoculation with four commercial products containing the arbuscular mycorrhizal fungus (AMF) strain Rhizophagus irregularis DAOM 197198. In parallel, potato roots were analysed using 454 GS-FLX+ sequencing of c . 800 bp of the nuclear LSU rRNA gene to assess the associated AMF communities. To evaluate inoculation success, sequence reads of R. irregularis on the root samples were compared between inoculated and not inoculated plants by analysing the frequency of occurrence (FO) and relative read abundance (RA). None of the commercial products significantly increased potato yield. Instead, the AMF communities were dominated by an unknown Acaulospora sp. (Sp14) found at high FO and RA in both localities. Rhizophagus irregularis was found in most of the roots of both inoculated and not inoculated plants at both localities. However, its abundance was unexpectedly low indicating poor inoculum establishment. Clearly, many factors have to be taken in consideration for the successful application of AMF-based inoculants. For the Ecuadorian field trials, several causes may explain the lack or poor establishment of R. irregularis such as inoculation technique, agricultural practices, biotic and abiotic conditions and competition with native AMF species.

Ming Tang - One of the best experts on this subject based on the ideXlab platform.

  • nutrient allocation and photochemical responses of populus canadensis neva to nitrogen fertilization and exogenous Rhizophagus irregularis inoculation
    Acta Physiologiae Plantarum, 2018
    Co-Authors: Haoqiang Zhang, Fengru Fang, Ming Tang
    Abstract:

    Arbuscular mycorrhizal fungi (AMF) can promote plant growth performance, but their effectiveness varies depending on soil nitrogen (N) availability. To clarify the effectiveness of exogenous AMF along an N-fertilization gradient (0, 2, 10, 20, and 30 mM), the impacts of exogenous Rhizophagus irregularis and N on the growth, photochemical activity, and nutritional status of Populus × canadensis ‘Neva’ in natural soil were evaluated in a pot experiment. The results showed that the 10 mM N level was the optimal fertilization regime with the highest promotion effect on plant growth and the maximum quantum yield of photosystem II (PSII) (Fv/Fm). Excess N (20 and 30 mM) fertilization reduced the actual quantum yield of PSII (ФPSII) and the Fv/Fm of the plants. Regardless of the N availability, inoculated plants exhibited greater Fv/Fm values than did non-inoculated plants. The biomass of inoculated plants was significantly higher compared with the control under low N levels (0 and 2 mM). Under high N levels, inoculated plants showed significant increases in ФPSII. Moreover, the nutrient imbalance of plants inoculated with exogenous R. irregularis was eased by increasing P, Fe, Mn and Cu uptake in roots and higher P, Ca, Mg, Fe, Mn and Zn concentrations in leaves. Moreover, the Fv/Fm and ФPSII exhibited positive correlations with P, Ca, Mg and Zn concentrations in leaves. In conclusion, inoculation with exogenous R. irregularis can benefit plant fitness by improving the photochemical capacity and nutrient composition of poplar under different N levels.

  • arbuscular mycorrhizal fungus Rhizophagus irregularis increased potassium content and expression of genes encoding potassium channels in lycium barbarum
    Frontiers in Plant Science, 2017
    Co-Authors: Haoqiang Zhang, Suzhen Wei, Longmin Xiao, Ming Tang
    Abstract:

    Potassium in plants accounts for up to 10% dry weight, and participates in different physiological processes. Under drought stress, plant requires more potassium but potassium availability in soil solutes is lowered by decreased soil water content. Forming symbiosis with arbuscular mycorrhizal (AM) fungi not only enlarges exploration range of plant for nutrient and water in soil, but also improves plant drought tolerance. However, the regulation of AM fungi on plant root potassium uptake and translocation from root to shoot was less reported. In current study, the effect of an AM fungus (Rhizophagus irregularis), potassium application (0 mM, 2 mM and 8 mM), and drought stress (30% field capacity) on Lycium barbarum growth and potassium status was evaluated. Ten weeks after inoculation, R. irregularis colonized more than 58% root of L. barbarum seedlings, and improved plant growth as well as potassium content. Potassium application increased colonization rate of R. irregularis, plant growth, potassium content, and decreased root/shoot ratio. Drought stress increased colonization rate of R. irregularis and potassium content. Expression of two putative potassium channel genes in root, LbKT1 and LbSKOR, was positively correlated with potassium content in root and leaves, as well as the colonization rate of R. irregularis. The increased L. barbarum growth, potassium content and genes expression, especially under drought stress, suggested that R. irregularis could improve L. barbarum root potassium uptake and translocation from root to shoot. Whether AM fungi could form a specific mycorrhizal pathway for plant potassium uptake deserves further studies.

  • effects of nitrogen and exogenous Rhizophagus irregularis on the nutrient status photosynthesis and leaf anatomy of populus canadensis neva
    Journal of Plant Growth Regulation, 2017
    Co-Authors: Haoqiang Zhang, Fengru Fang, Yongxin Zhang, Ming Tang
    Abstract:

    The productivity of poplar is associated with large nitrogen (N) requirements. Exogenous arbuscular mycorrhizal fungi (AMF) show potential for use as bio-fertilizers. Understanding the interaction between N and exogenous AMF has theoretical and practical significance for poplar plantation. A pot experiment was conducted to assess the effects of N and exogenous Rhizophagus irregularis on plant growth, nutrient uptake, photosynthesis, water status, and leaf anatomical properties of Populus × canadensis ‘Neva’ in natural soil. The results showed that N fertilization increased plant growth, net photosynthesis, water status and the conduit diameter of midribs. The concentrations of carbon (C) and N in leaves were increased, but the phosphorus (P) concentration was decreased by N fertilization. The effectiveness of exogenous R. irregularis varied under different N levels. Under low N levels, exogenous R. irregularis-inoculated plants grew faster and exhibited superior photosynthetic capacity, water status and leaf conduit diameters than non-inoculated plants. Under high N levels, C, N and P concentrations were enhanced by exogenous R. irregularis inoculation. Furthermore, the average conduit diameter of midribs presented a significant positive correlation with plant growth parameters, photosynthesis, relative water content (RWC) and leaf C and N concentrations. It was concluded that exogenous R. irregularis exerted the strongest positive effects under low N levels by promoting plant growth and photosynthesis, and the fungus promoted plant nutrition decoupled from the level of N fertilization. Moreover, the improvement of plant physiological traits due to N fertilization or exogenous R. irregularis inoculation was accompanied by changes in internal anatomical properties.

  • effects of Rhizophagus irregularis on photosynthesis and antioxidative enzymatic system in robinia pseudoacacia l under drought stress
    Frontiers in Plant Science, 2017
    Co-Authors: Min Sheng, Ming Tang
    Abstract:

    Black locust (Robinia pseudoacacia L.) is an important legume tree species that is widely used for revegetation in the arid and semi-arid areas of China, where it frequently encounters drought stress. This study investigated how the presence of AM fungi affected the photosynthesis and antioxidant gene-enzymes response of black locust seedlings to drought stress. Here, pot experiments were performed to investigate the effects of Rhizophagus irregularis (synonym for Glomus intraradices), an AM fungus, on the tissue water content, photosynthesis, reactive oxygen species (ROS) production, antioxidant enzyme activity and gene expression in black locust (Robinia pseudoacacia L.) seedlings which were subjected to well watered or moderate drought stress. Mycorrhizal symbiosis increased relative water content of plant roots and leaves, promoted the accumulation of biomass and chlorophyll (Chl) content, and improved photochemistry efficiency, regardless of watering regimes. Mycorrhizal plants had higher SOD, POD, CAT, APX, and GR activities, and the transcript levels of Cu/Zn-SOD, APX and GR, but lower O2, H2O2 and MDA concentrations in leaves and roots of black locust under drought and well watered conditions. Results from the present study indicate that AM fungus (R. irregularis) symbiosis can enhance photosynthesis and ROS scavenging capabilities and increase relative water content of leaves and roots to alleviate drought stress in black locust. Further research is needed to elucidate the relations among AM fungi and the metabolic pathways of antioxidant enzymes, and the function of antioxidant genes regulated by mycorrhizal symbiosis with the purpose of revealing the mechanisms of mycorrhiza-induced plant tolerance to drought stress.

  • effect of Rhizophagus irregularis on osmotic adjustment antioxidation and aquaporin pip genes expression of populus canadensis neva under drought stress
    Acta Physiologiae Plantarum, 2016
    Co-Authors: Ting Liu, Ming Tang, Chen Hui, Haoqiang Zhang
    Abstract:

    Drought is an abiotic stress that severely reduces plant growth. Responding to drought, plants would induce a series of physiological and biochemical changes. Colonization by arbuscular mycorrhizal (AM) fungi was reported beneficial in improving plants’ drought tolerance. However, the effect of AM fungi in improving drought tolerance of widely planted Populus spp. was rarely reported. The effect of AM fungus (Rhizophagus irregularis) on malondialdehyde (MDA) content, proline and soluble proteins content, antioxidative enzymes activates, relative water content (RWC) and water use efficiency (WUE), and the aquaporin PIP genes expression of Populus × canadensis ‘Neva’ leaves under well-watered and drought-stressed condition was evaluated. R. irregularis could colonize more than 80 % of poplar roots, reduce MDA and proline content, lower antioxidative enzymes activates, and down-regulate the expression of PIP2;1, PIP2;2. Meanwhile, R. irregularis could increase soluble protein content, increase RWC and WUE, and up-regulate the expression of PIP1;1, PIP1;3, PIP1;4, PIP1;5, PIP2;1, PIP2;2, and PIP2;3. In conclusion, R. irregularis could improve drought tolerance of P. canadensis by increasing RWC via regulation of aquaporin genes expression, and consequently increased WUE, lowered accumulation of osmotic adjustment molecule, reduced ROS accumulation and oxidative damage. Further studies focusing on the influence of AM fungi on specific aquaporin PIP gene location, function and expression in plant responding to drought stress are needed.

Ian R. Sanders - One of the best experts on this subject based on the ideXlab platform.

  • the model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome
    bioRxiv, 2021
    Co-Authors: Romain Savary, Frédéric G. Masclaux, Ian R. Sanders
    Abstract:

    Arbuscular mycorrhizal fungi (AMF; Glomeromycotina) are symbionts of most plant species that are known to possess unique intracytoplasmic endosymbiotic bacteria with an enigmatic role. Candidatus Moeniiplasma glomeromycotorum (CaMg) was shown to be widespread along the AMF phylogeny and present in most AMF species and isolates of those species. The model AMF species, Rhizophagus irregularis, that can be cultivated in vitro and for which a lot of genomic information now exists, would be the ideal model to study the true nature of the CaMg-AMF symbiosis. However, R. irregularis was never found to host endobacteria. Here we show by DNA sequencing that R. irregularis can, indeed, host CaMg (Ri-CaMg). However, this appears rare as only one R. irregularis isolate out of 58 hosted CaMg. In that isolate, the endosymbiotic bacterial population was genetically homogenous. By sequencing the complete genome of the bacteria, we found that its genome is among the smallest of all known CaMg and Mycoplasma-like genomes, with a highly reduced gene repertoire, suggesting a strong adaptation to the intracellular life. We discuss our findings in the light of previous literature on CaMg and on the same AMF isolates and suggest that these endosymbionts are more likely parasites than non-obligatory mutualists.

  • generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription
    New Phytologist, 2021
    Co-Authors: Chanz Robbins, Frédéric G. Masclaux, Consolée Aletti, Ivan D Mateus, Joaquim Cruz Corella, Rejane Seiler, Soonjae Lee, Ian R. Sanders
    Abstract:

    Arbuscular mycorrhizal fungi (AMF) form mutualisms with most plant species. The model AMF Rhizophagus irregularis is common in many ecosystems and naturally forms homokaryons and dikaryons. Quantitative variation in allele frequencies in clonally dikaryon offspring suggests they disproportionately inherit two distinct nuclear genotypes from their parent. This is interesting, because such progeny strongly and differentially affect plant growth. Neither the frequency and magnitude of this occurrence nor its effect on gene transcription are known. Using reduced representation genome sequencing, transcriptomics, and quantitative analysis tools, we show that progeny of homokaryons and dikaryons are qualitatively genetically identical to the parent. However, dikaryon progeny differ quantitatively due to unequal inheritance of nuclear genotypes. Allele frequencies of actively transcribed biallelic genes resembled the frequencies of the two nuclear genotypes. More biallelic genes showed transcription of both alleles than monoallelic transcription, but biallelic transcription was less likely with greater allelic divergence. Monoallelic transcription levels of biallelic genes were reduced compared with biallelic gene transcription, a finding consistent with genomic conflict. Given that genetic variation in R. irregularis is associated with plant growth, our results establish quantitative genetic variation as a future consideration when selecting AMF lines to improve plant production.

  • coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response
    The ISME Journal, 2020
    Co-Authors: Ivan D Mateus, Frédéric G. Masclaux, Consolée Aletti, Edward C Rojas, Romain Savary, Cindy Dupuis, Ian R. Sanders
    Abstract:

    Arbuscular mycorrhizal fungi (AMF) are of great ecological importance because of their effects on plant growth. Closely related genotypes of the same AMF species coexist in plant roots. However, almost nothing is known about the molecular interactions occurring during such coexistence. We compared in planta AMF gene transcription in single and coinoculation treatments with two genetically different isolates of Rhizophagus irregularis in symbiosis independently on three genetically different cassava genotypes. Remarkably few genes were specifically upregulated when the two fungi coexisted. Strikingly, almost all of the genes with an identifiable putative function were known to be involved in mating in other fungal species. Several genes were consistent across host plant genotypes but more upregulated genes involved in putative mating were observed in host genotype (COL2215) compared with the two other host genotypes. The AMF genes that we observed to be specifically upregulated during coexistence were either involved in the mating pheromone response, in meiosis, sexual sporulation or were homologs of MAT-locus genes known in other fungal species. We did not observe the upregulation of the expected homeodomain genes contained in a putative AMF MAT-locus, but observed upregulation of HMG-box genes similar to those known to be involved in mating in Mucoromycotina species. Finally, we demonstrated that coexistence between the two fungal genotypes in the coinoculation treatments explained the number of putative mating response genes activated in the different plant host genotypes. This study demonstrates experimentally the activation of genes involved in a putative mating response and represents an important step towards the understanding of coexistence and sexual reproduction in these important plant symbionts.

  • Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis
    2019
    Co-Authors: Frédéric G. Masclaux, Tania Wyss, Pawel Rosikiewicz, Marco Pagni, Ian R. Sanders
    Abstract:

    Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not match the proposed monokaryon or dikaryon state. We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in monosporic R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation exists. Bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome. In putative monokaryon isolates, very few bi-allelic transcripts could be found in the genome. In a putative dikaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative dikaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative monokaryon and dikaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in monokaryons. In contrast, within-fungus variation thought to be segregated among nuclei in a dikaryon isolate is indeed transcribed in a way that is proportional to that seen in the genome.

  • Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis
    Mycorrhiza, 2018
    Co-Authors: Frédéric G. Masclaux, Tania Wyss, Ivan D. Mateus-gonzalez, Consolée Aletti, Ian R. Sanders
    Abstract:

    The genetic state of the arbuscular mycorrhizal fungus species Rhizophagus irregularis differs among isolates, including both homokaryotic and dikaryotic isolates. Via the production of multi-nucleate axexual spores, siblings of dikaryotic isolates may inherit unequal frequencies of nucleotypes. Using bg112 , a microsatellite marker, previous studies revealed that lines deriving from single spores of the dikaryotic R. irregularis isolate C3 differed in their proportions of different alleles. A genomic study of single nuclei of R. irregularis , however, suggested that this marker was a multi-copy locus and that therefore it was inappropriate to study the inheritance of nuclei in dikaryotic isolates. In this study, we first analysed whole genome data of several R. irregularis isolates and demonstrated that bg112 is indeed a single copy locus in these genomes. Thus, the bg112 locus is a suitable marker to study the relative frequency of nucleotypes in R. irregularis . Second, by using amplicon sequencing, we confirmed the existence of one allele of bg112 in two homokaryotic isolates (DAOM197198 and C2) and two alleles in the dikaryotic isolate (C3). Finally, we found that the relative proportions of two bg112 alleles differed significantly among dikaryotic single-spore lines derived from isolate C3, indicating that genetically different nucleotypes are inherited unequally in this dikaryotic R. irregularis isolate.

Denis Beaudet - One of the best experts on this subject based on the ideXlab platform.

  • Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.
    The New phytologist, 2019
    Co-Authors: Emmanuelle Morin, Denis Beaudet, Shingo Miyauchi, Hélène San Clemente, Eric C. H. Chen, Adrian Pelin, Ivan De La Providencia, Steve Ndikumana, Mathieu Hainaut, Elodie Drula
    Abstract:

    Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.

  • Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina
    New Phytologist, 2019
    Co-Authors: Emmanuelle Morin, Denis Beaudet, Shingo Miyauchi, Hélène San Clemente, Eric C. H. Chen, Adrian Pelin, Ivan De La Providencia, Steve Ndikumana, Mathieu Hainaut, Elodie Drula
    Abstract:

    Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.

  • high intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
    New Phytologist, 2018
    Co-Authors: Eric C. H. Chen, Denis Beaudet, Emmanuelle Morin, Steve Ndikumana, Jessica Noel, Gokalp Yildirir, Philippe Charron, Camille Stonge, John M Giorgi, Manuela Kruger
    Abstract:

    Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.

  • molecular diagnostic toolkit for Rhizophagus irregularis isolate daom 197198 using quantitative pcr assay targeting the mitochondrial genome
    Mycorrhiza, 2016
    Co-Authors: Amine Badri, Denis Beaudet, Franck O P Stefani, Genevieve Lachance, Line Royarcand, Agathe Vialle, Mohamed Hijri
    Abstract:

    Rhizophagus irregularis (previously named Glomus irregulare) is one of the most widespread and common arbuscular mycorrhizal fungal (AMF) species. It has been recovered worldwide in agricultural and natural soils, and the isolate DAOM-197198 has been utilized as a commercial inoculant for two decades. Despite the ecological and economical importance of this taxon, specific markers for quantification of propagules by quantitative real-time PCR (qPCR) are extremely limited and none have been rigorously validated for quality control of manufactured products such as biofertilizers. From the sequencing of 14 complete AMF mitochondrial (mt) genomes, a qPCR assay using a hydrolysis probe designed in the single copy cox3-rnl intergenic region was tested and validated to specifically and accurately quantify the spores of R. irregularis isolate DAOM-197198. Specificity tests were performed using standard PCR and qPCR, and results clearly showed that the primers specifically amplified the isolate DAOM-197198, yielding a PCR product of 106 bp. According to the qPCR analyses on spores produced in vitro, the average copy number of mt genomes per spore was 3172 ± 304 SE (n = 6). Quantification assays were successfully undertaken on known and unknown samples in liquid suspensions and commercial dry formulations to show the accuracy, precision, robustness, and reproducibility of the qPCR assay. This study provides a powerful molecular toolkit specifically designed to quantify spores of the model AMF isolate DAOM-197198. The approach of molecular toolkit used in our study could be applied to other AMF taxa and will be useful to research institutions and governmental and industrial laboratories running routine quality control of AMF-based products.

  • independent mitochondrial and nuclear exchanges arising in Rhizophagus irregularis crossed isolates support the presence of a mitochondrial segregation mechanism
    BMC Microbiology, 2016
    Co-Authors: Laurence Daubois, Denis Beaudet, Mohamed Hijri, Ivan E De La Providencia
    Abstract:

    Background Arbuscular mycorrhizal fungi (AMF) are members of the phylum Glomeromycota, an early divergent fungal lineage that forms symbiotic associations with the large majority of land plants. These organisms are asexual obligate biotrophs, meaning that they cannot complete their life cycle in the absence of a suitable host. These fungi can exchange genetic information through hyphal fusions (i.e. anastomosis) with genetically compatible isolates belonging to the same species. The occurrence of transient mitochondrial length-heteroplasmy through anastomosis between geographically distant Rhizophagus irregularis isolates was previously demonstrated in single spores resulting from crossing experiments. However, (1) the persistence of this phenomenon in monosporal culture lines from crossed parental isolates, (2) its correlation with nuclear exchanges and (3) the potential mechanisms responsible for mitochondrial inheritance are still unknown. Using the AMF model organism R. irregularis, we tested whether the presence of a heteroplasmic state in progeny spores was linked to the occurrence of nuclear exchanges and whether the previously observed heteroplasmic state persisted in monosporal in vitro crossed-culture lines. We also investigated the presence of a putative mitochondrial segregation apparatus in Glomeromycota by identifying proteins similar to those found in other fungal groups.

Nuria Ferrol - One of the best experts on this subject based on the ideXlab platform.

  • the arbuscular mycorrhizal fungus Rhizophagus irregularis uses a reductive iron assimilation pathway for high affinity iron uptake
    Environmental Microbiology, 2018
    Co-Authors: Elisabeth Tamayo, Ascensión Valderas, Simon A B Knight, Andrew Dancis, Nuria Ferrol
    Abstract:

    Arbuscular mycorrhizal (AM) fungi can improve iron (Fe) acquisition of their host plants. Here, we report a characterization of two components of the high-affinity reductive Fe uptake system of Rhizophagus irregularis, the ferric reductase (RiFRE1) and the high affinity Fe permeases (RiFTR1-2). In the extraradical mycelia (ERM), Fe deficiency induced activation of a plasma membrane-localized ferric reductase, an enzyme that reduces Fe(III) sources to the more soluble Fe(II). Yeast mutant complementation assays showed that RiFRE1 encodes a functional ferric reductase and RiFTR1 an iron permease. In the heterologous system, RiFTR1 was expressed in the plasma membrane while RiFTR2 was expressed in the endomembranes. In the ERM, the highest expression levels of RiFTR1 were found in mycelia grown in media with 0.045 mM Fe, while RiFTR2 was upregulated under Fe-deficient conditions. RiFTR2 expression also increased in the intraradical mycelia (IRM) of maize plants grown without Fe. These data indicate that the Fe permease RiFTR1 plays a key role in Fe acquisition and that RiFTR2 is involved in Fe homeostasis under Fe-limiting conditions. RiFTR1 was highly expressed in the (IRM), which suggests that the maintenance of Fe homeostasis in the IRM might be essential for a successful symbiosis.

  • the arbuscular mycorrhizal fungus Rhizophagus irregularis differentially regulates the copper response of two maize cultivars differing in copper tolerance
    Plant Science, 2016
    Co-Authors: Ondrej Zitka, Miguel A Merlos, Adam Vojtech, Concepcion Azconaguilar, Nuria Ferrol
    Abstract:

    Abstract Arbuscular mycorrhiza can increase plant tolerance to heavy metals. The effects of arbuscular mycorrhiza on plant metal tolerance vary depending on the fungal and plant species involved. Here, we report the effect of the arbuscular mycorrhizal fungus Rhizophagus irregularis on the physiological and biochemical responses to Cu of two maize genotypes differing in Cu tolerance, the Cu-sensitive cv. Orense and the Cu-tolerant cv. Oropesa. Development of the symbiosis confers an increased Cu tolerance to cv. Orense. Root and shoot Cu concentrations were lower in mycorrhizal than in non-mycorrhizal plants of both cultivars. Shoot lipid peroxidation increased with soil Cu content only in non-mycorrhizal plants of the Cu-sensitive cultivar. Root lipid peroxidation increased with soil Cu content, except in mycorrhizal plants grown at 250 mg Cu kg−1soil. In shoots of mycorrhizal plants of both cultivars, superoxide dismutase, ascorbate peroxidase, catalase and glutathione reductase activities were not affected by soil Cu content. In Cu-supplemented soils, total phytochelatin content increased in shoots of mycorrhizal cv. Orense but decreased in cv. Oropesa. Overall, these data suggest that the increased Cu tolerance of mycorrhizal plants of cv. Orense could be due to an increased induction of shoot phytochelatin biosynthesis by the symbiosis in this cultivar.

  • GintAMT3 - a Low-Affinity Ammonium Transporter of the Arbuscular Mycorrhizal Rhizophagus irregularis.
    Frontiers in plant science, 2016
    Co-Authors: Silvia Calabrese, Daniel Wipf, Arthur Schüßler, Jacob Pérez-tienda, Matthias Ellerbeck, Christine Arnould, Odile Chatagnier, Thomas Boller, Andreas Brachmann, Nuria Ferrol
    Abstract:

    Nutrient acquisition and transfer are essential steps in the arbuscular mycorrhizal (AM) symbiosis, which is formed by the majority of land plants. Mineral nutrients are taken up by AM fungi from the soil and transferred to the plant partner. Within the cortical plant root cells the fungal hyphae form tree-like structures (arbuscules) where the nutrients are released to the plant-fungal interface, i.e. to the periarbuscular space, before being taken up by the plant. In exchange, the AM fungi receive valuable carbohydrates from the plant host. Besides the well-studied uptake of phosphorus (P), the uptake and transfer of nitrogen (N) plays a crucial role in this mutualistic interaction. In the AM fungus Rhizophagus irregularis (formerly called Glomus intraradices), two ammonium transporters (AMT) were previously described, namely GintAMT1 and GintAMT2. Here, we report the identification and characterization of a newly identified R. irregularis AMT, GintAMT3. Phylogenetic analyses revealed high sequence similarity to previously identified AM fungal AMTs and a clear separation from other fungal AMTs. Topological analysis indicated GintAMT3 to be a membrane bound pore forming protein, and GFP tagging showed it to be highly expressed in the intraradical mycelium (IRM) of a fully established AM symbiosis. Expression of GintAMT3 in yeast successfully complemented the yeast AMT triple deletion mutant (MATa ura3 mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2). GintAMT3 is characterized as a low affinity transport system with an apparent Km of 1.8 mM and a Vmax of 240 nmol-1 min-1 108 cells-1, which is regulated by substrate concentration and carbon supply.

  • characterization of three new glutaredoxin genes in the arbuscular mycorrhizal fungus Rhizophagus irregularis putative role of rigrx4 and rigrx5 in iron homeostasis
    PLOS ONE, 2016
    Co-Authors: Elisabeth Tamayo, Karim Benabdellah, Nuria Ferrol
    Abstract:

    Glutaredoxins (GRXs) are small ubiquitous oxidoreductases involved in the regulation of the redox state in living cells. In an attempt to identify the full complement of GRXs in the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis, three additional GRX homologs, besides the formerly characterized GintGRX1 (renamed here as RiGRX1), were identified. The three new GRXs (RiGRX4, RiGRX5 and RiGRX6) contain the CXXS domain of monothiol GRXs, but whereas RiGRX4 and RiGRX5 belong to class II GRXs, RiGRX6 belongs to class I together with RiGRX1. By using a yeast expression system, we observed that the newly identified homologs partially reverted sensitivity of the GRX deletion yeast strains to external oxidants. Furthermore, our results indicated that RiGRX4 and RiGRX5 play a role in iron homeostasis in yeast. Gene expression analyses revealed that RiGRX1 and RiGRX6 were more highly expressed in the intraradical (IRM) than in the extraradical mycelium (ERM). Exposure of the ERM to hydrogen peroxide induced up-regulation of RiGRX1, RiGRX4 and RiGRX5 gene expression. RiGRX4 expression was also up-regulated in the ERM when the fungus was grown in media supplemented with a high iron concentration. These data indicate the two monothiol class II GRXs, RiGRX4 and RiGRX5, might be involved in oxidative stress protection and in the regulation of fungal iron homeostasis. Increased expression of RiGRX1 and RiGRX6 in the IRM suggests that these GRXs should play a key role in oxidative stress protection of R. irregularis during its in planta phase.

  • Characterization of Three New Glutaredoxin Genes in the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis: Putative Role of RiGRX4 and RiGRX5 in Iron Homeostasis - Fig 1
    2016
    Co-Authors: Elisabeth Tamayo, Karim Benabdellah, Nuria Ferrol
    Abstract:

    A. Domain organization of the R. irregularis GRXs. Glutaredoxin domains are represented by black boxes. The thioredoxin-like (Trx) domain of RiGRX4, the mitochondrial location signal (MLS) of RiGRX5 and the domain of unknown function of RiGRX6 (white box) are also indicated. Numbers correspond to the position of the first cysteine in the active site in the GRX domains, the first glycine of the glutathione binding domains and the total length of the proteins. The position of the cysteine in the Trx domain of RiGRX4 is also indicated. B. Unrooted Nieghbor-Joining tree of the GRX family in fungi. Organisms: An, Aspergillus niger; Bc, Botrytis cinerea; Cc, Coprinopsis cinerea; Cn, Cryptococcus neoformans; Lb, Laccaria bicolor; Mg, Magnaporthe grisea; Nc, Neurospora crassa; Pc, Phanerochaete chrysosporium; Pg, Puccinia graminis; Ri, Rhizophagus irregularis; Ro, Rhizopus oryzae; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; Tm, Tuber melanosporum; Um, Ustilago maydis. R. irregularis GRXs are emphasized in bold. Protein JGI identification numbers are indicated. R. oryzae sequences were retrieved from the Broad Institute databases (http://www.broad.mit.edu/annotation/). Bootstrap values above 70 and supporting a node are indicated.