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ABSTRACT:
PROVIDER: PRJNA768887 | ENA |
REPOSITORIES: ENA
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Project description:Gluconacetobacter diazotrophicus has been the focus of several studies aiming to understand the mechanisms behind this endophytic diazotrophic bacterium. The present study is the first global analysis of the early transcriptional response of exponentially growing G. diazotrophicus to iron, an essential cofactor for many enzymes involved in various metabolic pathways. RNA-seq, targeted gene mutagenesis and computational motif discovery tools were used to define the G. diazotrophicus Fur regulon. The data analysis showed that genes encoding functions related to iron homeostasis, were significantly upregulated in response to iron limitation. Certain genes involved in the secondary metabolism were overexpressed under iron-limited conditions. In contrast, it was observed that the expression of genes involved in Fe-S cluster biosynthesis, flagellar biosynthesis and type IV secretion systems were downregulated in an iron-depleted culture medium. Our results support a model that control transcription in G. diazotrophicus by Fur function. The G. diazotrophicus Fur protein was able to complement an E. coli fur mutant. These results provide new insights into the effects of iron on the metabolism of G. diazotrophicus, as well as demonstrating the essentiality of this micronutrient for the main characteristic of plant growth promotion by G. diazotrophicus.
2021-01-09 | GSE164445 | GEO
Project description:Sugarcane plantlets from a variety with high inputs of N obtained from BNF (genotype SP70-1143, CTC, Brazil) free of microorganisms were obtained by sterile meristem culture and micropropagation according to the method of Hendre et al. (1983). In vitro-grown SP70-1143 rooted sugarcane plantlets were inoculated as described by James et al. (1994) with 0.1 ml of 106–107 bacterial suspension. Controls were inoculated with medium only. Endophytic diazotrophic bacteria used were Gluconacetobacter diazotrophicus (PAL5 strain) or a mixture of Herbaspirillum seropedicae (HRC54 strain) and H. rubrisubalbicans (HCC103 strain). All plants were maintained at 30°C with an irradiance of 60 µmol photons m–2 s–1 for 12 h d–1. One day after the inoculation, plant tissues were examined for bacterial colonization by the Most Probable Number (MPN) estimation, according to the methods of Reis et al. (1994) and plantlets were collected and immediately frozen in liquid nitrogen. Five plantlets were polled for each treatment. Extraction of total RNA was performed separately on each sample pool. Keywords: comparison of associations with different endophytic bacterias
2007-05-20 | GSE4970 | GEO
Project description:High ambient temperature regulated the plant systemic response to the beneficial endophytic fungus Serendipita indica. Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild type plants.
2022-02-26 | GSE197325 | GEO
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
2021-11-03 | GSE169629 | GEO
Project description:The recent release of a large number of genomes from ectomycorrhizal, orchid mycorrhizal and root endophytic fungi have provided deep insight into fungal lifestyle-associated genomic adaptation. Comparative analyses of symbiotic fungal taxa showed that similar outcomes of interactions in distant related root symbioses are examples of convergent evolution. The order Sebacinales represents a sister group to the Agaricomycetes (Basidiomycota) that is comprised of ectomycorrhizal, ericoid-, orchid- mycorrhizal, root endophytic fungi and saprotrophs (Oberwinkler et al., 2013). Sebacinoid taxa are widely distributed from arctic to temperate to tropical ecosystems and are among the most common and species-rich groups of ECM, OM and endophytic fungi (Tedersoo et al., 2012, Tedersoo et al., 2010, Oberwinkler et al., 2013). The root endophyte Piriformospora indica and the orchid mycorrhizal fungus S. vermifera (MAFF 305830) are non-obligate root symbionts which were shown to be able to interact with many different experimental hosts, including the non-mycorrhizal plant Arabidopsis thaliana. These two fungi display similar colonization strategies in barley and in Arabidopsis and the ability to establish beneficial interactions with different hosts (Deshmukh et al., 2006). Colonization of the roots by P. indica and S. vermifera results in enhanced seed germination and biomass production as well as increased resistance against biotic and abiotic stresses in its experimental hosts, including various members of the Brassicaceae family, barley, Nicotiana attenuata and switchgrass (Ghimire, 2011, Ghimire et al., 2009, Ghimire et al., 2011, Waller et al., 2008, Barazani et al., 2007, Deshmukh et al., 2006). Microarray experiments were performed to identify and characterize conserved sebacinoid genes as key determinants in the Sebacinales symbioses.
2015-06-01 | GSE60736 | GEO
Project description:Gluconacetobacter diazotrophicus PR 4 genome sequencing
| PRJNA536620 | ENA
Project description:Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq
2020-10-19 | GSE143635 | GEO
Project description:Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia
2017-12-06 | PRJEB23751 | EVA
Project description:Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction. We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the downregulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance.
2016-05-30 | GSE58771 | GEO
Project description:The endophytic fungus Piriformospora indica is a member of Sebacinales. It colonizes the roots of many plant species including the model plant Arabidospis thaliana (Peskan-Berghofer et al. 2004). P. indica promotes plant growth (Peskan-Berghofer et al. 2004), seed production (Shahollari et al. 2007) and confers resistance to biotic (Camehl et al. 2011) and abiotic stresses (Sherameti et al., 2008, Matsuo et al., 2015). Vadassery et al. (2009) have shown that a cell wall extract from P. indica induces cytoplasmic calcium elevation in Arabidopsis Col-0 roots. Johnson et al. (2017) isolated an ethylmethane-induced mutant cycam (cytoplasmic calcium elevation mutant) which fails to induce cytoplasmic calcium elevation in response to the cell wall preparation. The active compound was identified as cellotriose (CT) (Johnson et al., 2017). The cycam mutant shows a wild-type response to treatment with chitin. The expression profiles compare the response of WT and cycam roots to treatments with CT and chitin. References: Camehl I, Drzewiecki C, Vadassery J, Shahollari B, Sherameti I, Forzani C, Munnik T, Hirt H, Oelmüller R. (2011) The OXI1 kinase pathway mediates Piriformospora indica-induced growth promotion in Arabidopsis. PLoS Pathog. 7(5):e1002051. Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, Sherameti I, Dindas J, Mrozinska A, Paetz C, Scholz S, Furch A, Lipka V, Hedrich R, Schneider B, Svatoš S, Oelmüller R. (2017) Cellotriose-induced cytoplasmic calcium elevation is controlled by a poly(A) ribonuclease in Arabidopsis root. (submitted to elife). Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R. (2015) High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots. Mol Plant. 8(8):1253-73. Peškan-Berghöfer T, Shahollari B, Giang PH, Hehl S, Markert C, Blanke V, Varma AK, Oelmüller R. (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant–microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol. Plant. 122: 465–477. Shahollari B, Vadassery J, Varma A, Oelmüller R. (2007) A leucine-rich repeat protein is required for growth promotion and enhanced seed production mediated by the endophytic fungus Piriformospora indica in Arabidopsis thaliana. Plant J. 50(1):1-13. Sherameti, I., Tripathi, S., Varma, A., and Oelmüller, R. (2008). The root-colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress-related genes in leaves. Mol. Plant Microbe Interact. 21: 799-807. Vadassery, J., Ranf, S., Drzewiecki, C., Mithöfer, A., Mazars, C., Scheel, D., Lee, J., and Oelmüller, R. (2009) A cell wall extract from the endophytic fungus Piriformospora indica promotes growth of Arabidopsis seedlings and induces intracellular calcium elevation in roots. Plant J. 59: 193-206.
2018-02-09 | GSE98880 | GEO