Soil microbes and nutrient inputs influence root nodulation and tree performance in Alnus glutinosa
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PROVIDER: PRJEB90186 | ENA |
REPOSITORIES: ENA
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Project description:Soil microbes and nutrient inputs influence root nodulation and tree performance in Alnus glutinosa Raw sequence reads
| PRJNA1272542 | ENA
Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition.
2011-04-11 | GSE24153 | GEO
Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for A. glutinosa, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent
2011-04-11 | E-GEOD-24153 | biostudies-arrayexpress
Project description:Gene profiling during symbiosis between the actinorhizal tree Alnus glutinosa and the actinobacteria Frankia alni ACN14
| PRJNA130037 | ENA
Project description:The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'high-risk plants, plant products and other objects'. Taking into account the available scientific information, including the technical information provided by the applicant country, this Scientific Opinion covers the plant health risks posed by the following commodities: Alnus cordata, A. glutinosa and A. incana graftwood, bare-root plants and rooted plants in pots up to 7 years old imported into the EU from the UK. A list of pests potentially associated with the commodities was compiled. The relevance of each pest was assessed based on evidence following defined criteria. Two EU-quarantine pests (Entoleuca mammata, Phytophthora ramorum (non-EU isolates)) and one non-quarantine pest (Phytophthora siskiyouensis) were selected for further evaluation. For the selected pests, the risk mitigation measures implemented in the UK and specified in the technical dossier were evaluated taking into account the factors reducing their efficacy. For these pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The degree of pest freedom varies between the pests evaluated, with E. mammata being the pest most frequently expected on imported Alnus spp. small trees. Expert knowledge elicitation indicated, with 95% certainty, that between 9927 and 10,000 per 10,000 Alnus spp. small trees (bare-root plants or rooted plants in pots up to 7 years old) would be free from E. mammata.
| S-EPMC11736288 | biostudies-literature
Project description:Gene expression (RNAseq) of Alnus glutinosa after nodulation with Frankia alni ACN14a and infected (or not) with Phytophthora alni sp alni (root and leaf tissus)
| PRJEB61212 | ENA
Project description:Soybean (Glycine max) root nodulation is a symbiotic process that requires complex molecular and cellular coordination. The phloem plays a crucial role not only in nutrient transport but also in long-distance signaling that regulates nodulation. However, the molecular mechanisms underlying phloem-specific regulation during nodulation remain poorly characterized. Here, we developed a phloem-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) system to investigate the translational dynamics of phloem-associated genes during nodulation. Using a phloem-specific promoter (Glyma.01G040700) combined with the GAL4-UAS amplification system, we successfully captured the translatome of soybean root phloem at early (72 hours post-inoculation, hpi) and late (21 days post-inoculation, dpi) nodulation stages. Differential expression analysis revealed dynamic translational reprogramming, with 2,628 differentially expressed genes (DEGs) at 72 hpi and 8,422 DEGs at 21 dpi. Gene ontology and pathway enrichment analyses showed stage-specific regulatory shifts, including early activation of ethylene and defense pathways and late-stage enhancement of nutrient transport and vascular development. Transcription factor analysis identified GmbHLH121 as a key phloem-specific regulator of nodulation. Functional validation using RNAi knockdown and overexpression experiments demonstrated that GmbHLH121 negatively regulates nodule formation, likely acting downstream of or independently from early nodulation signaling pathways. Additionally, we uncovered dynamic regulation of cell wall-modifying enzymes (PME and PMEI) in the phloem, implicating their role in modulating plasmodesmata permeability and facilitating symplastic connectivity during nodulation. Our findings highlight the critical role of phloem-mediated translational regulation in coordinating root nodulation, emphasizing the phloem as an active regulatory hub for long-distance signaling and symbiotic efficiency. This study provides a foundational framework for future research on phloem-specific gene regulation and its impact on legume symbiosis.
2025-12-04 | GSE292049 | GEO
Project description:There are few data on fine root biomass and morphology change in relation to stand age. Based on chronosequences for beech (9-140 years old), oak (11-140 years) and alder (4-76 years old) we aimed to examine how stand age affects fine root biomass and morphology. Soil cores from depths of 0-15 cm and 16-30 cm were used for the study. In contrast to previously published studies that suggested that maximum fine root biomass is reached at the canopy closure stage of stand development, we found almost linear increases of fine root biomass over stand age within the chronosequences. We did not observe any fine root biomass peak in the canopy closure stage. However, we found statistically significant increases of mean fine root biomass for the average individual tree in each chronosequence. Mean fine root biomass (0-30 cm) differed significantly among tree species chronosequences studied and was 4.32 Mg ha(-1), 3.71 Mg ha(-1) and 1.53 Mg ha(-1), for beech, oak and alder stands, respectively. The highest fine root length, surface area, volume and number of fine root tips (0-30 cm soil depth), expressed on a stand area basis, occurred in beech stands, with medium values for oak stands and the lowest for alder stands. In the alder chronosequence all these values increased with stand age, in the beech chronosequence they decreased and in the oak chronosequence they increased until ca. 50 year old stands and then reached steady-state. Our study has proved statistically significant negative relationships between stand age and specific root length (SRL) in 0-30 cm soil depth for beech and oak chronosequences. Mean SRLs for each chronosequence were not significantly different among species for either soil depth studied. The results of this study indicate high fine root plasticity. Although only limited datasets are currently available, these data have provided valuable insight into fine root biomass and morphology of beech, oak and alder stands.
| S-EPMC4747558 | biostudies-literature