Ontology highlight
ABSTRACT:
PROVIDER: PRJNA493529 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:TThe seagrass microbiome (Biogeography and Plant-scale Dynamics): rRNA 16S amplicon sequencing
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Project description:Seagrass leaf reddening microbiome (16S amplicon sequencing)
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Project description:The seagrass microbiome (Light): rRNA 16S amplicon sequencing
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Project description:The seagrass microbiome (Disease): rRNA 16S amplicon sequencing
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Project description:Seagrass leaf microbiome associated with seagrass wasting disease (SWD, 16s amplicon sequencing)
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Project description:Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~104-108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This ‘epimutation-clock’ is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina, which represent the two primary modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
2024-01-11 | GSE223861 | GEO
Project description:Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~104-108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This ‘epimutation-clock’ is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina, which represent the two primary modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
2024-01-11 | GSE223810 | GEO
Project description:Positive and negative ecological interactions shape the dynamics and composition of natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein-based, are not well understood and only a small percentage of such interactions has been studied. We hypothesize that secreted proteins are a powerful and highly specific toolset to shape and defend a favorable plant niche. Here, we have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to inhibit and promote the growth of bacteria through secretion of proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the secreted proteome of Albugo candida combined with machine-learning predictors enabled the selection of candidates for heterologous expression and study of their inhibitory activity in vitro. We found that three of the candidate proteins showed a selective antimicrobial activity on several gram-positive bacterial strains isolated from Arabidopsis thaliana. We could ascribe the antibacterial activity of the candidates to their intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins that have an antimicrobial activity under apoplastic conditions and therefore are potential biocontrol tools for a targeted manipulation of the microbiome.
2023-05-31 | PXD031981 | Pride
Project description:The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and phenotypics, in their ability to reflect the full-scale anaerobic digestion microbiome. The phenotypic fingerprinting reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and phenotypic traits, yielded certain similar features yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, phenotypic fingerprinting is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
2021-05-26 | PXD024788 | Pride