Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
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PROVIDER: PRJNA968016 | ENA |
REPOSITORIES: ENA
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Project description:The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in-planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains’ abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
2023-11-03 | GSE231841 | GEO
Project description:The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
| S-EPMC10719396 | biostudies-literature
Project description:Genome-resolved metatranscriptomics reveals conserved root colonization strategies in a synthetic microbiota
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Project description:The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago. This symbiosis is still widely found across major land plant lineages, including bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. Here, we demonstrate that a broad AM genetic programme is conserved amongst land plants. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across three stages of symbiosis. Comparative analysis of transcriptional responses to symbiosis in the liverwort M. paleacea and the legume Medicago truncatula further revealed evolutionarily conserved expression patterns for genes underpinning pre-symbiotic signalling, intracellular colonization and nutrient exchange. This study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across land plants.
2024-08-08 | GSE245702 | GEO
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Project description:post-wash metatranscriptomics project
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Project description:Fungal interactions with plant roots, either beneficial or detrimental, have a major impact on agriculture and ecosystems1. The soil inhabiting ascomycete Fusarium oxysporum (Fo) constitutes a species complex of worldwide distribution causing vascular wilt in more than a hundred different crops2,3. Individual isolates of the fungus exhibit host-specific pathogenicity, determined by proteinaceous effectors termed secreted in xylem (SIX)4,5. However, such isolates can also colonize roots of non-host plants asymptomatically as endophytes, or even protect the plant against pathogenic isolates6,7. The molecular determinants of multi-host plant colonization are currently unknown. Here, we identified a set of fungal effectors termed ERCs (Early Root Compatibility effectors), which are secreted during early biotrophic growth of Fo on both host and non-host plants. In contrast to SIX effectors, which are encoded on lineage specific (LS) genomic regions5,8, ERCs are encoded on core genomic regions and broadly conserved across the Fo species complex. Targeted deletion of ERC genes in pathogenic Fo isolate resulted in reduced virulence on the host plant and rapid activation of plant immune responses, while in a non-pathogenic isolate it led to impaired root colonization and loss of biocontrol ability. Strikingly, some ERCs also contribute to Fo infection on the non-vascular land plant Marchantia polymorpha. Our results reveal an evolutionarily conserved mechanism for multi-host colonization by root infecting fungi.
2022-09-12 | PXD026400 | Pride