Bacterial communities associated with kelp hosts
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ABSTRACT:
PROVIDER: PRJEB50645 | ENA |
REPOSITORIES: ENA
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Project description:Bacterial communities associated with kelp hosts
| PRJEB50679 | ENA
Project description:Asteroidea-associated bacterial communities Metagenome
| PRJNA417960 | ENA
Project description:Root-associated bacterial and fungal communities
| PRJEB32926 | ENA
Project description:Diatom-derived polyunsaturated aldehydes (PUAs) significantly influence marine bacterial dy-namics, yet the underlying proteomic mechanisms remain elusive. We employed high-resolution comparative proteomics to decipher the functional reprogramming of two bacterial communi-ties—one naturally associated with a PUA-producing diatom (N-community) and another with a non-PUA producer (I-community)—under ecologically relevant PUA exposure. While growth rates and cell densities remained unaffected, indicating an absence of acute toxicity, proteomics revealed pronounced community-specific reorganization. N-communities displayed stable, regula-tion-oriented adjustments consistent with physiological accommodation, whereas I-communities exhibited dose-dependent stress responses, shifting toward protein repair and antioxidant defense. Our findings demonstrate that PUAs trigger profound proteomic reprogramming conditioned by the communities' prior ecological history. This functional divergence provides a molecular basis for understanding bacterial fitness and succession during diatom blooms, where PUA-mediated in-teractions could act as a selective filter shaping the phycosphere's microbial landscape. Polyunsaturated aldehydes (PUA) produced by diatoms have been proposed to exert a wide range of effects on marine bacteria, from inhibitory or stress-inducing responses to neutral or potentially beneficial effects. However, the bacterial proteomic responses remain elusive. Here, we employed a high-resolution comparative proteomic approach to decipher the functional reprogramming of two distinct bacterial communities under ecologically relevant PUA exposure. One community was composed by bacteria naturally associated with a PUA-producing diatom (N- communy and, a second community associated with a non-PUA-producing diatom (I-community). Bacterial growth rates and final cell densities were not significantly affected by any treatment, indicating the absence of toxic effects even at high PUA concentrations. Dissolved organic carbon consumption did not provide evidence that PUA was the relevant carbon source. Interestingly, comparative proteomic analyses revealed pronounced community-specific reorganization in response to PUA expo-sure.Our results show that PUAs trigger a profound proteomic reprogramming rather than a simple stress response. While I-community prioritized antioxidant defense and protein repair, N-community showed a metabolic shift towards energy conservation. These findings suggest that the metabolic history of bacterial assemblages determines their success in the phycosphere, providing a molecular basis for microbial succession during diatom blooms.
2026-06-04 | PXD075100 | Pride
Project description:Variations in Laminaria digitata associated bacterial communities
| PRJEB33998 | ENA
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
Project description:Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. Thus, DNA methylation seems to play an important role in kelp, which has not been reported before.
2018-07-17 | GSE117191 | GEO
Project description:Characterization of the mucosa-associated bacterial communities of abomasal ulcers by pyrosequencing
| PRJEB7320 | ENA
Project description:DIETARY AND DEVELOPMENTAL SHIFTS IN BUTTERFLY-ASSOCIATED BACTERIAL COMMUNITIES
| PRJEB21255 | ENA
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
2023-02-10 | GSE194276 | GEO