Microbiota of mediterranean orchids
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40289 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, large-scale transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of the terrestrial mixotrophic orchid Limodorum abortivum under natural conditions. Our results provide new insights into the mechanisms underlying plant-fungus interactions in orchids and in particular on the plant responses to the mycorrhizal symbiont(s) in adult roots. Comparison with gene expression in mycorrhizal roots of another orchid species, Oeceoclades maculata, suggests that amino acids may represent the main nitrogen source in both protocorms and adult orchids, at least for mixotrophic species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, suggests a common plant core of genes in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.
2021-01-31 | GSE159700 | GEO
Project description:MedSeA project 16S rRNA metabarcoding
| PRJEB58727 | ENA
Project description:Orchids form an endomycorrhizal association with fungal symbionts mainly belonging to Basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchange between the symbionts imply a modulation of gene expression. In this study, we used proteomic and transcriptomic approaches to identify changes in the steady-state levels of proteins and transcripts in roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals of O. maculata were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging (iTRAQ) and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways in mycorrhizal roots, as compared to non-mycorrhizal roots. Overall, proteomics and transcriptomics revealed in mycorrhizal roots increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggest that plant defense is reduced in mycorrhizal roots. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.
2020-08-07 | GSE155822 | GEO
Project description:Mycorrhizal fungi colonize orchid seed and induce the germination. This so-called symbiotic germination is a critical developmental process in the lifecycle of all orchids. However, the molecular changes taking place during the orchid seed symbiotic germination still remains largely unknown. To better understand the molecular mechanism of orchid seed germination, we performed comparative transcriptomic and proteomic analysis on Chinese traditional medicinal orchid plants, Dendrobium officinale to explore protein expression change at the different developmental stages between asymbiotic and symbiotic germination and identify the key proteins regulated symbiotic germination of orchid seeds. iTRAQ analysis from 8 samples identified 2256 plant proteins, of which, 308 proteins were differentially expressed across three developmental stages within asymbiotic or symbiotic accession and 229 proteins are differentially expressed in the symbiotic germination compared to asymbiotic germination. 32 proteins are co-upregulated in both proteomic and transcriptomic level for symbiotic germination compared to asymbiotic germination. Our results revealed that symbiotic germination of D. officinale seeds probably shares the common signal pathway with asymbiotic germination during the early germination stage.
2017-05-12 | PXD006102 | Pride
Project description:To compare the similarities and differences in species diversity of the gut microbiota between the patients with melasma and healthy subjects. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota.
2022-10-25 | GSE214430 | GEO
Project description:South African terrestrial orchid mycorrhizal fungi samples
| PRJNA631257 | ENA
Project description:Analysis of gingival crevicular fluid (GCF) samples may give information of the identity of unattached (planktonic) subgingival bacteria, the 35 forefront candidates for systemic dispersal via ulcerated periodontal pocket epithelium. Our study represents the first one targeting the identity of bacteria in gingival crevicular fluid. Methodology/Principal findings: We determined bacterial species diversity in GCF samples of a group of periodontitis patients and delineated contributing bacterial and host-associated factors. Subgingival paper point (PP) samples from the same sites were taken for comparison. After DNA extraction, 16S rRNA genes were PCR amplified and DNA-DNA hybridization was performed using a microarray for over 300 bacterial species or groups. Altogether 133 species from 41 genera and 8 phyla 45 were detected with 9 to 62 and 18 to 64 species in GCF and PP samples, respectively, 46 per patient. Projection to latent structures by means of partial least squares (PLS) was applied to the multivariate data analysis. PLS regression analysis showed that species of genera including Campylobacter, Selenomonas, Porphyromonas, Catonella, Tannerella, Dialister, Peptostreptococcus, Streptococcus and Eubacterium had significant positive correlations and the number of teeth with low-grade attachment loss a significant negative correlation to species diversity in GCF samples. OPLS/O2PLS discriminant analysis revealed significant positive correlations to GCF sample group membership for species of genera Campylobacter, Leptotrichia, Prevotella, Dialister, Tannerella, Haemophilus, Fusobacterium, Eubacterium, and Actinomyces. Conclusions/Significance: Among a variety of detected species those traditionally classified as Gram-negative anaerobes growing in mature subgingival biofilms were the main predictors for species diversity in GCF samples as well as responsible for distinguishing GCF samples from PP samples. GCF bacteria may provide new prospects for studying dynamic properties of subgingival biofilms. The microbial profiles of GCF and subgingival plaque were analyzed from 17 subjects with periodontal disease.
2010-05-21 | E-GEOD-21929 | biostudies-arrayexpress
Project description:Pollinator specificity has traditionally been considered the main reproductive isolation mechanism in orchids. Among Mediterranean orchids, however, many species attract and deceive pollinators by mimicking nectar-rewarding plants. To test the extent to which deceptive orchid species share pollinators, we collected and identified hemipollinaria-carrying insects, and used ribosomal sequences to identify the orchid species from which hemipollinaria were removed. We found that social and solitary bees, and also flies, carried hemipollinaria belonging to nine orchid species with different degrees of specialization. In particular, Anacamptis morio, Dactylorhiza romana and Orchis mascula used a large set of pollinator species, whereas others such as Orchis quadripunctata seemed to be pollinated by one pollinator species only. Out of the insects with hemipollinaria, 19% were found to carry hemipollinaria from more than one orchid species, indicating that sympatric food-deceptive orchids can share pollinators. This sharing was apparent even among orchid sister-species, thus revealing an effective overlap in pollinator sets among closely related species. These results suggest varying degrees of pollinator specificity in these orchids, and indicate that pollinator specificity cannot always act as the main isolation mechanism in food-deceptive temperate orchids.
| S-EPMC1564100 | biostudies-literature