Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lake water metagenome

ABSTRACT: Targeted isolation approaches combined with environmental sequencing unveil ecological interactions and seasonality of chytrid fungi

PROVIDER: PRJNA682007 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13207841_1.fastq.gz	Fastqsanger.gz
	SRR13207841_2.fastq.gz	Fastqsanger.gz
	SRR13207842_1.fastq.gz	Fastqsanger.gz
	SRR13207842_2.fastq.gz	Fastqsanger.gz
	SRR13207843_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 114

Similar Datasets

Homolaphlyctis polyrhiza

Project description:Chytrid fungi

| PRJNA68391 | ENA

Project description:Seasonality in honeybees interactions

| PRJNA887226 | ENA

Incipient speciation by divergent adaptation and antagonistic epistasis in yeast

Project description:Understanding the conditions that promote the evolution of reproductive isolation, and thus speciation. Here we empirically test some of the key predictions of speciation theory (Coyne 2004; Kohn 2005) by experimentally evolving the initial stages of speciation in yeast. After allowing replicate populations to adapt to two divergent environments, we observed the consistent, de novo evolution of two forms of postzygotic isolation: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. In general, divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by ecological speciation theory. Our experimental system allowed for the first controlled comparison of the relative importance of ecological and genetic mechanisms of isolation, and the novel ability to quantify the effects of antagonistic epistasis. For mitotic reproduction, hybrid inferiority was conditional upon the selective environments and was both ecological and genetic in basis. In contrast, isolation associated with meiotic reproduction was unconditional and was caused solely by genetic mechanisms. Overall, our results show that adaption to divergent environments promotes the evolution of isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature (Schluter 2000,2001: Funk 2006) Keywords: Speciation, antagonistic epistasis, divergent adaptation

2007-06-21 | GSE6870 | GEO

RNA-seq analysis of Coprinopsis cinerea mycelium challenged with gram negative and gram positive bacteria

Project description:During growth in their ecological niche fungi encounter many (micro)organisms that compete for nutrients and /or have antagonistic activity. However, little is known about responses of fungi upon exposure to other microbes. In this project we want to gain insight in induced responses of C. cinerea towards bacteria through comparison of the transcriptome of vegetative C. cinerea mycelium either grown alone or exposed to the bacterial species Escherichia coli or Bacillus subtilis

2018-09-30 | E-MTAB-6876 | biostudies-arrayexpress

Survey functional genes in Arctic marine sediment communities

Project description:The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment. These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms. Ultimately, these data suggest that marine fungi could be as important in oceanic ecosystems as they are in freshwater environments.

2020-07-14 | GSE117831 | GEO

High-throughput transcriptomics of water extracts detects reductions in biological activity with water treatment processes

Project description:The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations including chemical coverage and high cost, and broad-coverage in vitro assays such as transcriptomics may further improve water quality monitoring by assessing a large range of possible effects. Here, we used high-throughput transcriptomics to assess the activity induced by field-derived water extracts in MCF7 breast carcinoma cells.

2024-03-05 | GSE252117 | GEO

ena-DATASET-CBMSO-16-05-2019-08:09:24:047-226 - samples

Project description:Isolation of fungi in infected neural tissues in patients with Parkinson's disease. Here we used next generation sequencing of Internal Transcribed Spacer (ITS) regions, by PCR amplicons (NGS ITS amplicon analysis).

| EGAD00001005025 | EGA

Presence of fungal infection in brains of patients with Parkinsons disease (PD)

| EGAS00001003644 | EGA

Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth.

Project description:Lipo-chitooligosaccharides (LCOs) are historically known for their role as microbial-derived signaling molecules that shape plant symbiosis with beneficial rhizobia or mycorrhizal fungi. Recent studies showing that LCOs are widespread across the fungal kingdom have raised questions about the ecological function of these compounds in organisms that do not form symbiotic relationships with plants. To elucidate the ecological function of these compounds, we investigate the metabolomic response of the ubiquitous human pathogen, Aspergillus fumigatus, to LCOs. Our metabolomics data revealed that exogenous application of various types of LCOs to A. fumigatus resulted in significant shifts in fungal metabolic profile, with marked changes in the production of specialized metabolites known to mediate ecological interactions. Using network analyses, we identify specific types of LCOs with the most significant effect on the abundance of known metabolites. Extracts of several LCO-induced metabolic profiles significantly impact the growth rates of diverse bacterial species. These findings suggest that LCOs may play an important role in the competitive dynamics of non-plant-symbiotic fungi and bacteria. This study identifies specific metabolomic profiles induced by these ubiquitously produced chemicals and creates a foundation for future studies into the potential roles of LCOs as modulators of interkingdom competition.

2022-10-21 | MSV000090566 | MassIVE

Mechanisms of interaction between ectomycorrhizal fungi and the mycorrhiza helper bacterium Pseudomonas fluorescens BBc6R8

Project description:Mycorrhiza helper bacteria (MHB) promote the formation of ectomycorrhizae between tree roots and ectomycorrhizal fungi. Despite the high relevance of MHB for forestry and for sustainable tree production in tree nurseries, little is known about the properties of the bacteria that contribute to their helper abilities. The MHB strain Pseudomonas fluorescens BBc6R8 is used as a model to study the mechanisms of the helper effect. We took advantage of new technologies to obtain, for the first time, the whole genome sequence of an MHB. Analyses reveal an important plasticity of the genome with numerous functions acquired by horizontal gene tranfer. Genome mining was combined with transcriptomic and mutagenesis approaches to reveal molecular determinants of the helper effect. The data suggest that the production of helper molecules is likely to be constitutive in vitro. The helper effect appears to be pleiotropic and to rely, for a substantial part, on trophic interactions. Despite its helper abilities, the bacterium is also able in specific conditions to outcompete ectomycorrhizal fungi and inhibit their growth. We conclude that the helper bacterium possess a broad range of properties whose expression depending on the biotic and abiotic conditions can result in either a beneficial, neutral or antagonistic interaction between the plant, the ectomycorrhizal fungus and the bacterium. The study was performed along a kinetic with three sampling times: before contact between the bacterial colonies and the fungus (14 days after inoculation), at the time of contact (16 days after inoculation) and after an extended period of contact (21 days). For each time, three independent replicates were performed. A control treatment without the fungus was performed in triplicate and sampled at 14 days.

2014-06-12 | E-GEOD-38243 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data