MUSHROOM CULTIVATION
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589209 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The white button mushroom Agaricus bisporus is the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. Growth profiling suggested different abilities for several A. bisporus strains to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.
2018-05-22 | GSE99928 | GEO
Project description:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential genes expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved.
2012-08-13 | GSE39559 | GEO
Project description:Five commercial strains of the culinary and medicinal mushroom Agaricus subrufescens were grown under two cultivation systems (outdoor versus indoor). Polar and lipid extracts of mushroom dry powders were extracted with a mixture of solvents (water:methanol:methyl tert-buthyl ether) and analyzed by UHPLC-ESI-HRMS-based untargeted metabolomics. A Nexera X2 UHPLC system (Shimadzu) equipped with an Acquity UPLC HSS T3 column (2.1 mm x 100 mm x 1.8 um) (Waters) was employed coupled to a MaXis 4G Q-TOF MS analyzer (Bruker Daltonics) through an electrospray ionization source. Data was acquired in positive ion mode.
2021-05-06 | MSV000087377 | MassIVE
Project description:Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from extra- and intracellular resources becomes mobilized to fuel fungal self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential genes expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a comprehensive framework for further elucidation of the interrelation and interplay of the individual cellular events involved. for each post-exponential time point (Day1, Day3 and Day6 post-carbon depletion), biological duplicates were performed.
2012-08-12 | E-GEOD-39559 | biostudies-arrayexpress
Project description:The effect of respiration (aerobic cultivation in the presence of heme and vitamin K2) was compared with unsupplemented aerobic cultivation with Lactobacillus plantarum.
2010-01-01 | GSE18432 | GEO
Project description:Lasting 24hr transcriptomic response of adult Drosophila mushroom body nuclei following odors only (odors) or odors+ethanol (trained) treatment.
2018-10-25 | GSE108525 | GEO
Project description:Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. Herein, we employed co-cultivation approach to identify cryptic biosynthetic gene clusters (BGCs) from fungal genomes eliciting the expression of genes that are silent or poorly transcribed in axenic cultures. Fungi were isolated from sphagnum peat bog samples collected from different regions of North-eastern USA because aspects of this ecological niche reflect the critical microenvironment of the human tuberculosis granuloma and are a natural habitat for slow growing mycobacterial species that compete for limited nutrients with other microbes. Bioactivity-guided assay led us to identify three unique fungal isolates that selectively produce growth inhibitory metabolites during co-cultivation with Mtb. Fungal mRNA sequencing from co-cultured isolates facilitated the identification of elicited Type I Polyketide Synthase BGCs that were silent/cryptic in monoculture conditions. Bioinformatic analyses followed by chemical validation identified these molecules to be patulin, citrinin and nidulalin A. Interestingly, these induced fungal metabolites led to a highly responsive redox-stress homeostasis within Mtb. Our study thus, illustrates a co-cultivation mediated elicitation of unique fungal NPs resulting in a thiol-burst oxidative stress mediated killing of Mtb. We believe that the identification of vulnerable drug targets may yield insights into further understanding of this essential thiol stress mediated killing of the mycobacteria
2024-10-15 | GSE255435 | GEO
Project description:We performed mRNA-seq of dissected Drosophila mushroom bodies, comparing to whole brain and testis mRNA seq of MB, brain and testis
2012-02-01 | E-GEOD-33783 | biostudies-arrayexpress