Fungi and bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA693472 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria and fungi sequences of wood and soil
| PRJNA633292 | ENA
Project description:Metagenomics analysis reveals co-infection of fungi and bacteria isolated from different regions of brain tissue from elderly persons and patients with Alzheimer's disease.
| EGAS00001002766 | EGA
Project description:Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely E. glandulosa showed little differential response to the experimental treatments. By demonstrating temperature dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes.
2021-06-03 | PXD026003 | Pride
Project description:Brown rot fungi play an essential role in carbon cycling by decomposing lignocellulose into substrates usable by themselves and other microbes. Interactions between bacteria and fungi can be competitive or beneficial, but these relationships are not well understood because of a lack of good model systems. To model cross-feeding between fungi and bacteria, wood decayed by the brown rot fungus Rhodonia placenta was used as a carbon source for the phototrophic bacterium Rhodopseudomonas palustris. We found that fungal decay products generated by Rda. placenta could be used by R. palustris for growth, and later decay stages contained more usable substrates than early stages. Mass spectrometry identified a range of aromatic and non-aromatic acids, but after 95 days of bacterial growth, R. palustris only consumed non-aromatic acids over the aromatic lignin monomers. Genes involved with aromatic compound degradation were unimportant for growth and RNA sequencing revealed that aromatic compound degradation genes were repressed on decayed wood extract. Randomly barcoded transposon sequencing failed to identify a solitary catabolic pathway used by R. palustris, suggestive of substrate co-utilization, and surprisingly showed that genes involved with copper toxicity were essential. Finally, we found genes involved with biosynthesis of certain cofactors were non-essential on decayed wood extract, suggesting these nutrients were scavenged, and implicating these resources in supporting microbial communities in the environment. This study helps lay the foundation for a model fungal-bacterial system to study interactions that govern these relationships which will be valuable for understanding ecological interactions and industrially relevant co-culture systems.
2026-06-08 | GSE311457 | GEO
Project description:This study looks at the gene expression of two chain-elongating bacteria, Pseudoramibacter alactolyticus and Megasphaera elsdenii, in monoculture and in coculture with anaerobic gut fungi (Neocallimastix lanati). P. alactolyticus in particular has appeared stable in synthetic cocultures with anaerobic fungi based on metabolic output, and this RNA-seq study was designed to further assess that stability. Additionally, chain-elongating bacteria can use fungal fermentation products to generate short- and medium-chain fatty acids, and this study was employed to see how genes involved in this process (reverse beta oxidation) were regulated in coculture compared to monoculture.
2026-01-06 | GSE291899 | GEO
Project description:Bacteria, Fungi, Protist Raw sequence reads
| PRJNA1270755 | ENA