Sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA400449 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5985530_1.fastq.gz | Fastqsanger.gz | |||
| SRR5985530_2.fastq.gz | Fastqsanger.gz | |||
| SRR5985540_1.fastq.gz | Fastqsanger.gz | |||
| SRR5985540_2.fastq.gz | Fastqsanger.gz | |||
| SRR5985531_1.fastq.gz | Fastqsanger.gz |
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Project description:Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant. To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonium carbonate. A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154. At day 31, the preservative was still protecting the wood, which showed no strength loss. At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss. Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4). Transcripts that showed higher expression levels at the early time point were controlling increased oxalate metabolism, laccase for hydroquinone-driven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response. Transcripts that showed higher expression levels at the late time point were involved in degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism, catabolism of laccase substrates, extracellular proton reduction, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH.
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Project description:16S amplicon pool analyses of the four gut sections of the wood-feeding beetle, Odontotaenius disjunctus The beetle is purely wood feeding, and we aim to first characterize the community that exist within the gut sections
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Project description:The decomposition of large woody material is an important process in forest carbon cycling and nutrient release. Cord-forming saprotrophic basidiomycete fungi create non-resource limited mycelial networks between decomposing branches, logs and tree stumps on the forest floor where colonisation of new resource is often associated with the replacement of incumbent decay communities. Cord-forming species often dominate competition hierarchies in controlled paired antagonism experiments and have been shown to translocate resource to support colonisation and produce inhibitory metabolites. To date, antagonism experiments have mostly placed competing fungi in direct contact, while in nature cord-forming saprobes encounter colonised wood as mycelia in a network. Here we used soil-based microcosms that allowed foraging cord-forming Hypholoma fasciculare to encounter a wood block colonised by Trametes versicolor and conducted transcriptomic and proteomic analysis of the interaction. Cellular processes and metabolic responses to the competitive interaction were identified, where protein turnover featured strongly for both species. H. fasciculare demonstrated an exploitative profile with increased transcription of enzymes that targeted carbohydrate polymers of the substrate and in RNA and ribosome processing. T. versicolor showed a shift in signalling, energy generation and amino acid metabolism. Putative genes involved in secondary metabolite production were identified in both species. This study highlights the importance of ecologically-relevant experimental design when considering complex processes such as community development during wood decomposition
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Project description:Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Beyond the gene expression on glucose, 1129 genes were upregulated on cellulose and 1516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included GH12, GH131, CE1, AA3_1, AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these genes in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
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