Diversity of wood-inhabiting bacteria in boreal peat forest
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR198835.fastq.gz | Fastqsanger.gz | |||
| ERR198836.fastq.gz | Fastqsanger.gz | |||
| ERR198837.fastq.gz | Fastqsanger.gz | |||
| ERR198838.fastq.gz | Fastqsanger.gz | |||
| ERR198839.fastq.gz | Fastqsanger.gz |
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Project description:Deadwood plays a crucial role in forest ecosystems, but we have limited information about the specific fungal taxa and extracellular lignocellulolytic enzymes that are actively involved in the decomposition process in situ. To investigate this, we studied the fungal metaproteome of twelve deadwood tree species in a replicated, eight-year experiment. Key fungi observed included genera of white-rot fungi (Basidiomycota, e.g. Armillaria, Hypholoma, Mycena, Ischnoderma, Resinicium), brown-rot fungi (Basidiomycota, e.g. Fomitopsis, Antrodia), diverse Ascomycota including xylariacous soft-rot fungi (e.g. Xylaria, Annulohypoxylon, Nemania) and various wood-associated endophytes and saprotrophs (Ascocoryne, Trichoderma, Talaromyces). These fungi used a whole range of extracellular lignocellulolytic enzymes, such as peroxidases, peroxide-producing enzymes, laccases, cellulases, glucosidases, hemicellulases (xylanases) and lytic polysaccharide monooxygenases (LPMOs). Both the fungi and enzymes were tree-specific, with specialists and generalists being distinguished by network analysis. The extracellular enzymatic system was highly redundant, with many enzyme classes of different origins present simultaneously in all decaying logs. Strong correlations were found between peroxide-producing enzymes (oxidases) and peroxidases as well as LPMOs, and between ligninolytic, cellulolytic and hemicellulolytic enzymes. The overall protein abundance of lignocellulolytic enzymes was reduced by up to -30% in gymnosperm logs compared to angiosperm logs, and gymnosperms lacked ascomycetous enzymes, which may have contributed to the lower decomposition of gymnosperm wood. In summary, we have obtained a comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in several temperate forest tree species, which can help to improve our understanding of the complex ecological processes in forest ecosystems.
2024-04-22 | PXD041962 | Pride
Project description:metagenome of microorganis inhabiting decaying wood
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Project description:The increasing human impact on the earth's biosphere is inflicting changes at all spatial scales. As well as deterioration and fragmentation of natural biological systems, these changes also led to other, unprecedented effects and emergence of novel habitats. In boreal zone, intensive forest management has negatively impacted a multitude of deadwood-associated species. This is especially alarming given the important role wood-inhabiting fungi have in the natural decay processes. In the boreal zone, natural broad-leaved-dominated, herb-rich forests are threatened habitats which have high wood-inhabiting fungal species richness. Fungal diversity in other broadleaved forest habitat types is poorly known. Traditional wood pastures and man-made afforested fields are novel habitats that could potentially be important for wood-inhabiting fungi. This study compares species richness and fungal community composition across the aforementioned habitat types, based on data collected for wood-inhabiting fungi occupying all deadwood diameter fractions. Corticioid and polyporoid fungi were surveyed from 67 130 deadwood particles in four natural herb-rich forests, four birch-dominated wood pastures, and four birch-dominated afforested field sites in central Finland. As predicted, natural herb-rich forests were the most species-rich habitat. However, afforested fields also had considerably higher overall species richness than wood pastures. Many rare or rarely collected species were detected in each forest type. Finally, fungal community composition showed some divergence not only among the different habitat types, but also among deadwood diameter fractions. Synthesis and applications: In order to maintain biodiversity at both local and regional scales, conserving threatened natural habitat types and managing traditional landscapes is essential. Man-made secondary woody habitats could provide the necessary resources and serve as surrogate habitats for many broadleaved deadwood-associated species, and thus complement the existing conservation network of natural forests.
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Project description:Biochar is considered to be a possible means of carbon sequestration to alleviate climate change. However, the dynamics of the microbial community during wood decomposition after biochar application remain poorly understood. In this study, the wood-inhabiting bacterial community composition and its potential functions during a two-year decomposition period after the addition of different amounts of biochar (0.5 kg m-2 and 1.0 kg m-2), and at different biochar pyrolysis temperatures (500 °C and 650 °C), in a boreal Scots pine forest, were analyzed using Illumina NovaSeq sequencing combined with Functional Annotation of Prokaryotic Taxa (FAPROTAX). The results showed that the wood decomposition rates increased after biochar addition to the soil surface in the second year. Treatment with biochar produced at high temperatures increased the diversity of wood-inhabiting bacteria more than that produced at low temperatures (P < 0.05). The wood-inhabiting bacterial diversity and species richness decreased with decomposition time. The biochar treatments changed the wood-inhabiting bacterial community structure during the decomposition period. The pyrolysis temperature and the amount of applied biochar had no effect on the bacterial community structure but shifted the abundance of certain bacterial taxa. Similarly, biochar application shifted the wood-inhabiting bacterial community function in the first year, but not in the second year. The wood-inhabiting bacterial community and function were affected by soil pH, soil water content, and soil total nitrogen. The results provide useful information on biochar application for future forest management practices. Long-term monitoring is needed to better understand the effects of biochar application on nutrient cycling in boreal forests.
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Project description:Boreal toads (Anaxyrus boreas boreas) of the Southern Rocky Mountain population are declining due to the introduction of the chytrid fungus Batrachochytrium dendrobatidis (Bd). Boreal toads in Colorado are generally susceptible to Bd infection, but some Bd-tolerant populations persist in parts of the Southern Rocky Mountain and broader Eastern boreal toad population. We conducted a Bd challenge with lab-reared sibling toads from Bd-susceptible Colorado and purportedly Bd-tolerant Utah populations and report on transcriptomic responses to Bd during late infection in skin and liver tissue. Fewer immune genes were expressed in response to Bd in Colorado toads, but with greater upregulation compared to Utah toads, indicating a dysregulated immune response. Signatures of Bd-tolerance in Utah toads included more moderate upregulation in immune gene expression and a significantly enriched suite of gene functions related to innate and adaptive immune responses. Our transcriptomic results support the notion that Utah toads are tolerant to Bd, rather than resistant, carrying Bd loads similar to Colorado yet having a unique transcriptomic profile and presenting minimal clinical signs of chytridiomycosis. We conclude that closely related populations have divergent transcriptomic responses to Bd with a dysregulated immune response in Bd-susceptible toads.
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Project description:Microeukaryotes of undisturbed soil and treated areas of northern Alberta boreal forest.
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