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Microbial metaproteome data from decayed beech dead wood.

ABSTRACT: Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota at a given point in time. In this dataset, we provide data of an exemplary beech wood log and applied different extraction methods to provide the proteome profile of beech dead wood and their corresponding fungal-bacterial community.

SUBMITTER: Kipping L

PROVIDER: S-EPMC7038588 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Microbial metaproteome data from decayed beech dead wood.

Kipping Lydia L Holzscheck Nicholas N Maurer Florian F Muszynski Sarah S Noll Matthias M Jehmlich Nico N

Data in brief 20200214

Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota a ...[more]

PMID: 32123712

Similar Datasets

Microbial metaproteome data from decayed beech dead wood

Project description:Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota at a given point in time. In this dataset, we provide data of an exemplary beech wood log and applied different extraction methods to provide the proteome profile of beech dead wood and their corresponding fungal-bacterial community.

2020-05-27 | PXD016801 | Pride

decayed wood

Project description:decayed wood Raw sequence reads

| PRJNA593777 | ENA

Bark coverage shifts assembly processes of microbial decomposer communities in dead wood.

Project description:Bark protects living trees against environmental influences but may promote wood decomposition by fungi and bacteria after tree death. However, the mechanisms by which bark determines the assembly process and biodiversity of decomposers remain unknown. Therefore, we partially or completely removed bark from experimentally felled trees and tested with null modelling whether assembly processes were determined by bark coverage and if biodiversity of molecularly sampled fungi and bacteria generally benefited from increasing bark cover. The community composition of fungi, wood-decaying fungi (subset of all fungi) and bacteria clearly separated between completely debarked, partly debarked and control trees. Bacterial species richness was higher on control trees than on either partly or completely debarked trees, whereas the species richness of all fungi did not differ. However, the species richness of wood-decaying fungi was higher on partially and completely debarked trees than on control trees. Deterministic assembly processes were most important in completely debarked trees, a pattern consistent for fungi and bacteria. Our findings suggest that human disturbances in forests shift the dominant assembly mechanism from stochastic to deterministic processes and thus alter the diversity of wood-inhabiting microorganisms.

| S-EPMC6790774 | biostudies-literature

Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms.

Project description:Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.

| S-EPMC9227542 | biostudies-literature

Molecular Screening of Microorganisms Associated with Discolored Wood in Dead European Beech Trees Suffered from Extreme Drought Event Using Next Generation Sequencing.

Project description:Drought events weaken trees and make them vulnerable to attacks by diverse plant pathogens. Here, we propose a molecular method for fast screening of microorganisms associated with European beech decline after an extreme drought period (2018) in a forest of Thuringia, Germany. We used Illumina sequencing with a recent bioinformatics approach based on DADA2 to identify archaeal, bacterial, and fungal ASVs (amplicon sequence variants) based on bacterial and archaeal 16S and fungal ITS genes. We show that symptomatic beech trees are associated with both bacterial and fungal plant pathogens. Although the plant pathogen sequences were detected in both discolored and non-discolored wood areas, they were highly enriched in the discolored wood areas. We show that almost each individual tree was associated with a different combination of pathogens. Cytospora spp. and Neonectria coccinea were among the most frequently detected fungal pathogens, whereas Erwinia spp. and Pseudomonas spp. were the dominant bacterial plant pathogens. We demonstrate that bacterial plant pathogens may be of major importance in beech decline.

| S-EPMC8537330 | biostudies-literature

Decayed wood - metagenomic - Proteomic characterization of proteins from organisms feeding on decayed wood from Montana

Project description:Proteomic characterization of proteins from organisms feeding on decayed wood from Montana

2017-10-04 | PXD007727 | Pride

Improving Fire Retardancy of Beech Wood by Graphene.

Project description:The aim of this paper was to improve the fire retardancy of beech wood by graphene. Six fire properties, namely time to onset of ignition, time to onset of glowing, back-darkening time, back-holing time, burnt area and weight loss were measured using a newly developed apparatus with piloted ignition. A set of specimens was treated with nano-wollastonite (NW) for comparison with the results of graphene-treated specimens. Graphene and NW were mixed in a water-based paint and brushed on the front and back surface of specimens. Results demonstrated significant improving effects of graphene on times to onset of ignition and glowing. Moreover, graphene drastically decreased the burnt area. Comparison between graphene- and NW-treated specimens demonstrated the superiority of graphene in all six fire properties measured here. Fire retardancy impact of graphene was attributed to its very low reaction ability with oxygen, as well as its high and low thermal conductivity in in-plane and cross-section directions, respectively. The improved fire-retardancy properties by the addition of graphene in paint implied its effectiveness in hindering the spread of fire in buildings and structures, providing a longer timespan to extinguish a fire, and ultimately reducing the loss of life and property. Based on the improvements in fire properties achieved in graphene-treated specimens, it was concluded that graphene has a great potential to be used as a fire retardant in solid wood species.

| S-EPMC7077454 | biostudies-literature

Surface Characteristics of One-Sided Charred Beech Wood.

Project description:The aim of this paper was to analyze selected properties of beech wood (Fagus sylvatica L.) treated by one-sided surface charring. Specimens were one-side charred with a hot plate using several time-temperature combinations (from 200 to 400 °C). Characteristics such as colour, discoloration, surface roughness, fire resistance, total carbohydrate content at several wood layers and decay resistance were evaluated. Surface charring was applied to the radial and tangential surfaces. Colour measurements showed that the surface of the wood turned grey due to charring. In addition to colour measurements, other experiments showed significant differences between radial and tangential specimens due to their different structures. The higher the temperature used in treating them, the lower the roughness values for radial specimens, while the trend for tangential specimens was the opposite. A smoother surface is more fire resistant, so radial specimens are generally better in this regard. Tangential specimens are more susceptible during preparation to forming cracks that impair flame resistance because a continuous protective densified layer is not formed. The determination of total carbohydrates revealed significant changes at various wood depths after surface charring. These changes were more predictable in radial specimens due to the annual ring orientation, because each layer consisted of a similar earlywood/latewood ratio. Finally, when decay resistance was assessed, weight loss was found to be lower in all specimens than in the references. The results suggest that charring at a particular combination of temperature and time improved the investigated properties of the surface-modified beech.

| S-EPMC8151175 | biostudies-literature

Priority effects during fungal community establishment in beech wood.

Project description:Assembly history of fungal communities has a crucial role in the decomposition of woody resources, and hence nutrient cycling and ecosystem function. However, it has not been clearly determined whether the fungal species that arrive first may, potentially, dictate the subsequent pathway of community development, that is, whether there is a priority effect at the species level. We used traditional culture-based techniques coupled with sequencing of amplified genetic markers to profile the fungal communities in beech (Fagus sylvatica) disks that had been pre-colonised separately with nine species from various stages of fungal succession. Clear differences in community composition were evident following pre-colonisation by different species with three distinct successor communities identified, indicating that individual species may have pivotal effects in driving assembly history. Priority effects may be linked to biochemical alteration of the resource and combative ability of the predecessor.

| S-EPMC4579477 | biostudies-literature

Niche partitioning among dead wood-dependent beetles.

Project description:Niche partitioning among species with virtually the same requirements is a fundamental concept in ecology. Nevertheless, some authors suggest that niches have little involvement in structuring communities. This study was done in the Pardubice Region (Czech Republic) on saproxylic beetles with morphologically similar larvae and very specific requirements, which are related to their obligatory dependence on dead wood material: Cucujus cinnaberinus, Pyrochroa coccinea, and Schizotus pectinicornis. This work was performed on 232 dead wood pieces at the landscape scale over six years. Based on the factors studied, the relationships among these species indicated that their co-occurrence based on species presence and absence was low, which indicated niche partitioning. However, based on analyses of habitat requirements and species composition using observed species abundances, there was no strong evidence for niche partitioning at either studied habitat levels, the tree and the microhabitat. The most likely reasons for the lack of strong niche partitioning were that dead wood is a rich resource and co-occurrence of saproxylic community was not driven by resource competition. This might be consistent with the theory that biodiversity could be controlled by the neutral drift of species abundance. Nevertheless, niche partitioning could be ongoing, meaning that the expanding C. cinnaberinus may have an advantage over the pyrochroids and could dominate in the long term.

| S-EPMC8313673 | biostudies-literature

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