Forest gap
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25917 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2505410.fastq.gz | Fastqsanger.gz | |||
| ERR2505420.fastq.gz | Fastqsanger.gz | |||
| ERR2505411.fastq.gz | Fastqsanger.gz | |||
| ERR2505421.fastq.gz | Fastqsanger.gz | |||
| ERR2505412.fastq.gz | Fastqsanger.gz |
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Project description:Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.
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Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
2014-07-22 | GSE59620 | GEO
Project description:The database consists of 248 HPLC-QTOF-HRMS/MS analyses of microscopic fungi isolated from soil samples collected in 2021, in the cloud forest of central Veracruz, Mexico. Soil samples were collected from around of 17 ant nests, from inside of 15 anthills, and from two transit areas. Also entomogenic fungi of ants. The two best represented ants were Solenopsis geminata and Atta mexicana, the others were Dorymyrmex bicolor, Nomamyrmex esenbeckii, Cheliomyrmex morosus, and Camponotus sericeiventris. Growth media and solvents analyses are available.
Dataset license: CC BY-NC-ND 4.0
2024-04-08 | MSV000094490 | MassIVE
Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.
2021-02-02 | PXD005447 | Pride
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients. 12 samples were collected from two long-term polluted areas (Olkusz and Miasteczko M-EM-^ZlM-DM-^Eskie) in Southern Poland. In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised
2014-07-22 | E-GEOD-59620 | biostudies-arrayexpress
Project description:forest disturbance on soil fungi Raw sequence reads
| PRJNA412774 | ENA
Project description:Forest soil bacterial community Raw sequence reads
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Project description:Soils are a huge reservoir of organic C, and the efflux of CO2 from soils is one of the largest fluxes in the global C cycle. Out of all natural environments, soils probably contain the greatest microbial biomass and diversity, which classifies them as one of the most challenging habitats for microbiologists (Mocali and Benedetti, 2010). Until today, it is not well understood how soil microorganisms will respond to a warmer climate. Warming may give competitive advantage to species adapted to higher temperatures (Rinnan et al., 2009). The mechanisms behind temperature adaptations of soil microbes could be shifts within the microbial community. How microbial communities will ultimately respond to climate change, however, is still a matter of speculation. As a post-genomic approach in nature, metaproteomics allows the simultaneous examination of various protein functions and responses, and therefore is perfectly suited to investigate the complex interplay between respiration dynamics, microbial community architecture, and ecosystem functioning in a changing environment (Bastida et al., 2012). Thereby we will gain new insights into responses to climate change from a microbial perspective. Our study site was located at 910 m a.s.l. in the North Tyrolean Limestone Alps, near Achenkirch, Austria The 130 year-old mountain forests consist of Norway spruce (Picea abies) with inter-spread of European beech (Fagus sylvatica) and silver fir (Abies alba). Three experimental plots with 2 × 2 m warmed- and control- subplots were installed in 2004. The temperature difference between control and warmed plots was set to 4 °C at 5 cm soil depth. Soil was warmed during snow-free seasons. In order to extract proteins from forest soil samples, the SDS–phenol method was adopted as previously described by Keiblinger et al. (2012). Protein extractions were performed from each subplot soil samples. The abundance of protein-assigned microbial phylogenetic and functional groups, were calculated based on the normalized spectral abundance factor (NSAF, Zybailov et al., 2006).
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