Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666757 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12755644_1.fastq.gz | Fastqsanger.gz | |||
| SRR12755644_2.fastq.gz | Fastqsanger.gz | |||
| SRR12755645_1.fastq.gz | Fastqsanger.gz | |||
| SRR12755645_2.fastq.gz | Fastqsanger.gz | |||
| SRR12755646_1.fastq.gz | Fastqsanger.gz |
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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:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. nirS gene diversity from two salt marsh experiments, GSM (4 treatments, 8 samples, duplicate arrays, four replicate blocks per array, 8 arrays per slide) and PIE (2 treatments, 16 samples, duplicate arrays four replicate blocks per array, 8 arrays per slide)
2010-11-13 | E-GEOD-25227 | biostudies-arrayexpress
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
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.
2022-03-01 | GSE147041 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in EarthM-bM-^@M-^Ys biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling. Fifty four samples were collected from three soil types (Phaeozem,Cambisol,Acrisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; Both with and without maize cropping in each site; Three replicates in every treatments.
2013-10-30 | E-GEOD-51592 | biostudies-arrayexpress
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
2013-07-13 | GSE48820 | GEO
Project description:A comparision of soil microbial functional genes of three types of subtropical broad-leaved forests Microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher alpha-diversity of functional genes but lower beta-diversity, and showed more complex functional gene networks.
2021-01-29 | GSE165723 | GEO
Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO
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).
2022-03-14 | PXD004428 | Pride