Microbial community from different tea plantation
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PROVIDER: PRJNA551933 | ENA |
REPOSITORIES: ENA
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Project description:tea plantation soil from different province Raw sequence reads
| PRJNA722620 | ENA
Project description:Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq. Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA). Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data. Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.
2022-08-17 | GSE198198 | GEO
Project description:Parkinson’s Disease (PD) is a disease of the central nervous system that progressively affects the motor system. Epidemiological studies have provided evidence that exposure to agriculture-related occupations or agrichemicals elevate a person’s risk for PD. Here, we sought to examine the possible epigenetic changes associated with working on a plantation on Oahu, HI and/or exposure to organochlorines (OGC) in PD cases. We measured genome-wide DNA methylation using the Illumina Infinium HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n=20) assessed for years of plantation work and presence of organochlorines in brain tissue. The comparison of 10+ to 0 years of plantation work exposure detected 7 and 123 differentially methylated loci (DML) in brain and blood DNA, respectively (P<0.0001). The comparison of cases with 4+ to 0-2 detectable levels of OGC, identified 8 and 18 DML in brain and blood DNA, respectively (P <0.0001). Pathway analyses revealed links to key neurotoxic and neuropathologic pathways related to impaired immune and proinflammatory responses as well as impaired clearance of damaged proteins, as found in the predominantly glial cell population in these environmental exposure-related PD cases.
2020-05-29 | GSE151355 | GEO
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:Total bacterial DNA was isolated from water and sediment samples from a local watershed and 16S rRNA sequences were analyzed using the Illumina MiSeq v3 platform in order to generate snapshots of bacterial community profiles. A total of 56 samples were collected that represent water and sediment samples from 14 sample sites over two different time points (November 18 and 25, 2011).
2016-07-03 | E-GEOD-73842 | biostudies-arrayexpress
Project description:Pu-erh tea has attracted increasing attention worldwide because of its special flavor and health effects, but its impact on composition and function of the gut microbiota remains unclear. The aim of this study was to investigate effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and metaproteomic investigation of the microbial communities in cecal samples taken from obese rats administrated with or without extracts of raw and ripe Pu-erh tea. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that, despite differences in the chemical compositions of the raw and ripe Pu-erh tea, administration of either at two different doses (0.15 and 0.40 g/Kg body weight), significantly (P<0.05) increased community diversity, and changed the composition of the cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes including sucrose metabolism, glycolysis, syntheses of proteins, rRNA and antibiotics were significantly (P<0.05), or had a tendency (0.10<P<0.05) to be, promoted by enriching relevant enzymes. Furthermore, evidences from population, molecular and metabolic levels have shown that polyphenols of raw Pu-erh tea and their metabolites can promote potentially the growth of Akkermansia municiphila by stimulating the type II and III secretion system protein, elongation factor Tu, and glyceraldehyde-3-phosphate dehydrogenase. This study has provided new evidences for the prebiotic effects of Pu-erh tea.
2022-03-03 | PXD010972 | Pride
Project description:To understand microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and the effects of environmental factors on their structure, 12 activated sludge samples were collected from four WWTPs in Beijing. GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes. The results showed that, for each gene category, such as egl, amyA, nir, ppx, dsrA sox and benAB, there were a number of microorganisms shared by all 12 samples, suggestive of the presence of a core microbial community in the activated sludge of four WWTPs. Variance partitioning analyses (VPA) showed that a total of 53% of microbial community variation can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.
2014-01-15 | GSE54055 | GEO