Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.
Project description:This study began with 72 male 4-week-old BALB/c mice. The mice were split evenly into one of four cohorts: Control, River, Pine, and Road. The control mice were raised with standard corn cob bedding whereas the remaining mice were raised with clean bedding amended with 300 mL of one of three different types of soil. The soil exposure continued throughout the experiment, with 300 mL of new soil added with bi-weekly cage changes. The soils used to amend the cage bedding were previously characterized as having high (Pine), medium (River), and low (Road) diversity. The River and Pine soil were collected from Duke Forest and the Road soil was collected adjacent to Highway 15-501 in Chapel Hill, North Carolina. All mice were given a standard diet and the cages were distributed reverse osmosis treated water through a centralized Lixit® system that was fed to each cage in parallel. After 32 days of standard rearing with amended soils, the mice were exposed via oropharyngeal aspiration to either live influenza A (PR8) virus or heat inactivated (HI) virus.
Project description:This study examined how transcriptomics tools can be included in a Triad-based soil quality assessment to assess the toxicity of soils from river banks polluted by metals. To that end we measured chemical soil properties and used the standardized ISO guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod, Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher tier testing in soil quality. One of the least polluted soils showed toxicity in the bioassay that could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that another factor than metals (most likely of biological origin) caused the toxicity. This study demonstrates the feasibility and advantages of integrating transcriptomics into Triad-based soil quality assessment. Combining molecular and organismal life-history trait’s stress responses helps identifying causes of adverse effect in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress.
Project description:This study examined how transcriptomics tools can be included in a Triad-based soil quality assessment to assess the toxicity of soils from river banks polluted by metals. To that end we measured chemical soil properties and used the standardized ISO guideline for ecotoxicological tests and a newly developed microarray for gene expression in the indicator soil arthropod, Folsomia candida. Microarray analysis revealed that the oxidative stress response pathway was significantly affected in all soils except one. The data indicate that changes in cell redox homeostasis are a significant signature of metal stress. Finally, 32 genes showed significant dose-dependent expression with metal concentrations. They are promising genetic markers providing an early indication of the need for higher tier testing in soil quality. One of the least polluted soils showed toxicity in the bioassay that could be removed by sterilization. The gene expression profile for this soil did not show a metal-related signature, confirming that another factor than metals (most likely of biological origin) caused the toxicity. This study demonstrates the feasibility and advantages of integrating transcriptomics into Triad-based soil quality assessment. Combining molecular and organismal life-history traitM-bM-^@M-^Ys stress responses helps identifying causes of adverse effect in bioassays. Further validation is needed for verifying the set of genes with dose-dependent expression patterns linked with toxic stress. We used a one-color microarray design where each sample was hybridized to a single array
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.
Project description:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant