Soil invertebrate communities in two forest types
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA724931 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19582400_1.fastq.gz | Fastqsanger.gz | |||
| SRR19582400_2.fastq.gz | Fastqsanger.gz | |||
| SRR19582500_1.fastq.gz | Fastqsanger.gz | |||
| SRR19582500_2.fastq.gz | Fastqsanger.gz | |||
| SRR19582600_1.fastq.gz | Fastqsanger.gz |
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Project description:Polycyclic Aromatic Hydrocarbons (PAHs) continue to cause environmental challenges due to their release in the environment by a great variety of anthropogenic activities and their accumulation in soil ecosystems. Here we studied the toxicological effect of the model PAH phenanthrene (Phe) on the soil invertebrate model Enchytraeus crypticus at the individual, tissue and molecular level. Organisms were exposed to Phe for 2 and 21 days to the (previously estimated) EC10 and EC50 (population reproduction over 3 weeks). Gene expression profiling did not reveal a typical Phe-induced biotransfor-mation signature, as it usually does in arthropods and vertebrates. Instead, we observed only general metabolic processes to be affected after 2 days of exposure, such as translation and ATP synthesis-coupled electron transport. Histological sections of tissues of 2-day exposed animals did not show any deviations from the control situation. In contrast, prolonged exposure up to 21 days showed histopathological effects: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among soil invertebrate communities, which restricts read-across and extrapolation in the context of soil ecological risk assessment.
2015-12-18 | GSE74114 | GEO
Project description:Polycyclic Aromatic Hydrocarbons (PAHs) continue to cause environmental challenges due to their release in the environment by a great variety of anthropogenic activities and their accumulation in soil ecosystems. Here we studied the toxicological effect of the model PAH phenanthrene (Phe) on the soil invertebrate model Enchytraeus crypticus at the individual, tissue and molecular level. Organisms were exposed to Phe for 2 and 21 days to the (previously estimated) EC10 and EC50 (population reproduction over 3 weeks). Gene expression profiling did not reveal a typical Phe-induced biotransfor-mation signature, as it usually does in arthropods and vertebrates. Instead, we observed only general metabolic processes to be affected after 2 days of exposure, such as translation and ATP synthesis-coupled electron transport. Histological sections of tissues of 2-day exposed animals did not show any deviations from the control situation. In contrast, prolonged exposure up to 21 days showed histopathological effects: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among soil invertebrate communities, which restricts read-across and extrapolation in the context of soil ecological risk assessment. The data presented in our manuscript is an exposure experiment where E. cryticus is exposed to phenanthrene EC10 and EC50 on reproduction for 2 and 21 days. A single channel, interwoven loop design was used to test animals. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. The platform is a 4*180k Agilent platform containing some 86k E. crypticus probes in duplicate. However, only a subset of the probes (23k) was used for the analysis. To see which probes were used in the analysis see the raw data files control type column, only probes which are denoted with a 0 were used.
2015-12-18 | E-GEOD-74114 | biostudies-arrayexpress
Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.
2015-03-26 | PRD000542 | Pride
Project description:Pentachlorophenol (PCP) as a widely used pesticide is also considered to be an endocrine disruptor. Molecular effects of chemicals with endocrine disrupting potential on soil invertebrates are largely unknown. Collembola (Folsomia candida) has been used as a model organism in ecotoxicity and in this study we explored the transcriptional expression changes of Folsomia candida in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure time and majority of them were found to be down-regulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially genes. Analyses of Gene Ontology (GO) annotation and enrichment revealed that cell cycle related transcripts were significantly induced by PCP, indicating it can stimulated the cell proliferation in springtail as reported in human breast cancer cells. We also observed enrichment of functional terms related to steroid receptor and particularly twenty significant differential expressed genes involved in Chitin metabolism in response to PCP exposure. Combined with the confirmation by qPCR, our results appears that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and molting associated genes may serve as possible biomarkers for toxicological effects. In general, analysis of changes in the gene expression profiles of springtails in response to PCP exposure is useful for obtaining information on endocrine disruptor exposure of soil invertebrate and may contribute to the classification and risk assessment of relative chemicals.
2016-10-30 | GSE52893 | GEO
Project description:Temperature is an important ecological condition, and sudden temperature changes in soil can induce stress in soil-dwelling invertebrates. Soil animals can move to more favorable habitats and/or adapt physiologically to a stressful environment. Hyperthermic conditions will impact gene expression as one of the first steps. We use a transcriptomics approach to identify the transcripts of which expression changed in response to heat stress in the springtail Folsomia candida using a 5,131 probe microarray. A temperature shift from 20°C to 30°C for 30 minutes significantly altered the expression of 142 genes, of which 116 were upregulated, and 26 downregulated. Many upregulated genes encoded heat shock proteins (Hsps) or enzymes involved in the synthesis of ATP, such as members of the electron transport chain. Furthermore, genes involved in oxidative stress and anion-transporting ATPases were upregulated. Downregulated were glycoside hydrolases, involved in catalysis of certain disaccharides, which indicate an accumulation of stress-protective disaccharides. The microarray results from this study, which were validated using quantitative RT PCR, reveal a mild response to heat shock in this soil invertebrate, relative to other organisms. This may be due to specific ecological factors during evolution of soil invertebrates, such as the relatively stable temperatures in the soil habitat. This study presents potential candidate genes for future functional studies concerning thermal stress in soil-dwelling invertebrates, like e.g., the investigation of the heat hardening process. Folsomia candida was first acclimated to LUFA 2.2 soil at 20 C for two days. Then animals were either exposed to 30 C for 30 minutes (heat shock treated), or were not heat shocked (reference). For each treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or heat shock. Each unique heat shock treated sample was hybridized to a unique reference sample. In total in 4 hybridizations of 8 samples, was performed. The dyes were evenly distributed, which means that for each treatment two samples were labeled with cy3 and the other two with cy5.
2010-06-24 | E-GEOD-17024 | biostudies-arrayexpress
Project description:Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.
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