Anthropogenic soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA809221 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress
2024-02-01 | GSE251706 | 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:Burkholderia pseudomallei can adapt to and thrive in a variety of environments, including soil and water, and also can infect different hosts, including humans, leading to the tropical disease melioidosis. Modulation of gene and protein expression is one of this pathogen's adaptive survival mechanisms, which could lead to changes in the bacteria's cell membrane, metabolism, and virulence. To better understand bacterial adaptation and host-pathogen interactions, this study compared the expression profiles of B. pseudomallei from infected mice to B. pseudomallei cultivated in soil extract media. B. pseudomallei in vivo was created by infecting mice through the intraperitoneal route and harvesting the spleens on day 5 post infection. Total RNA was isolated and sequenced from the harvested spleen. Sequence reads were mapped to the B. pseudomallei UKMD286 strain genome sequence.
2022-07-22 | E-MTAB-11200 | biostudies-arrayexpress
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: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