Ontology highlight
ABSTRACT:
PROVIDER: PRJNA557209 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9855785.fastq.gz | Fastqsanger.gz |
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Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning.
2010-12-30 | GSE22825 | GEO
Project description:The goal of this study was to measure the effect of heat stress on the transcriptome of a cold-adapted fish species - Trematomus bernacchii - an Antarctic fish species. Keywords: Stress response
2007-12-14 | GSE9871 | GEO
Project description:The malate shuttle is traditionally known to maintain the NAD+/NADH balance between the cytosol and mitochondria. Whether the malate shuttle has additional functions was unknown. Here we show that chronic viral infections induced the expression of GOT1, the key enzyme in the malate shuttle, in CD8+ T cells. Got1 deficiency indeed decreased the NAD+/NADH ratio and dampened antiviral CD8+ T cell responses to chronic infection; however, increasing the NAD+/NADH ratio did not restore antiviral T cell responses. Got1 deficiency reduced the production of the ammonia scavenger 2-ketoglutarate and led to toxic ammonia accumulation in CD8+ T cells. Supplementation with 2-ketoglutarate assimilated and detoxified ammonia in Got1-deficient T cells and restored antiviral responses. This study suggests that the major function of the malate shuttle in CD8+ T cells is not to maintain the NAD+/NADH ratio, but rather to detoxify ammonia and enable sustainable ammonia-neutral glutamine catabolism in CD8+ T cells during chronic infections.
2023-09-01 | GSE220876 | GEO
Project description:Nitrogen fixation is a highly energy-demanding process and highly regulated at multiple levels. The two major signals that regulate nitrogen fixation in most diazotrophs are oxygen and ammonia. In order to study the complex regulated mechanism and to highlight the complete nitrogen fixing system in genome level, here we present the transcriptional profiles of the nitrogen fixation genes of P.stutzeri A1501 in different growth conditions with a genome-wide DNA microarray. In this study, the three samples of "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension","P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments, while, the other three samples of "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-1", "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments. The gene expressions under these two growth phases were compared to investigate which genes' expression were effected by different ammonia concentrations. Keywords: nitrogen fixation, nitrogen repression
2007-04-20 | GSE6572 | GEO
Project description:Using RNAseq of small RNA libraries isolated from the gill tissue of the Antarctic fish Trematomus bernacchii we have characterized the termal sensitivity of miRNA homologues in these highly stenothermic fish.
2019-04-02 | GSE128132 | GEO
Project description:Abstract: Atmospheric ammonia is a common problem in poultry industry. High concentrations of aerial ammonia cause great harm to broilers' health and production. For the consideration of human health, the limit exposure concentration of ammonia in houses is set at 25 ppm. Previous reports have shown that 25 ppm is still detrimental to livestock, especially the gastrointestinal tract and respiratory tract, but the negative relationship between ammonia exposure and the tissue of breast muscle of broilers is still unknown. In the present study, 25 ppm ammonia in poultry houses was found to lower slaughter performance and breast yield. Then, high-throughput RNA sequencing was utilized to identify differentially expressed genes in breast muscle of broiler chickens exposed to high (25 ppm) or low (3 ppm) levels of atmospheric ammonia. The transcriptome analysis showed that 163 genes (fold change ≥ 2 or ≤ 0.5; P-value < 0.05) were differentially expressed between Ammonia25 (treatment group) and Ammonia3 (control group), including 96 down-regulated and 67 up-regulated genes. qRT-PCR analysis validated the transcriptomic results of RNA sequencing. Gene Ontology (GO) functional annotation analysis revealed potential genes, processes and pathways with putative involvement in growth and development inhibition of breast muscle in broilers caused by aerial ammonia exposure. This study facilitates understanding of the genetic architecture of the chicken breast muscle transcriptome, and has identified candidate genes for breast muscle response to atmospheric ammonia exposure.
2016-08-19 | GSE85786 | GEO
Project description:Community structure of ammonia oxidizing microorganism in East Antarctic soil
| PRJDB8665 | ENA
Project description:Abstract: Ammonia is one of the most prominent air pollutants in poultry houses. High levels of ammonia have adverse effects on respiratory health, growth performance, meat production of broilers, and breast meat growth and yield are critical important in the broiler industry. To date, studies focus on the negative relationship of ammonia exposure and breast muscle tissue are still very limited, and the underlying molecular mechanisms remain poorly understood. In this study, high concentrations of atmospheric ammonia were found to lower slaughter rate and broiler breast meat yield significantly (P < 0.05). To explore the candidate genes that ammonia regulates breast meat yield of broilers, high throughout RNA-Seq was used to compare the transcriptome of breast muscle with different ammonia exposure (50 ppm vs 3 ppm). In total, 129 differentially expressed genes (DEGs) were identified (P-value < 0.05; fold-change ≥ 2), among which 87 genes were significantly down-regulated and 42 were up-regulated. Bioinformatics analysis suggested that DEGs (such as PDK4, ACSL1, GLUL, FBXO32) were involved in fatty acid degradation/metabolism, nitrogen metabolism, PPAR signaling and adipocytokine signaling pathways. Functional annotation showed that DEGs were mainly enriched in reactive oxygen species metabolic process and muscle contraction. It can be concluded that decreased meat yield was due to the DEGs participating in above biological processes and pathways. This study provides novel insights into transcriptional differences in breast meat between high- and low-ammonia exposed broiler chickens.
2017-10-14 | GSE104941 | GEO
Project description:Investigation of the whole genome gene expression level changes relative to exponential phase growth in Nitrosomonas europaea ATCC19718 after 12 hours ammonia starvation, 144 hours ammonia starvation, and 20 minutes following ammonia addition to starved cells. The ammonia monooxygenase of chemolithotrophic ammonia oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2). Several AOB, including N. europaea, also posess a divergent monocistronic copy of amoC (amoC3) of unknown function. Previous work suggested a possible functional role for amoC3 in N. europaea during recovery from extended ammonia starvation as part of the σE- stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC3 is part of a general post-starvation cellular response system in N. europaea. We also found that amoC3 is required for efficient exit from prolonged ammonia starvation, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon also plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. A twelve chip study using total RNA recovered from four timepoints for each of three biological replicates of wild-type cultures of Nitrosomonas europaea ATCC 19718. Total RNA was obtained from each biological culture replicate during exponential growth, following 12 hours ammonia starvation, 144 hours ammonia starvations, and 20 minutes following ammonia addition to starved cells.
2012-08-02 | E-GEOD-35122 | biostudies-arrayexpress