Ontology highlight
ABSTRACT:
PROVIDER: PRJNA750859 | ENA |
REPOSITORIES: ENA
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Project description:Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated microbial community profiles as well as directly assayed nitrogen cycling genes that encode the enzymes responsible for overall nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms responsible for production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that elevated rates of nitrous oxide production and consumption are the result of changes in community structure, not simply changes in microbial activity.
2018-01-13 | GSE108888 | GEO
Project description:This study describes a transcriptome-phenotype matching approach in which the starter L. lactis MG1363 was fermented under a variety of conditions that differed in the levels of oxygen and/or salt, as well as the fermentation pH and temperature. Samples derived from these fermentations in the exponential phase of bacterial growth were analyzed by full-genome transcriptomics and the assessment of heat and oxidative stress phenotypes. Variations in the fermentation conditions resulted in up to 1000-fold differences in survival during heat and oxidative stress. More specifically, aeration during fermentation induced protection against heat stress, whereas a relatively high fermentation temperature resulted in enhanced robustness towards oxidative stress. Concomitantly, oxygen levels and fermentation temperature induced differential expression of markedly more genes when compared with the other fermentation parameters. Correlation analysis of robustness phenotypes and gene expression levels revealed transcriptome signatures for oxidative and/or heat stress survival, including the metC-cysK operon involved in methionine and cysteine metabolism. To validate this transcriptome-phenotype association we grew L. lactis MG1363 in the absence of cysteine which led to enhanced robustness towards oxidative stress. Conclusions Overall, we demonstrated the importance of careful selection of fermentation parameters prior to industrial processing of starter cultures. Furthermore, established stress genes as well as novel genes were associated with robustness towards heat and/or oxidative stress. Assessment of the expression levels of this group of genes could function as an indicator for enhanced selection of fermentation parameters resulting in improved robustness during spray drying. The increased robustness after growth without cysteine appeared to confirm the role of expression of the metC-cysK operon as an indicator of robustness and suggests that sulfur amino acid metabolism plays a pivotal role in oxidative stress survival.
2014-08-01 | GSE58284 | GEO
Project description:During its progression from nasopharynx to other sterile and non-sterile niches of its human host, Streptococcus pneumoniae must cope with changes in temperature. We hypothesized that the pneumococcal temperature adaptation is an important facet of pneumococcal in host survival. Here we evaluate the effect of temperature on the phenotype of pneumococcus and the role of glutamate dehydrogenase (GdhA) during thermal stress adaptation associated with virulence and survival. Microarray analysis revealed a significant transcriptional response to temperature changes, affecting the expression of 132 and 119 genes at 34°C and 40°C, respectively, at mid-exponential growth phase relative to at 37ºC. One of the differentially regulated genes was gdhA, which is upregulated at 40°C while downregulated at 34°C relative to 37°C. Mutation of gdhA attenuated the growth, cell size, biofilm formation, pH survival, and virulence factor generation in a temperature dependent manner. Moreover, we identify that both D39 and ΔgdhA strains showed homo-lactic fermentation in glucose, however, ΔgdhA had higher formate production than D39 at all temperatures, which raised the hypothesis that gdhA involves in the regulation of pyruvate formate lyase (pflB) which is activated by catabolite control protein A (CcpA). In silico analysis pointed that a putative CcpA binding site (cre) was found in two proximal regions of -gdhA-coding sequence. The CcpA binding to the putative promoter region of gdhA was confirmed by EMSA. Furthermore, the transcriptional regulation of gdhA by CcpA, was temperature dependent. Finally, ΔgdhA grown at 34°C or 40°C was less virulent in Galleria mellonella infection model, suggesting that GdhA is required for pneumococcal virulence in fluctuating temperatures. These data demonstrated that temperature is an important parameter that affects physiology of S. pneumoniae and GdhA plays a significant role in temperature adaptation.
2021-11-24 | GSE154888 | GEO