Project description:Climate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern-central African origin and recent worldwide colonization. Desiccation stress response is a complex and extensively studied trait, however the natural variation in tolerance, and the underlying transcriptomic and physiological mechanisms are still not clear. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains from cold semi-arid climates are more tolerant compared with the ones from hot summer mediterranean climate zones. Moreover, the variance in the tolerance of the strains correlates with the interaction of altitude and evaporation. We found that the tolerant strains had a lower level of initial water content and lose less water during desiccation stress. The reduction in the water loss is probably due to the decrease in the respiration rate in desiccation stress conditions, and to the cuticular hydrocarbon composition found in tolerant strains. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. Furthermore, we identified several desiccation candidate genes unique for the tolerant strains that can be targeted by tRNA derived fragments, known to be important in post-transcriptional gene regulation in several stress responses. We also looked for transposable element insertions possibly affecting the expression of genes relevant in desiccation tolerance, however, except for four insertions, there is no clear association between the presence of the TE insertions and the tolerance level of the strains. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains and puts tRFs in the scope of desiccation related studies as possible regulators of desiccation tolerance.

Project description:Climate change is one of the main factors shaping the distributions and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are specially threatened by these challenging dry environments, thanks to their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern African origin and recent and fast worldwide spreading. Desiccation stress response is a complex and extensively studied trait, however the natural variation and underlying molecular and physiological mechanisms responsible for the tolerance in natural European D. melanogaster populations has never been studied. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains belonging to the cold semi-arid climates are more tolerant compared to the others, and that this tolerance can be explained by the combination of altitude and evaporation. The tolerant strains had a lower level of initial water content and lost less water during desiccation stress. We found that the reduction in the water loss happens through a decrease in the respiration rate in desiccation stress conditions, and by having a less permeable cuticle prior the stress exposure. The decreased rate of respiration in the tolerant strains is a consequence of the down-regulation of genes related to diverse metabolic processes. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. We also identified four transposable element insertions, which might be responsible for changes in gene expression. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains, and generated a list of putative mutations shaping desiccation stress response.

Project description:The growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. In this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of Bradyrhizobium japonicum to drought. Desiccation of cells resulted in the differential expression of 15 to 20% of the 8,480 B. japonicum open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed genes. While 225 genes were universally up-regulated at all three incubation times in response to desiccation, an additional 43 and 403 up-regulated genes were common to the 4/24- and 24/72-h incubation times, respectively. Desiccating conditions resulted in the significant induction (>2.0-fold) of the trehalose-6-phosphate synthetase (otsA), trehalose-6-phosphate phosphatase (otsB), and trehalose synthase (treS) genes, which encode two of the three trehalose synthesis pathways found in B. japonicum. Gene induction was correlated with an elevated intracellular concentration of trehalose and increased activity of trehalose-6-phosphate synthetase, collectively supporting the hypothesis that this disaccharide plays a prominent and important role in promoting desiccation tolerance in B. japonicum. Microarray data also indicated that sigma(54)- and sigma(24)-associated transcriptional regulators and genes encoding isocitrate lyase, oxidative stress responses, the synthesis and transport of exopolysaccharides, heat shock response proteins, enzymes for the modification and repair of nucleic acids, and the synthesis of pili and flagella are also involved in the response of B. japonicum to desiccation. Polyethylene glycol-generated osmotic stress induced significantly fewer genes than those transcriptionally activated by desiccation. However, 67 genes were commonly induced under both conditions. Taken together, these results suggest that B. japonicum directly responds to desiccation by adapting to changes imparted by reduced water activity, such as the synthesis of trehalose and polysaccharides and, secondarily, by the induction of a wide variety of proteins involved in protection of the cell membrane, repair of DNA damage, stability and integrity of proteins, and oxidative stress responses. Keywords: stress response; time course

Project description:Spingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. The objectives of this study were to characterize how strain RW1 responses to changes in different components of the total water potential (solute and matric potential) and to then connect these responses to more realistic scenarios of soil desiccation. To accomplish this task, transcriptome profiling was used to investigate the effects of decreasing the solute potential with sodium chloride (solute stress), decreasing the matric potential with high-molecular weight polyethylene glycol (matric stress), or inoculating cells directly into unsaturated sand (sand desiccation stress). Transcriptome profiling revealed a general response to solute, matric, and sand desiccation stress that involved synthesizing trehalose and modifying the composition of exopolysaccarides. Transcriptome profiling also revealed responses that were unique to each stress. Only solute and matric stress triggered the down-regulation of flagella genes. Only solute and sand desiccation stress triggered the up-regulation of two RNA polymerase ECF-type sigma factors along with several membrane proteins, mechanosensitive channels, and solute transporters. Finally, only matric stress triggered the up-regulation of the RNA polymerase sigma-32 factor along with several molecular chaperones. Together, this study revealed a general response to solute, matric and sand desiccation stress but also unique responses to only a subset of these stresses, suggesting that each stress affects strain RW1 in a fundamentally different way. Comparative transcriptome profiling was performed to assess the effects of acute (30 min) solute and matric stress (3 samples for acute solute stress, 3 samples for acute matric stress, 3 controls), the effects of chronic (24 hours) solute and matric stress (3 samples for chronic solute stress, 3 samples for chronic matric stress, 3 controls), and the effects of sand desiccation stress (4 samples for sand desiccation treatment, 3 controls).

			Action	DRS
	SRR20068422_1.fastq.gz	Fastqsanger.gz
	SRR20068422_2.fastq.gz	Fastqsanger.gz
	SRR20068423_1.fastq.gz	Fastqsanger.gz
	SRR20068423_2.fastq.gz	Fastqsanger.gz

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Transcriptomic response of Nostoc sp. MG11 under desiccation stress

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