Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies
Ontology highlight
ABSTRACT:
ORGANISM(S): Mesorhizobium sp. N33
PROVIDER: GSE60710 | GEO | 2015/05/08
SECONDARY ACCESSION(S): PRJNA259352
REPOSITORIES: GEO
Similar Datasets
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general.
2011-06-01 | GSE26306 | GEO
Project description:Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies
| PRJNA259352 | ENA
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.
2011-07-05 | GSE29610 | GEO
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general. 18 microarray slides representing 6 individuals from 3 treatment groups (Intolerant, Tolerant and Control). One test cDNA labeled with cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide Reference design: 18 slides (6 x Tolerant fish, 6x Intolerant fish, 6x Control fish) were used.
2011-06-01 | E-GEOD-26306 | biostudies-arrayexpress
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions. 24 microarray slides representing 6 individuals from 4 treatment groups (Control, During, After and Recovery). One test cDNA labeled with Cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide. Reference design: 6x control fish, 6x group D fish, 6x group A fish, 6x group R fish.
2011-07-05 | E-GEOD-29610 | biostudies-arrayexpress
Project description:Analysis of gene expression changes of Mesorhizobium alhagi CCNWXJ12-2 under high salt stress. Mesorhizobium alhagi CCNWXJ12-2 is isolated from Alhagi sparsifolia in northwest of China.
2014-05-06 | GSE57306 | GEO
Project description: Not available
| S-EPMC4432818 | biostudies-literature
Project description:Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes.
2013-04-02 | GSE45693 | GEO
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
2010-05-15 | E-GEOD-17517 | biostudies-arrayexpress
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
2010-06-19 | E-GEOD-17532 | biostudies-arrayexpress