Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.

Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated. Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.

Project description:Temperature is an important ecological condition, and sudden temperature changes in soil can induce stress in soil-dwelling invertebrates. Soil animals can move to more favorable habitats and/or adapt physiologically to a stressful environment. Hyperthermic conditions will impact gene expression as one of the first steps. We use a transcriptomics approach to identify the transcripts of which expression changed in response to heat stress in the springtail Folsomia candida using a 5,131 probe microarray. A temperature shift from 20Â°C to 30Â°C for 30 minutes significantly altered the expression of 142 genes, of which 116 were upregulated, and 26 downregulated. Many upregulated genes encoded heat shock proteins (Hsps) or enzymes involved in the synthesis of ATP, such as members of the electron transport chain. Furthermore, genes involved in oxidative stress and anion-transporting ATPases were upregulated. Downregulated were glycoside hydrolases, involved in catalysis of certain disaccharides, which indicate an accumulation of stress-protective disaccharides. The microarray results from this study, which were validated using quantitative RT PCR, reveal a mild response to heat shock in this soil invertebrate, relative to other organisms. This may be due to specific ecological factors during evolution of soil invertebrates, such as the relatively stable temperatures in the soil habitat. This study presents potential candidate genes for future functional studies concerning thermal stress in soil-dwelling invertebrates, like e.g., the investigation of the heat hardening process. Folsomia candida was first acclimated to LUFA 2.2 soil at 20 C for two days. Then animals were either exposed to 30 C for 30 minutes (heat shock treated), or were not heat shocked (reference). For each treatment 4 biological replicates were used, replicate samples consisted of total RNA extracted from ~30 animals exposed in the same jar to either reference or heat shock. Each unique heat shock treated sample was hybridized to a unique reference sample. In total in 4 hybridizations of 8 samples, was performed. The dyes were evenly distributed, which means that for each treatment two samples were labeled with cy3 and the other two with cy5.

Project description:Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity. However, metabolic acclimatization occurs over multiple levels of the biological hierarchy, from the enzyme and cellular level, through organ systems, to whole-organism metabolic rate. Previous studies have focused on one or a few biological hierarchy levels, leaving us without a general understanding of how metabolic acclimatization might differ between tropical and temperate species. Here, we investigate thermal acclimatization of 3 species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism, organ, mitochondria, metabolome and proteome. As predicted by the climate variability hypothesis, the 2 temperate species T. septentrionalis and T. wolteri had an enhanced acclimation response at the whole organism level compared to the tropical species T. sexlineatus, as measured by respiratory gas exchange rates. However, the mechanisms by which whole organism performance was modified was strikingly different in the 2 temperate species: widespread T. septentrionalis modified organ sizes, while the narrowly distributed T. wolteri relied on mitochondrial, proteomic and metabolomic regulation. We suggest that these 2 mechanisms of thermal acclimatization may represent general strategies used by ectotherms, with distinct ecological costs and benefits. Lacking either of these mechanisms of thermal acclimatization capacity, the tropical species is likely to have increased vulnerability to climate change.

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Soil metagenome

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