Dataset Information

Soil Metaproteomics LC-MS

ABSTRACT: Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of microbial populations (metaproteomics), yet not their genomic abundance (16S rRNA gene amplicon sequencing), supporting the hypothesis that metabolic activity may be more closely linked to climate than community composition.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Nico Jehmlich

LAB HEAD: Nico Jehmlich

PROVIDER: PXD009773 | Pride | 2022-03-01

REPOSITORIES: Pride

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Publications

Climate shapes the protein abundance of dominant soil bacteria.

Bastida Felipe F Crowther Tom W TW Prieto Iván I Routh Devin D García Carlos C Jehmlich Nico N

The Science of the total environment 20180528

Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of Actinobacteria, Planctomycetes and Proteobacteria, supporting the hypothesis that metabolic activity of some dominant phyla may be closely linked to climate. These results may improve our capacity to construct microbial models that better predict the ...[more]

PMID: 29852443

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Project description:Soils are a huge reservoir of organic C, and the efflux of CO2 from soils is one of the largest fluxes in the global C cycle. Out of all natural environments, soils probably contain the greatest microbial biomass and diversity, which classifies them as one of the most challenging habitats for microbiologists (Mocali and Benedetti, 2010). Until today, it is not well understood how soil microorganisms will respond to a warmer climate. Warming may give competitive advantage to species adapted to higher temperatures (Rinnan et al., 2009). The mechanisms behind temperature adaptations of soil microbes could be shifts within the microbial community. How microbial communities will ultimately respond to climate change, however, is still a matter of speculation. As a post-genomic approach in nature, metaproteomics allows the simultaneous examination of various protein functions and responses, and therefore is perfectly suited to investigate the complex interplay between respiration dynamics, microbial community architecture, and ecosystem functioning in a changing environment (Bastida et al., 2012). Thereby we will gain new insights into responses to climate change from a microbial perspective. Our study site was located at 910 m a.s.l. in the North Tyrolean Limestone Alps, near Achenkirch, Austria The 130 year-old mountain forests consist of Norway spruce (Picea abies) with inter-spread of European beech (Fagus sylvatica) and silver fir (Abies alba). Three experimental plots with 2 × 2 m warmed- and control- subplots were installed in 2004. The temperature difference between control and warmed plots was set to 4 °C at 5 cm soil depth. Soil was warmed during snow-free seasons. In order to extract proteins from forest soil samples, the SDS–phenol method was adopted as previously described by Keiblinger et al. (2012). Protein extractions were performed from each subplot soil samples. The abundance of protein-assigned microbial phylogenetic and functional groups, were calculated based on the normalized spectral abundance factor (NSAF, Zybailov et al., 2006).

Project description:Genome-wide transcriptional profiling of Arabidopsis thaliana to a combination of heatwave and drought under ambient and elevated CO2. Goal of this study was elucidate the transcriptional responses to a combination of heat wave and drought, and to see how these responses are modifed under future climate (high) CO2. Climate changes increasingly threaten plant growth and productivity. Such changes are complex and involve multiple environmental factors, including rising CO2 levels and climate extreme events. As the molecular and physiological mechanisms underlying plant responses to realistic future climate extreme conditions are still poorly understood, a multiple organizational level-analysis (i.e. eco-physiological, biochemical and transcriptional) was performed, using Arabidopsis exposed to incremental heat wave and water deficit under elevated CO2.The climate extreme resulted in biomass reduction, photosynthesis inhibition, and considerable increases in stress parameters. Photosynthesis was a major target as demonstrated at the physiological and transcriptional levels. In contrast, the climate extreme treatment induced a protective effect on oxidative membrane damage, most likely as a result of strongly increased lipophilic antioxidants and membrane-protecting enzymes. Elevated CO2 significantly mitigated the negative impact of a combined heat and drought, as apparent in biomass reduction, photosynthesis inhibition, chlorophyll fluorescence decline, H2O2 production and protein oxidation. Analysis of enzymatic and molecular antioxidants revealed that the stress-mitigating CO2 effect operates through up-regulation of antioxidant defense metabolism, as well as by reduced photorespiration resulting in lowered oxidative pressure. Therefore, exposure to future climate extreme episodes will negatively impact plant growth and production, but elevated CO2 is likely to mitigate this effect. Transcriptome analysis was performed by Agilent Arabidopsis (V4) 4x44K platform which represented all known genes in the Arabidopsisgenome. Experiments were performed using a modified loop design (Knapen et al., 2009). This design consisted of total 8 arrays; sample from each treatment was labelled once and has 4 biological replicates, two of which were labelled in red and two in green

Dataset Information

Soil Metaproteomics LC-MS

Publications

Climate shapes the protein abundance of dominant soil bacteria.

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