Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan C.; Shah, Manesh; Chavarría, Krystle L.; Tom, Lauren M.; Brodie, Eoin L.; Hettich, Robert L.

doi:10.1021/pr100787q

Cited by 175 publications

(177 citation statements)

References 39 publications

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“…Cryosols at 5-cm depth from 1-week cores, with in situ water saturation conditions, were subsampled and kept frozen at − 20°C. Three grams of cryosol was mixed with sodium dodecyl sulfate-based lysis buffer, and the slurry were subjected to protein extraction and trypsin proteolysis described earlier (Chourey et al, 2010). Digested peptides were separated on an in-house packed SCX (Luna)-C18 (Aqua) column and analyzed by an LTQ-Orbitrap (Thermo Fisher Scientific, San Jose, CA, USA) coupled to an Ultimate 3000 HPLC system (Dionex, Thermo Fisher Scientific Inc., Waltham, MA, USA).…”

Section: Identification Of Pmmo In Metaproteomementioning

confidence: 99%

An active atmospheric methane sink in high Arctic mineral cryosols

et al. 2015

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Methane (CH 4 ) emission by carbon-rich cryosols at the high latitudes in Northern Hemisphere has been studied extensively. In contrast, data on the CH 4 emission potential of carbon-poor cryosols is limited, despite their spatial predominance. This work employs CH 4 flux measurements in the field and under laboratory conditions to show that the mineral cryosols at Axel Heiberg Island in the Canadian high Arctic consistently consume atmospheric CH 4 . Omics analyses present the first molecular evidence of active atmospheric CH 4 -oxidizing bacteria (atmMOB) in permafrost-affected cryosols, with the prevalent atmMOB genotype in our acidic mineral cryosols being closely related to Upland Soil Cluster α. The atmospheric (atm) CH 4 uptake at the study site increases with ground temperature between 0°C and 18°C. Consequently, the atm CH 4 sink strength is predicted to increase by a factor of 5-30 as the Arctic warms by 5-15°C over a century. We demonstrate that acidic mineral cryosols are a previously unrecognized potential of CH 4 sink that requires further investigation to determine its potential impact on larger scales. This study also calls attention to the poleward distribution of atmMOB, as well as to the potential influence of microbial atm CH 4 oxidation, in the context of regional CH 4 flux models and global warming.

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Section: Identification Of Pmmo In Metaproteomementioning

confidence: 99%

An active atmospheric methane sink in high Arctic mineral cryosols

et al. 2015

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“…Total RNA was extracted from ground tissue of young maize (B73) seedlings as described previously (Chourey et al, 2010). For cloning of ZmKSL4, ZmCYP71Z18, and ZmTPS11, 5 mg of total RNA was reverse transcribed using qScript cDNA SuperMix (Quanta Biosciences) followed by PCR amplification of the target genes with gene-specific oligonucleotides (Supplemental Table S1).…”

Section: Isolation and Cloning Of Cdnasmentioning

confidence: 99%

Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize

et al. 2018

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“…Proteins were extracted from the biofilms using an SDS protein extraction protocol based on previously reported methodology (Chourey et al, 2010). Biofilm from each sample was split into two, representing extraction replicates.…”

Section: Protein Extractionmentioning

confidence: 99%

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

et al. 2014

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Microbial communities that underpin global biogeochemical cycles will likely be influenced by elevated temperature associated with environmental change. Here, we test an approach to measure how elevated temperature impacts the physiology of individual microbial groups in a community context, using a model microbial-based ecosystem. The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 1C. Elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entire community. Proteins from related organisms differed in their relative abundance and functional responses to temperature. Elevated temperature repressed carbon fixation proteins from two Leptospirillum genotypes, whereas carbon fixation proteins were significantly upregulated at higher temperature by a third member of this genus. Leptospirillum group III bacteria may have been subject to viral stress at elevated temperature, which could lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, these findings highlight the utility of proteomics-enabled community-based physiology studies, and provide a methodological framework for possible extension to additional mixed culture and environmental sample analyses.

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Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

Cited by 175 publications

References 39 publications

An active atmospheric methane sink in high Arctic mineral cryosols

An active atmospheric methane sink in high Arctic mineral cryosols

Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

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