Analyzing Microorganisms in Environmental Samples Using Stable Isotope Probing with H218O

2009 ◽  
Vol 2009 (12) ◽  
pp. pdb.prot5341-pdb.prot5341 ◽  
Author(s):  
E. Schwartz
Keyword(s):  
Stable Isotope ◽  
Environmental Samples ◽  
Stable Isotope Probing

scholarly journals Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples

2016 ◽  
Vol 41 ◽  
pp. 14-18 ◽  
Author(s):  
Egbert Schwartz ◽  
Michaela Hayer ◽  
Bruce A Hungate ◽  
Benjamin J Koch ◽  
Theresa A McHugh ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Environmental Samples ◽  
Microbial Growth ◽  
Stable Isotope Probing

scholarly journals Acetate Repression of Methane Oxidation by Supplemental Methylocella silvestris in a Peat Soil Microcosm

2011 ◽  
Vol 77 (12) ◽  
pp. 4234-4236 ◽  
Author(s):  
M. Tanvir Rahman ◽  
Andrew Crombie ◽  
Hélène Moussard ◽  
Yin Chen ◽  
J. Colin Murrell
Keyword(s):  
Stable Isotope ◽  
Methane Oxidation ◽  
Environmental Samples ◽  
Peat Soil ◽  
Methane Monooxygenase ◽  
Laboratory Culture ◽  
Stable Isotope Probing ◽  
Soil Microcosm ◽  
Content Type

ABSTRACTMethylocellaspp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase ofMethylocella silvestrisin laboratory culture. DNA stable-isotope probing (DNA-SIP) using13C-methane and12C-acetate, carried out withMethylocella-spiked peat soil, showed that acetate also repressed methane oxidation byMethylocellain environmental samples.

RNA-Stable Isotope Probing v2

2021 ◽  
Author(s):  
Roey Angel ◽  
Eva Petrova ◽  
Ana Lara
Keyword(s):  
Stable Isotope ◽  
Nucleic Acids ◽  
Density Gradient ◽  
Environmental Sample ◽  
Environmental Samples ◽  
Enrichment Culture ◽  
Stable Isotope Probing ◽  
Recent Book ◽  
The Subject ◽  
Comprehensive Discussion

The following protocol describes how to perform an RNA-Stable Isotope Probing experiment. The scope of this protocol only covers the parts involving separating labelled RNA from unlabelled RNA using ultracentrifugation in a caesium trifluoroacetate density gradient and downstream quantification to evaluate whether the labelling and separation of the RNA were successful. Total RNA should be extracted from an environmental sample or an enrichment culture that was incubated with an isotopically-labelled substrate. Labelling can be of the carbon, oxygen or nitrogen in the RNA (or any combination of the 3). For environmental samples, we recommend extracting RNA using our protocol Total Nucleic Acids Extraction from Soil and purifying it using the Purification of RNA from Crude NA Extract protocol. This protocol is based on the following papers: Whiteley et al. (2007); Dumont et al. (2011); Angel and Conrad (2013). For a comprehensive discussion on how to design a SIP experiment and how to analyse the resulting data, we recommend referring to the recent book on the subject: Stable Isotope Probing: Methods and Protocols, especially chapters: 1-3 and 9-18.

RNA-Stable Isotope Probing v2

2021 ◽  
Author(s):  
Roey Angel ◽  
Eva Petrova ◽  
Ana Lara
Keyword(s):  
Stable Isotope ◽  
Nucleic Acids ◽  
Density Gradient ◽  
Environmental Sample ◽  
Environmental Samples ◽  
Enrichment Culture ◽  
Stable Isotope Probing ◽  
Recent Book ◽  
The Subject ◽  
Comprehensive Discussion

The following protocol describes how to perform an RNA-Stable Isotope Probing experiment. The scope of this protocol only covers the parts involving separating labelled RNA from unlabelled RNA using ultracentrifugation in a caesium trifluoroacetate density gradient and downstream quantification to evaluate whether the labelling and separation of the RNA were successful. Total RNA should be extracted from an environmental sample or an enrichment culture that was incubated with an isotopically-labelled substrate. Labelling can be of the carbon, oxygen or nitrogen in the RNA (or any combination of the 3). For environmental samples, we recommend extracting RNA using our protocol Total Nucleic Acids Extraction from Soil and purifying it using the Purification of RNA from Crude NA Extract protocol. This protocol is based on the following papers: Whiteley et al. (2007); Dumont et al. (2011); Angel and Conrad (2013). For a comprehensive discussion on how to design a SIP experiment and how to analyse the resulting data, we recommend referring to the recent book on the subject: Stable Isotope Probing: Methods and Protocols, especially chapters: 1-3 and 9-18.

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