Soil pretreatment boosts protein recovery for microbial community studies

Oct 23, 2013
Soil pretreatment boosts protein recovery for microbial community studies

Scientists have significantly boosted the recovery and identification of proteins expressed by soil-dwelling microbes over what was previously possible, thanks to a new method of soil pretreatment being used at EMSL in Richland, Wash. The new strategy for processing samples reveals additional insight into the function of microbial communities in their native environments.

Studying the proteins expressed by -dwelling microbial communities helps to define their fundamental biogeochemical roles in carbon cycling, nitrogen cycling, phosphorus cycling, and climate regulation.  It also helps to determine how microbial communities might assist with environmental cleanup—for example, bacterial expression could be used to remediate sites contaminated with toxic metals or radionuclides.

Metaproteomics studies, or the characterization of all proteins in a cellular community, are imperative for understanding the function of that live in soil—but it is sticky business.  Methods for protein recovery and identification that rely on simply lysing microbes in place results in the proteins binding irretrievably to the soil, and attempts to separate bacteria from soil prior to lysis are incomplete at best.  To address this issue, PNNL staff tested a variety of methods and found that recovery and identification of proteins is significantly enhanced if, before lysis, soil samples are treated with both a cocktail of polar positive amino acids, which bind to soil and block protein binding sites, and desorption buffer, which enhances the release of proteins from the soil/solution mixture.  This method proved effective in a model system consisting of E. coli and uncontaminated soil samples from Rifle, Colorado; a variety of having different sand and silt compositions; and an indigenous soil sample contaminated with diesel oil from King George, Antarctica. The method does not interfere with mass spectrometry analyses, and in the model system, the research team showed that the polar positive amino acid/desorption buffer pretreatment improved protein identification by nearly an order of magnitude compared to using no pretreatment at all. 

Explore further: The failing freezer: How soil microbes affect global climate

More information: Nicora, C. et al. 2013. Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies, Proteomics. DOI: 10.1002/pmic.201300003

add to favorites email to friend print save as pdf

Related Stories

Fingerprinting fugitive dust

Jul 21, 2011

Each community of soil microbes has a unique fingerprint that can potentially be used to track soil back to its source, right down to whether it came from dust from a rural road or from a farm field, according to a U.S. Department ...

ORNL researchers improve soil carbon cycling models

Aug 16, 2012

A new carbon cycling model developed at the U.S. Department of Energy's (DOE) Oak Ridge National Laboratory better accounts for the carbon dioxide-releasing activity of microbes in the ground, improving scientists' understanding ...

Recommended for you

Shell files new plan to drill in Arctic

Aug 29, 2014

Royal Dutch Shell has submitted a new plan for drilling in the Arctic offshore Alaska, more than one year after halting its program following several embarrassing mishaps.

Reducing water scarcity possible by 2050

Aug 29, 2014

Water scarcity is not a problem just for the developing world. In California, legislators are currently proposing a $7.5 billion emergency water plan to their voters; and U.S. federal officials last year ...

User comments : 0