Soil protein extractions - comparative evaluation of pooling strategy for metaproteome analysis

Wien

2014

S. 18

Artikel aus einer ZeitschriftUnselbständiges Werk

200190105

Soil metaproteomic studies present a major challenge since the soil matrix is spatially and temporally heterogeneous. The objective of the present study was the evaluation of pooling strategy by taking independent and spatially separated soil samples to obtain a consistent sample that encompasses variability. The application of pooling for protein extraction aimed to reduce time and costs of soil metaproteome analysis. A pooling experiment was conducted to evaluate the applicability and suitability for the analysis of the soil metaproteome in field plots of a mature beech stand. To this end, we pooled five individual soil samples (2 g each) to form a composite of 10 g sample before the protein extraction procedure was conducted. This was compared with the results obtained from the five individual samples (5 g each), replicated twice. Individual replicate soil samples from small plots on the larger plot scale were analyzed and put together into one pooled sample prior to protein extraction. Proteins were analyzed by 1D PAGE followed by liquid chromatography/tandem mass spectrometry (LC-MS/MS), and peptides were assigned to protein groups for each sample. We found that most abundant microbial taxa and functions were present in the pooled sample: (a) In the pooled sample individual species or functions were well representative compared to separate individual samples. (b) The functional categorization of proteins within the pooled sample was similar to the individual samples. Our study demonstrated that pooling strategy for soil protein extraction protocol resulted in similar results to those of analyses of individual soil samples. Generally it will be necessary to test soils from each site or experiment individually if pooling is not suitable. We conclude that, the application of pooling for extraction purpoes should be considered for metaproteomics from field studies that do not focus on within-site variability.