Sampling is a critical stage of any research study.  Your analysis and results can only be as good as your sample. There are few in situ methods for sampling microbial population that do not require further analysis in lab to produce data.  Standard assessment methods involve taking soil cores from field sites and assessing microbial communities through biological markers (such as lipids) or rates of processes (such as enzymatic activity). A single soil core (or several closely spaced samples) may be used for analyses. The specificity of the biomarker methods vary greatly as some biomarkers can give very specific information (such as DNA analysis), while others methods give more general information (such as phospholipid fatty acids – PLFA analysis). These biomarker identification methods can then be correlated with measurements of microbial activity obtained on the same soil sample.