Environmental Sample Collection and Processing

Environmental matrices are diverse and typically heterogeneous, and therefore different strategies are employed to obtain representative environmental samples that allow for subsequent microbial characterization in terms of types, abundance and activities. For soils that are extremely heterogeneous, different sampling strategies and methods are described for sampling both surface soils and subsurface vadose zones. Information is also provided on optimum methods of storage and subsequent processing of samples depending on whether cultural or molecular (nucleic acid-based) analyses are to be conducted, and whether the target microbes are bacteria, fungi or viruses. Similar methodologies are described for sampling municipal wastes, sediment and water, with particular emphasis on human pathogens including viruses and protozoan parasites. Finally, information is presented on sampling air for microbial characterization, and the detection of microorganisms on fomites.