Listed here are a number of references relevant to the problem of sampling design in microbial ecology. Additional suggestions welcome!
“Pseudoreplication and the Design of Ecological Field Experiments” (Hurlbert 1984)
“A primer of Ecological Statistics” (2004, book available for purchase)
“Experimental Design for the Life Sciences” (2003, book available for purchase)
“Design and Analysis of Ecological Experiments” (1989, book available for purchase)
Primer-E (A statistical software package that also offers regular workshops)
“Basic Survey Design” website produced by the National Statistical Service (Australia)