Algae farming in shallow open ponds requires little technology, with low capital and operating expenditures. In relatively uncontrolled ponds there is a high likelihood that microbial contamination will affect algal yield. We are interested in understanding natural contamination as an ecological process to better control the trajectory of microbial community assembly. Nannochloropsis salina was grown in small open ponds (100L). Extracted metagenomic DNA was subjected to PCR for amplification of 16S and 18S rRNA genes with the products examined by denaturing gradient gel electrophoresis (DGGE) and excised bands were sequenced. DGGE fingerprints can provide a measure of relatedness between communities that will indicate whether the assembly process is mainly stochastic or deterministic.