Assay of lipid and cell wall components can readily provide differentiation in reciprocal mixtures of bacteria and fungal monocultures. To test natural microbial assemblies, small plastic sheets were exposed in a subtropical estuary. The sheets were then transferred to a laboratory where estuarine environments that inhibit prokaryotic growth and stimulated fungal growth were compared with and environment where eukaryotic growth was inhibited and prokaryotic growth was stimulated. The morphology determined by scanning electron microscopy showed typical mycelial networks where eukaryotic growth was stimulated and none were inhibited. The stimulation of eukaryotic growth produced a greater biomass measured in terms of lipid phosphate, respiratory activity or extractable adenosine nucleotides, but with a slower synthesis of phospholipids and DNA and a smaller concentration of muramaic acid (a unique prokaryote wall component). The stimulation of eukaryotic growth increased the rate of sulpholipid synthesis relative to DNA or phospholipid synthesis.