Bacterial and protozoan populations were monitored in orchard soil amended with Brassica napus seed meal. Numbers of fluorescent pseudomonads peaked one week following incorporation of the amendment and declined thereafter, whereas populations of Streptomyces spp. increased to stable levels nearly 20-fold higher than in non-treated soil. The amoeba-flagellate Naegleria americana, isolated from the amended soil, showed a marked feeding preference in culture for fluorescent pseudomonads relative to Streptomyces spp. Amended soils showed rapid declines in RSM-derived cis-oleic acid that paralleled increases in the numbers of bacteria and proportion of bacterial fatty acid markers in the soil. Arachidonic acid, which reached peak levels one week after seed meal incorporation, was found in Pythium spp. and Mortierella spp. but not in the two most abundant protozoa isolated from soil. These data indicate that arachidonic acid is not a suitable marker for protozoan quantification.