According to guidelines for the approval of pesticides, side-effects on soi
l microorganisms should be determined by studying functional parameters suc
h as carbon or nitrogen mineralisation. However, the microbial diversity ma
y have been markedly changed following pesticide use despite unaltered meta
bolism, and such changes may affect soil fertility. This review evaluates n
ew methods for measuring pesticide effects on bacterial diversity, and disc
usses how sampling should take temporal and spatial heterogeneity into acco
unt. Future research on pesticide approval protocols should establish the r
elationships between mineralisation assays and new and rapid bacterial dive
rsity profiling methods, and should include the possible ecological implica
tions of altered bacterial diversity for soil fertility.