Although microorganisms are largely responsible for organic matter decomposition, earthworms may also affect the rates of decomposition directly by feeding on and digesting organic matter and microorganisms, or indirectly affect them through their interactions with the microorganisms, basically involving stimulation or depression of the microbial populations. We tested the general hypothesis that microbial populations, and especially fungi, are enhanced by earthworm activity, and also whether earthworms are able to modify the biodiversity of microbial populations, and its relation to the function of the system. In addition, we examined the metabolic quotient and the effect of labile organic C to assess the relationships between earthworm and microbes. We found that decomposition of pig manure has two stages characterized by the presence or absence of earthworms. Thus, the presence of earthworms was related with increases in overall microbial biomass and activity, which decreased when earthworms left the substrate; the same pattern was observed for fungi. Furthermore, earthworms modified the physiological profiles of microbial communities of pig manure, increasing the diversity of substrates utilized. In addition, earthworms promoted a more efficient use of energy of microbial communities, as the metabolic quotient showed. The rate of carbon loss was almost twice where earthworms were present, revealing faster decomposition. Our data match with the recent findings that to maintain essential processes the functional properties of present species are at least as important as the number of species per se. This is in accordance with the "insurance hypothesis," which states that a large number of species is probably essential for maintaining stable processes in changing environments, as the presence of earthworms would have promoted in pig manure.