When presented with ferrous ions and tetrathionate in growth media, individual archaeal species, Acidianus brierleyi, Metallosphaera hakonensis and Sulfolobus metallicus, exhibited different patterns of substrate utilisation and cell growth. Total cell numbers for A. brierleyi were about 60% of those for M. hakonensis and S. metallicus after complete substrate utilisation, and specific growth rates were affected by substrate concentration and cell growth history. High iron(II) concentrations inhibited S. metallicus growth. In relation to mixed microbial communities in high-temperature bioleaching reactors, the results are consistent with the hypothesis that specific growth rates of different species grown on different substrates strongly influence community structure. The combination of T-RFLP with substrate analysis and cell counts is a valuable analytical tool for the discrimination and semi-quantitative estimation of species in mixed cultures that can be used to gain better understanding of community structures and population dynamics in complex bioleaching systems. (C) 2012 Elsevier Ltd. All rights reserved.