Water is a scarce and unevenly distributed national resource and it is, therefore, important to reduce water consumption in paper mills. Closure of water systems for reuse, however, directly and indirectly results in an increase in the numbers and types of microorganisms resulting in poor runnability, lower production rates and increased safety hazards. The aim of this study was to investigate the microbiology of paper-mill water systems in South Africa to aid in closure of water systems whilst controlling microbial fouling. Different environmental parameters monitored at paper mills were reviewed together with microbial enumeration techniques employed by industry and characterisation and identification methods to study bacteria. Various environmental and process parameters could play an important role in the number and type of microorganisms in a paper-mill water system. The highest correlation between an environmental parameter and biological activity was found for oxidation-reduction potential and the numbers of culturable aerobic bacteria. Other environmental parameters that significantly influenced microbial numbers were temperature, dissolved oxygen, dissolved solids, chemical oxygen demand, nitrogen, phosphorous, specific water consumption, pulp furnish, biocide class and retention time. The characterisation and identification of problematic bacteria in paper mills could enable better control since the correct biocides could be applied to minimise microbiologically associated problems. Prevalent bacteria that were isolated from the water systems of 14 paper machines were typed into 35 distinct groups using ERIC-PCR and PCR-RFLP and identified with sequence analysis. Eleven of the 35 types were identified to species level, 20 types were identified to genus level and the remaining four types were identified to family level. It was found that the majority of bacteria belonged to the genera Acinetobacter and Pseudomonas that contain well-known slime-forming bacterial species. Traditional methods employed to investigate bacteria in industrial water systems often do not accurately represent the composition and diversity of bacterial communities. DGGE analysis could provide a powerful tool for monitoring bacterial diversity, since it is able to discriminate between identical sizes of PCR-amplified DNA fragments that differ in their sequence content. The use of DGGE to monitor changes in microbial populations could improve control of microbial fouling, but more analyses would be needed to validate the results of the present study. / Dissertation (MSc (Microbiology))--University of Pretoria, 2008. / Microbiology and Plant Pathology / unrestricted