The microbial populations of aquaculture prawn ponds waters and sediments wereinvestigated using a range of microbiological and microscopical techniques.There were twice as many microorganisms in the sediment in the inner parts of theaquaculture ponds (15.5 x 109 microorganisms/g sediment dry weight) than there werein the outer parts (8.1 x 109 microorganisms/g sediment dry weight) when acridineorange staining of microorganisms followed by manual cell counting was carried out.This result is most likely to be due to smaller particles (e.g. microorganisms) beingcarried to the centre of the ponds by the water currents produced by aerators as heavierparticles would be deposited in the outer pond regions. Also, the larger number ofmicroorganisms in the inner regions is likely to be influenced by the amount of feed(organic carbon and nitrogen) placed in the ponds. Visualisation of cells byfluorescence in situ hybridisation was attempted, however, the strong autofluorescenceexhibited by sediment samples and cells in the samples prevented probe detection.A new microbial genomic DNA extraction method was devised because whenpreviously published protocols were employed, either no DNA was extracted or thatextracted was unable to be used as a template in PCR. The new method allows theextraction of high molecular weight genomic DNA from sediment samples as small as0.25 g. It primarily relies upon the addition of herring sperm DNA to bind to clayparticles in the sediment samples and extended incubations with high concentrations oflysozyme and proteinase K. PCR of the 16S rDNA was successful from the extractedDNA using the new protocol.The bacterial composition of the water column of a pond from a subtropical locationwas investigated using PCR amplification of the bacterial community 16S rDNA forclone library analysis. The clone library was analysed by clone insert and phylogeneticanalysis. A total of 55 clones were analysed. The closest relatives of the dominantclone types were heterotrophic bacteria, from which it was concluded that heterotrophswere the dominant type of bacteria in the water column.A total of 85.7% of recovered clones were from the Gammaproteobacteria phylum(majority from Pseudoalteromonas), 12.5% of clones from the Alphaproteobacteriaphylum, and 1.8% from the Bacteroidetes phylum. No clones in this pond water hadknown nitrifiers as their closest relatives.The bacterial diversity in three pond sediments was investigated by the clone librarytechnique. Few clones were highly similar to any previously published sequence. Thecommunity composition for all clone libraries was determined to be very complex withrepresentatives from the Actinobacteria, Bacteroidetes, Chloroflexi, candidate divisionOS-K, Planctomycetales and relatives, and Proteobacteria being common to alllibraries. Nitrifiers were absent while sulfate reducers were present in substantialnumbers in all clone libraries. Some clones represent novel phylum-level lineageseither by themselves or within known or candidate divisions.The numbers of Deltaproteobacteria detected in the 16S rDNA sediment clone librarieswas substantial and the detection of sulfate reducing bacteria (SRB) in one pond wasachieved through the use of PCR amplification and cloning of the genes coding fordissimilatory sulfite reductase (dsrAB; DSR). PCR amplification yielded two bands,however, cloning the 1.9 kb band determined it to be DSR. New primers facilitatingsequencing the full length of the DSR clones were designed. This clone library revealedtwo distinct groups of SRB designated A and B. The group A DSR clones correlatedwith the deltaproteobacterial 16S rDNA sequences from the Desulfobulbaceae in thesame pond. The group B DSR clones were determined to be from a novel group ofSRB related to cloned DSR genes from the Guaymas Basin after analysis of the genedata.The biogeochemical roles of the microorganisms detected in the three sediment 16SrDNA clone libraries were extrapolated from the sequence data. The possibleinvolvement in the cycles of carbon, nitrogen, and sulfur were hypothesised. Thepotential roles in the carbon cycle are photosynthesis, fermentation and oxidation ofcarbohydrates and fatty acid oxidation. In the nitrogen cycle, ammonium assimilation,deamination, and nitrogen fixation are possible activities occurring in prawn ponds. Inthe sulfur cycle, dissimilatory sulfate reduction, assimilatory sulfate reduction, sulfideoxidation, and liberation of sulfide from organic sulfur compounds are most likely to beoccurring.