The extreme conditions within extreme environmental niche present within full scale autothermal thermophilic aerobic digester(ATAD) system characterised by the selective pressure of high temperature, alkaline environment coupled to the presence ofrecalcitrant or slowly metabolisable substrates and, low oxygen solubility and availability.Niche is unique, and of high interest for biotechnology and engineering industries as a for its ability to select a phylogeneticallystable community physiologically adapted to the conditions, suitable for that operational design and do sustain an excellentbiodegradation functions at extreme conditions. Also, sustainability of an advanced biological wastewater treatment processesATAD system is dependent on the long-term stability of the ecosystem and the activity of the microbial consortia within it, which in turn is highly dependent on the ATAD design and operation.We have addressed crucial issues in optimisation of the analysis and have highlighted particularly the errors and limitations thatcan be associated with the novel and complex environmental niches ecosystems monitoring and analysis at elevated temperatures using the ATAD model. This may be of particular use for ecologists, microbiologists and molecular biologists who operate in multidisciplinary areas however unaware of all the issues associated with utility of such methodology. The study and methodology applied offer a significant advancement to the prior body of knowledge and tools regarding ATAD microbialconsortia.For the first time to date, we have evaluated the efficiency of molecular techniques such as genera-specific PCR and PCR-DGGEto monitor biodiversity indexes within the ATAD ecosystem and examined microbial dynamics in response to elevatedtemperatures response to elevated temperatures and high pH during processing. We have demonstrated that diversity recovery is afeature of the optimisation of the molecular approaches used and is essential for optimum species identification in extremeenvironments. The community associated with ATAD thermophilic stage (23hrs) were analysed via rDNA-PCR, clone libraryconstruction, phylogenetic analysis and systematic ccomparative analysis to all organism identified to date within other worldwideATAD systems. The list of organisms and techniques indentified and collected will be of great help for further exploitation,recovery of organisms, and their utilisation for ATAD bioaugmentation and ATAD performance. The particular findings in regardto cellulose degraders, metal reducing anaerobes, capnophiles (entrapment and utilization of CO2 produced during digestion) andsymbiotic organisms within tested ATAD systems is extremely innovative and will undoubtedly trigger new research in thebiotechnological and engineering in academia and industry.