Advancement and further standardization of contemporary municipal wastewater and sludge treatment facilities is underway in order to increase their efficiency and promote environmentally safe sustainable practices. Practically, a dual stage aerobic/anaerobic–anaerobic system has always been a more viable approach in tackling wastewater of domestic origin. Typically, the amount and the quality of sludge generation and the effective temperature management keeping in view the cost-effectiveness and environmental health during treatment of domestic wastewater and sludge are vital. A more comprehensive approach to deal with wastewater and its sludge along with production of biogas and Class A biosolids is desired. Therefore, the study is aimed at improving the efficiency of the dual digestion system (sequential aerobic/anaerobic-anaerobic) for wastewater and sludge, producing Class A biosolids coupled with energy (biogas) generation under optimum environmental conditions. Besides, a detailed investigation of culture and molecular based bacterial diversity and density was also carried to highlight the involvement of specific bacteria. In the 1st phase, laboratory scale sequential aerobic and anaerobic system was developed for the treatment of domestic wastewater under the influence of low to slightly high temperature regime (5, 25 and 45°C) and different aerobic retention times (1-3 days). Overall, the treatment efficiency varied from 92-100 % in terms of biochemical oxygen demand (BOD), Chemical oxygen demand (COD), turbidity and nitrite nitrogen (NO2-N) removal in total retention time of 14 days (2 days aerobic and 12 days anaerobic digestion). Increase in aerobic retention time from 1-3 days improved the treatment efficiency by 5-20 %. However, a slight increase though non- significant in COD (94 - 97.1%) and BOD (95.1 - 96.7%) reduction was observed under treatment from 25 to 45°C of temperature. Whereas, nearly 60% decrease in treatment efficiency was observed in terms of BOD and COD removal when temperature reduced from 45-5°C. The low temperature (5°C) treatment efficiency of the whole system was recovered to maximum within 6-8 days when reactor was bioaugmented with activated sludge. A significant decrease (98-99%) in pathogenic bacteria (HPC/mL) (Escherichia coli, Salmonella typhimurium, Shigella dysenteriae, and Pseudomonas aeruginosa) was observed in the remaining biomass (sludge) after treatment. Likewise, the MPN index of fecal coliforms and E. coli in the sludge also showed considerable reduction. Further changes in pollution indicators such as pH and nitrites (2.86–0.01± 0.05 mg/L), nitrates (0.98–0.02 ± 0.05 mg/L), phosphates (0.847–0.50 ± 0.05 mg/L) and sulphates (0.721-0.28 ± 0.03 mg/L) indicated involvement of the other key bacterial species in digestion of wastewater. In the 2nd phase, beneficial nitrifying bacteria were isolated and identified as Nitrososmonas sp. and Nitrobacter sp. from the raw wastewater and activated sludge (feed/influent). Besides, their specific activities were also determined based on different substrates utilization rates. Further beneficial nitrifying, sulphur oxidizing and phosphate accumulating bacteria were successfully screened in the biomass from aerobic phase of sequential aerobic-anaerobic treatment facility at 25°C. In the stable operating conditions, over 98% removal rate for total nitrogen was observed with and without activated sludge seeding. Moreover, COD removal rate reached up to 93%, indicating both organic matter and ammonia removal. Autotrophic bacteria viz. ammonia, nitrite and sulphur oxidizers and phosphate accumulating bacteria were isolated through culture enrichment techniques demonstrated about 49-72% of NH3-N, 60-94% of nitrite, 18-30% sulphur and 25-59% phosphorus removal was observed in activated sludge biomass. These results were also confirmed and correlated with the activities of different hydrolytic enzyme such as Hydroxylamine oxidase, nitrite oxidase, sulphur oxidase and alkaline phosphatase in the activated sludge. In the 3rd phase, the influence of thermal pretreatment (55°C for 2 days) on the mesophilic anaerobic digestion (35 ± 2°C) of secondary and primary-secondary combination of sludge was studied. Besides, the treatment efficiency was also investigated for biogas yield, sludge stabilization and pathogen reduction at 12 and 20 days of solid retention times respectively. The thermal pretreatment (55°C for 2 days) subsequently with mesophilic anaerobic digestion at 35±2°C of secondary and primary/secondary sludge combinations improved the removal of VS by 35-38%, TCOD by 38-43% and SCOD by 37-47% with an overall yield of biogas by 31-34% (0.162-0.174NL/gVSreducecd), methane (0.082- 0.103NL/gVSreduced). However, treatment of secondary sludge showed a slight increase in COD solubilization (1-4%), organic matter reduction (10-11%) and specific biogas yield of 10-20% compared to primary-secondary sludge combinations. Moreover, this sequential mode of treatment helped removal of pathogenic bacteria by 7.6 - 8.1 log10 units thereby meeting the U.S. standard for Class A biosolids. The last phase of the study evaluated the comparative performance of dual stage 45°C thermophilic-mesophilic temperature phased anaerobic digestion system and 55°C thermophilic- mesophilic TPAD system with respect to sludge hydrolysis and methane production under the same operational conditions (6.5% of Total Solid content and 12.5 days total Solid Retention Time). The overall performance of TPAD-I system achieved 77% reduction in volatile solids i.e. only 5% higher than TPAD-II system. There were observed no ammonia inhibition and excessive level of volatile fatty acids accumulation and consequently the two phase digesters were able to yield significantly higher rate of methane production ((45°C, 3.55±0.47 L CH4/L.day; 35°C, 1.44 ± 0.12 L CH4/L.day) than TPAD-II. TPAD-II system suffered from certain degree of instability such as high VFAs accumulation (6087 ± 1578 mg/L), low buffering capacity and increased level of total NH3 (2982 ± 219mg/L) and free NH3 (226 ± 25 mg/L), reduced level of methane production (1.69 ± 0.1 L/L.d) was seen rather than being stopped. The bacterial and archaeal population were investigated using high through-put 454 pyrosequencing and Illumina sequencing respectively. In both TPAD systems, the associated bacterial population was dominated by Firmicutes (45.5-60.9%), Bacteriodetes (20-26.5%), Proteobacteria (8.6- 36%), Synergistetes (2.1-10.6%) and Actiniobacteria (1.9-7.2%), while archaeal community was dominated by Methanomicrobia (Genus Methanosarcina: 74-84%) and Methanobacteria (Genus Methanobacterium: 15-27%). In particular, there was observed a progression from genus Clostridium to Coprothermobacter and Tepidanaerobacter, and Methanocarcina to Methanothermobacter and Methanobacterium in 55°C TPAD. Variation in the composition of microbial populations in the first thermophilic stage at 55°C was attributed to the temperature, that of second mesophilic stage associated bacterial communities was related to the influent coming from first thermophilic stage. This study determined the key bacterial species that were involved with enhanced performance of TPAD systems at different temperature regimes. The overall results proved that dual digestion system has a great potential to be up-scaled at large scale for handling wastewater and sludge for small communities in developing countries even at low temperature conditions. It will not only support to mend the public health in terms of removal of unwanted organic/in-organic compounds and pathogens from wastewater and sludge producing Class A biosolids for large scale safe application in croplands