Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Biogas production from waste materials has emerged as a promising avenue for sustainable energy generation, offering a dual benefit of waste management and renewable energy production. The selection and preparation of waste feedstocks, including agricultural residues, food waste, animal manure, and municipal solid wastes, are important for this process, while the microbial communities are majorly responsible for bioconversions. This review explores the role of complex microbial communities and their functions responsible for the anaerobic digestion of wastes. It covers the crucial physiological processes including hydrolysis, acidogenesis, acetogenesis, and methanogenesis, elucidating the microbial activities and metabolic pathways involved in the prospects of improving the efficiency of biogas production. This article further discusses the influence of recent progress in molecular techniques, including genomics, metagenomics, meta-transcriptomics, and stable isotope probing. These advancements have greatly improved our understanding of microbial communities and their capabilities of biogas production from waste materials. The integration of these techniques with process monitoring and control strategies has been elaborated to offer possibilities for optimizing biogas production and ensuring process stability. Microbial additives, co-digestion of diverse feedstocks, and process optimization through microbial community engineering have been discussed as effective approaches to enhance the efficiency of biogas production. This review also outlines the emerging trends and future prospects in microbial-based biogas production, including the utilization of synthetic biology tools for engineering novel microbial strains and consortia, harnessing microbiomes from extreme environments, and integrating biogas production with other biotechnological processes. While there are several reviews regarding the technical aspects of biogas production, this article stands out by offering up-to-date insights and recommendations for leveraging the potential of microbial communities, and their physiological roles for efficient biogas production. These insights emphasize the pivotal role of microbes in enhancing biogas production, ultimately contributing to the advancement of a sustainable and carbon-neutral future.