“The role of the infinitely small in nature is infinitely great” opined Louis Pasteur. Indeed, since microbes have inhabited earth, they have played crucial roles in ecosystems. They have been sine qua non to natural biological cycles and systems including the carbon, nitrogen and sulfur cycles. In addition, they have been at the centre of engineered bioprocesses such as biological wastewater treatment and fermentation. However, understanding and dissecting the complex microbial community structure, composition, spatial distribution and dynamics in ecosystems are highly challenging considering the salient limitations of traditional or conventional culture-dependent techniques. Although with the emergence of molecular methods such as Terminal Restriction Fragment Length Polymorphism (TRFLP), Automated rRNA Intergenic Spacer Analysis (ARISA), Random Amplified Polymorphic DNA (RAPD), Denaturing Gradient Gel Electrophoresis, Single Strand Conformation Polymorphism (SSCP), microautoradiography (MAR) and Fluorescent in situ Hybridization (FISH) among others, enormous strides have been leaped towards the understanding of alpha, beta and gamma microbial diversity, still limitations persist in terms of gaining adequate coverage, and application to field-scale environments and ecosystems. Many molecular methods provide incomplete analysis as they do not capture the entire complexities of microbial communities. In order to unravel the unparalleled taxonomic diversity of microbial communities in ecological niches, high sample throughput and coverage of phylotypes at high as well as at low abundance are highly desirable.