Abstract

Culture-based methods are important in studying the microbial ecology of natural and man-made environments, but they are extremely biased in assessing microbial genetic diversity by selecting a particular population of microorganisms. With the recent advances in genomics and sequencing technologies, microbial community analyzes using culture-independent molecular techniques have ushered in a new era in microbial ecology. Molecular analyzes of environmental communities have shown that the cultivable fraction represents <1% of the total number of prokaryotic species in a given sample. Molecular approaches such as genetic fingerprinting, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics are critical to discovering and characterizing the enormous microbial diversity and understanding its interactions with biotic and abiotic environmental factors. This Review summarizes recent advances in molecular microbial ecology with an emphasis on novel techniques and approaches that provide new insights into the phylogenetic and functional diversity of microbial aggregates. The potential applications of the individual molecular techniques and their combination for a more comprehensive assessment of microbial diversity were illustrated using example studies.