Anaerobic technology has been applied for the treatment of solid wastes and wastewater since the 1880s. This chapter reviews the most recent advance in molecular microbial characterization techniques, i.e., metagenomics, as well as its applications in anaerobic technology, from the exploration of the intriguing science of anaerobes to industrial engineering applications. With the rapidly decreasing cost of high-throughput sequencing technologies and timely updating of state-of-the-art bioinformatics analysis tools, metagenomics has revolutionized the study of microbiology and demonstrated the great potential of the development of novel microbial resources (e.g., industrial biomolecules and enzymes and biodegradation genes), as it discloses unprecedented genetic information of uncultivated microorganisms at an amazingly fast rate. This chapter gives a detailed introduction to the technical procedures of metagenomics, from preliminary molecular experiments to high-throughput sequencing, as well as its application in environmental anaerobic technology.

Anaerobic technology has been applied to sludge digestion for over 50 years and to wastewater treatment for nearly 30 years. This chapter reviews the nucleic acids-based molecular methods for the analysis of microbial communities, and their applications for the microbial communities in anaerobic reactors. At first, nucleic acid extraction and selection of nucleic acid biomarkers are discussed with emphasis on special aspects related to anaerobic sludge samples. Second, the common nucleic acids-based methods are introduced, including cloning and sequencing for characterization, quantitative real-time polymerase chain (qRT-PCR) for quantification, fluorescence in situ hybridization (FISH) for visualization, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) for screening/typing/monitoring, and stable isotope probing (SIP) and microautoradiography-FISH to link the microbial identity with the specific functions. Finally, applications of the aforementioned molecular methods in anaerobic technology are summarized, focusing on identification of new species in the anaerobic process, characterization of microbial compositions in the anaerobic reactors, visualization of layered structure of anaerobic granular sludge, etc.