High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

ABSTRACT Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format ” and “closed-format ” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complemen-tary high-throughput molecular technologies to address important ecological questions. Microorganisms inhabit almost every imaginable environ-ment in the biosphere, play integral and unique roles in ecosystems, and are involved in the biogeochemical cycling of essential elements, such as carbon, oxygen, nitrogen, sulfur, phos-phorus, and variousmetals. Their structure, function, interaction, and dynamics are critical to our existence, yet their detection, identification, characterization, and quantification pose severa