title: 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 complementary high-throughput molecular technologies to address important ecological questions.
authors: jzhou@ou.edu.
authors: Jizhong
authors: J
authors: Zhou
authors: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA.
authors: Zhili
authors: Z
authors: He
authors: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
authors: Yunfeng
authors: Y
authors: Yang
authors: Ye
authors: Y
authors: Deng
authors: Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors: Susannah G
authors: SG
authors: Tringe
authors: Lisa
authors: L
authors: Alvarez-Cohen
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D017753:Ecosystem; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D012988:Soil Microbiology
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