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Molecular techniques have revolutionized microbial ecology and constant advances in next-generation sequencing have dramatically improved our ability to explore both dominant and rare members of microbial communities at ever-greater depths. Until recently, shotgun metagenomics of complex communities was largely restricted to gene-centric analyses that highlighted important functional distinctions between communities, but not between individual populations within those communities. Current gigabase and even terabase scale projects are overcoming the obstacles to genome assembly from complex metagenome data and enabling new levels of functional exploration. I will review the sequencing technologies in use for metagenomics and describe their application to complex communities including soils and sediments.<p><p>Keywords: