Many studies have shown that the rhizosphere soil comprises several plant growth-promoting microbes. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion, is important for improving soil fertility and crop productivity. Microbial communities are found across diverse environments. As many microbes are culturable in the lab, there is a gap in study on their diversity, especially in the sequencing of DNA from within the constituent community. The construction and screening of metagenomic expression libraries have great potential to identify novel genes and their functions. In this chapter, we describe briefly metagenomic library preparation from rhizosphere bacterial DNA, screening of libraries for growth-promoting genes, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.