This book provides essential molecular techniques and protocols for analyzing microbes that are useful for developing novel bio-chemicals, such as medicines, biofuels, and plant protection substances. The topics and techniques covered include: microbial diversity and composition; microorganisms in the food industry; mass cultivation of sebacinales; host-microbe interaction; targeted gene disruption; function-based metagenomics to reveal the rhizosphere microbiome; mycotoxin biosynthetic pathways; legume-rhizobium symbioses; multidrug transporters of yeast; drug-resistant bacteria; the fungal endophyte piriformospora indica; medicinal plants; arbuscular mycorrhizal fungi; biosurfactants in microbial enhanced oil recovery; and biocontrol of the soybean cyst nematode with root endophytic fungi; as well as microbe-mediated drought tolerance in plants.