The invention provides methods of isolating and characterizing previously unknown microbial organisms by efficiently culturing and recovering microbes through the use of a gnotobiotic rhizobacterial isolation plant system (GRIPS). A GRIPS contains seedlings grown from surface-sterilized seeds using aseptic techniques. By inoculating GRIPS with microbes, the system supports the growth of unique microbes that form close relationships with a plant host. This approach facilitates recovery of beneficial microbes that would not be culturable with conventional methods.