The invention relates to methods for the screening, identification and/or application of microorganisms of use in imparting beneficial properties to plants. In one embodiment, the method involves a) subjecting plants to a growth medium in the presence of a first set of microorganisms； b) selecting one or more plants following step a) on the basis of one or more phenotypic traits； c) acquiring a second set of microorganisms associated with one or more plants selected in step b)； d) subjecting the first set of microorganisms prior to step a) and/or the second set of microorganisms acquired in step c) to a targeted or random genetic modification； and e) repeating steps a) to d) one or more times, wherein the second set of microorganisms are used in step a) of any successive repeat. In a second embodiment, the method involves a) subjecting one or more plants to a growth medium in the presence of a first set of one or more microorganisms； b) applying one or more selective pressures during step a)； c) selecting one or more plants following step b) on the basis of one or more phenotypic traits； and d) acquiring a second set of one or more microorganisms associated with one or more plants selected in step c)； and wherein the first set of one or more microorganisms has been subjected to a targeted or random genetic modification prior to step a) and/or the second set of one or more microorganisms acquired in step d) are subjected to a targeted or random genetic modification
