Endophytic microorganisms depend on the nutrient supplied by host plants, so parameters affect plant nutrient supplies will consequently influent endophytic communities. Thus physical factors, such as temperature, rainfall, edaphic factors and UV radiation will affect endophytic communities indirectly. Those factors will influence the microorganisms from rhizophere and phylloplane in a similar way.
In addition, soil physical and chemical factors also have an indirect effect on the endophytic communities. The factors, including pH, salinity and soil texture can alter the saprophytic bacteria in rhizosphere, resulting in preselecting the endophytic bacterial source.