The present invention relates to the process of constructing plant-site specific functional microbiomes to screen, identify plant and soil microbes with beneficial traits, and to apply the functional microbiome, microbe or microbial consortia for improving the growth and health of plants cultivated on normal, stressed or marginal lands and for improving soil health, the removal and/or stabilisation of organic and inorganic pollutants, and the enhancement of soil microbial ecosystem functions.