I am happy to contribute a bit to this massive effort by my friend Yang Bai from Peking University.
Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns: Cell https://www.cell.com/cell/fulltext/S0092-8674%2825%2900198-9
Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns: Cell https://www.cell.com/cell/fulltext/S0092-8674%2825%2900198-9
Comments
Although taxonomy varies a lot between crops and soils the bacterial gene functions are quite stable between crops and soils!
https://www.nature.com/articles/nature11234/figures/2