Hypophosphite is used to inhibit syntrophic methanogenesis or growth of hydrogenotrophic methanogens, plants are genetically engineered to comprise and express a heterologous hypophosphite/2-oxoglutarate dioxygenase htxa gene to enable the use of the reduced phosphorus, such as hypophosphite as a phosphorus source, and hypophosphite and phosphite fertilizer amendments are utilized as phosphorus sources by soil microorganisms, to increase carbon storage in deep sediments.