There is a wealth of unexplored knowledge about microbe's ecosystem functioning impacts on food security, climate change mitigation and sustainable agriculture with focus on cassava cultivation in the tropics using biofertilizer.The rhizosphere modified by biofertilizer as agronomic management during cassava cultivation by the inoculants for microbiome engineering for integrated soil fertility management by the release of plant root exudates and microbial metabolites.Microbiome and the cassava crop are highly dependent on each other as the microbiome contributes a significant portion of the secondary genome of the host plant like quorum quenching strategies that suppress the virulence of pathogens, enhance high yielding cultivars and favorable environments for development.Rhizosphere engineering using biofertilizer can reduce and improves chemical dependant agriculture for resilience agriculture.Cassava genetic engineering integrated with biofertilizer can transforms the use of cassava cultivar for polluted soils phytoremediation and bio-energy crop cultivation in the tropics as re-generative agriculture technique for xenobiotic pollution management.The economic impacts will be development of remediation-to-biofuel economy of restorated polluted soils by conversion of the bioenergy crop cultivated into bioethanol.Cassava cultivation with biofertilizer accentuate regenerative agriculture as an integral potential for food security and sustainable development goals (SDG).