Plant–microbe interactions are central to sustainable agriculture.

Nitrogen metabolites play essential roles in plant-growth promotion.

Pyridoxal-5′-phosphate-dependent enzymes mediate a variety of nitrogen metabolism.

Engineering microbes is a promising way for the indirect control of plant metabolism.

Microbiome engineering helps control plant growth and stress response systematically.

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5′-phosphate-dependent enzymes, which have pivotal roles in microbe–microbe and plant–microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

© 2022 The Authors. Published by Elsevier Ltd.