From the Air We Breathe to the Food We Eat: The Future of Self-Fertilizing Crops

By:  Lorenz B. Mapote | Kataegis 

Before the sun could even illuminate the field, our farmers  are already at work-- tending to crops that, more than ever, depend on something they cannot readily get: nitrogen. 

Modern agriculture runs on nitrogen fertilizers. Yet the vast majority of it does not come from organic sources, but from factories that synthesize  nitrogen compounds like urea - products whose prices have sharply risen with trends in global energy markets and the current crisis in the Middle East. In countries like the Philippines, which  imports around 90% of its fertilizer supplies, the cost and stability of these supplies are more than of economic concerns - it is a vulnerability in the system itself.

But a humble revolution is taking place in laboratories around the world. Scientists are now attempting to engineer crops that can partner with microbes to utilize nitrogen directly from the air we breathe - effectively fertilizing themselves reducing dependency on synthetic fertilizers.

In legumes such as Lotus japonicus, symbiotic relationship with nitrogen-fixing soil bacteria (rhizobia) is well-established.  This association is controlled by processes of signal exchanges between the legumes and the rhizobia. 

This process begins with the LysM receptor-like kinases, a group of membrane bound receptors on root cell surfaces that detect microbial signals in the soil. When rhizobia release signals known as Nod Factors, Nod Factor Receptor 1 (NFR1) and Nod Factor Receptor 5 (NFR 5) recognize these compounds and initiate signal pathways promoting symbiosis, allowing bacterial entry and formation of root nodules. These nodules are specialized, tumor-like organs on the root of legumes, housing the nitrogen-fixing bacteria inside.

In contrast, related LysM receptors including CERK-family kinases, primarily detect chitin-like molecules, activating immune responses against microbial invasions. In non-legumes, however, these receptors are predominantly specialized in immunity rather than symbiosis.

A recent study revealed how subtle the distinction between defense and cooperation can be. Researchers identified a conserved amino acid sequence within the intracellular kinase domains of these receptors called SD1 or Symbiosis Determinant 1 and C-terminal region of NFR1. Within these critical regions are two amino acid residues that act as a switch, determining whether the receptor activates immune signaling to reject the microbes or symbiotic signaling to accommodate them.

By introducing two amino acid substitutions, T304M (Threonine to Methionine) and D306A (Aspartic acid to Alanine) into an immune receptor CERK6 researchers were able to partially reprogram receptors to accept rhizobia. In L. japonicus, the resulting mutation enabled the immune receptors to induce early symbiotic responses. This includes formation of infection threads in roots, and initiation of nodule organogenesis, where the cells in the root cortex divide rapidly to form a nodule.

When researchers tried to apply the equivalent amino acid substitutions in the barley immune receptor RLK4, resembling the NFR1 sequence from L. japonicus, the outcome is not enhanced symbiosis but a partial reprogramming of immune signaling. When expressed in L. japonicus, the resulting responses include formation of early-infection-like structures, and  limited activation of symbiosis pathways. Without the mutation, the barley receptor perceives these factors as a potential threat.

While the study did not produce a fully nitrogen-fixing non-legume plant, it revealed that engineering certain protein receptors may allow us to control symbiotic and immune mechanisms of a plant. This discovery highlights that minimal alterations are significant towards engineering beneficial symbiotic traits. Rather than engineering an entirely new biological system, we might just be editing what’s already there.

The implications of receptor editing extend far beyond the laboratory. The dependence on synthetically produced nitrogen comes at a great environmental cost. Research in 2022 estimates that their production and usage constitutes 2.1% of the global greenhouse gas emissions and  2% of worldwide fossil fuel usage, making them a significant contributor to climate change. 

If such strategies in plant engineering were to be applied to major crops, the impact could be revolutionary. Produce may be controlled to exhibit beneficial traits which may reduce reliance on unsustainable fertilizers, while improving yield and developing resilience to environmental stress.