Developments in Biobased Fertilizers for Achieving Low CI Score Crops

By: Joel Stone,  President,  Climate Systems Solutions

An October 24 article in MIT Technology Review, Why agriculture is a tough climate problem to solve, inspired me to take a deeper dive into the use of fertilizers to reduce Scope 1 emissions in Agriculture.

This article offers a briefing on the impact that developments in synthetic biology can have toward solutions in agriculture to result in low CI Score crops and significantly impact our atmospheric carbon through smart agriculture practices. Synthetic fertilizers contribute significantly to Scope 1 emissions in agriculture. Scope 1 emissions are direct emissions from sources that are controlled or owned by an organization, which, in agriculture, includes emissions directly from farmland and associated agricultural activities.

Here’s how synthetic fertilizers contribute to Scope 1 emissions:

1. Nitrous Oxide Emissions from Soil: Synthetic nitrogen fertilizers, when applied to soil, can stimulate the production of nitrous oxide (N₂O), a potent greenhouse gas with a global warming potential nearly 300 times that of carbon dioxide. This occurs through microbial processes like nitrification and denitrification, where nitrogen compounds are converted into nitrous oxide. These emissions happen directly on the farm, making them Scope 1 emissions.
2. Application Processes: Fertilizer application processes, such as spreading or injecting fertilizers, often involve fuel-powered machinery, which also produces CO₂ emissions directly on-site. This also falls under Scope 1 emissions as it’s a direct emission from agricultural activities.
3. Fertilizer Breakdown and Chemical Reactions: When fertilizers are applied to fields, chemical breakdown processes release various greenhouse gases directly from the soil. For example, urea-based fertilizers release ammonia, which can indirectly lead to nitrous oxide emissions when it’s redeposited in nearby soils and water bodies.
4. Residue Management and Fertilizer Application on Pasture Land: When synthetic fertilizers are used on pasture land for livestock feed, the decomposition of grass or crop residue that has absorbed synthetic fertilizers can contribute to further emissions, either through nitrogenous gas emissions directly from the soil or via animal excretion, which adds more nitrogen to the soil.

By contributing directly to emissions on the farm, synthetic fertilizers are an important factor in Scope 1 emissions in agriculture. Reducing reliance on synthetic nitrogen fertilizers, through practices like synthetic biology-driven biological solutions, can directly mitigate these emissions.

Synthetic biology offers promising solutions to reduce synthetic fertilizer use by engineering microorganisms to enhance plant nutrient uptake, fix atmospheric nitrogen, and improve soil health. Here are some key approaches:

1. Engineering Nitrogen-Fixing Microorganisms: Plants primarily rely on nitrogen for growth, typically sourced from synthetic fertilizers. Synthetic biology can engineer soil microbes (e.g., Rhizobium or Azotobacter) to more efficiently fix atmospheric nitrogen into forms plants can absorb. Bioengineering enables these microbes to be more resilient in diverse soil types, potentially helping reduce the need for nitrogen-based fertilizers.
2. Phosphorus-Solubilizing Microbes: Phosphorus is another essential nutrient for plants, often locked in soil minerals and unavailable to plants. By engineering soil microbes to secrete enzymes that release this bound phosphorus, plants can gain access to more of it naturally. This approach can reduce the need for synthetic phosphorus fertilizers and improve soil nutrient cycling.
3. Microbial Consortia for Plant Health and Growth: Instead of single microorganisms, synthetic biology can design microbial consortia that synergistically promote plant growth. This consortium could contain engineered strains that help with nitrogen fixation, phosphorus solubilization, and even the production of growth-promoting compounds, creating a more resilient and nutrient-rich soil microbiome.
4. Bioengineering Crops for Symbiotic Relationships: Another approach is to modify crops themselves to better host nitrogen-fixing bacteria. For example, engineering crops to develop root nodules (typically seen in legumes) can allow them to naturally acquire nitrogen from symbiotic bacteria. This can reduce fertilizer use, particularly in major grain crops like wheat or corn, which do not typically host nitrogen-fixing bacteria.
5. Biostimulants and Metabolite Production: Synthetic biology can help produce biostimulants or specific metabolites that boost plant nutrient uptake or improve resistance to environmental stresses. Engineered microbes can be applied as biostimulants, enhancing nutrient uptake efficiency in plants without the need for synthetic fertilizers.
6. Soil Carbon Sequestration and Microbial Engineering: By enhancing soil microbial populations to better sequester carbon, synthetic biology can improve soil structure and nutrient content over time. Healthier soils with higher carbon levels often require fewer fertilizers, as they can retain nutrients more effectively and promote sustained plant growth.
7. Developing Phytomicrobiome Manipulation Techniques: Leveraging synthetic biology to customize plant microbiomes (the community of microbes associated with plants) can make plants more resilient, efficient, and nutrient-hungry, reducing fertilizer needs over time.

Together, these approaches harness synthetic biology’s precision to create environmentally-friendly, sustainable alternatives to synthetic fertilizers, ultimately helping agriculture move toward regenerative practices that benefit soil health and reduce greenhouse gas emissions.

One of the largest single emitters of CO2 that contributes to the CO2 footprint is the the production of synthetic fertilizers from natural gas. To reduce nitrogen-based synthetic fertilizer use, synthetic biology can be used to optimize natural processes that supply nitrogen to plants, particularly by enhancing biological nitrogen fixation. Here are some promising approaches:

1. Engineering Nitrogen-Fixing Microbes for Non-Leguminous Crops: Naturally, nitrogen-fixing bacteria like Rhizobium form symbiotic relationships with legumes (e.g., soybeans) but not with most staple crops like wheat or corn. Synthetic biology can modify nitrogen-fixing microbes, enabling them to associate with the roots of non-leguminous crops or enhancing their nitrogen-fixing efficiency, providing plants with a more consistent nitrogen supply.
2. Transferring Nitrogen-Fixation Genes into Non-Symbiotic Bacteria: Certain bacteria, like Azotobacter and Gluconacetobacter, live freely in the soil and produce nitrogen on their own. Synthetic biology can insert nitrogen-fixation genes into these microbes to boost their nitrogen-fixing capabilities, creating biofertilizers that work in different soil types and agricultural systems.
3. Bioengineering Crops to Host Nitrogen-Fixing Bacteria: Through genetic engineering, we can modify crops themselves to form root nodules that naturally host nitrogen-fixing bacteria. While legumes naturally have these nodules, efforts are underway to modify cereals to develop them as well, potentially allowing crops like rice or maize to rely less on synthetic nitrogen fertilizers.
4. Optimizing Bacterial Efficiency for Nitrogen Fixation: Nitrogenase, the enzyme responsible for nitrogen fixation, is energy-intensive and sensitive to oxygen. Synthetic biology can help optimize this process by altering bacterial metabolic pathways to make nitrogen fixation more efficient under various environmental conditions. By improving the bacterial capacity to thrive in different soil pH, moisture levels, and temperatures, engineered bacteria can provide plants with nitrogen more reliably.
5. Developing Synthetic Nitrogen-Fixing Consortia: Microbial consortia involve multiple engineered microorganisms working together to maximize nitrogen fixation while supporting each other's growth. By designing consortia where different microbes specialize in nitrogen fixation, nutrient uptake, or supporting soil health, plants can benefit from a more sustainable nutrient supply with a reduced need for synthetic fertilizers.
6. Gene Editing for Nitrogen Efficiency in Plants: Some plants naturally use nitrogen more efficiently than others. Synthetic biology tools like CRISPR can edit crops’ genomes to enhance nitrogen uptake, reduce nitrogen loss, and increase nitrogen-use efficiency. Engineering crops to use nitrogen more efficiently can minimize the amount of nitrogen they require, further reducing the need for nitrogen-based fertilizers.
7. Enhancing Microbial Colonization in Soil: Engineered microbes can be designed with properties that enhance their survival, colonization, and proliferation in different soil environments. By ensuring they survive and thrive longer, plants have a more reliable supply of nitrogen over the growing season.

These synthetic biology approaches aim to harness natural nitrogen-fixing processes or engineer plants and microbes to better access and utilize nitrogen. This approach not only cuts down on nitrogen-based fertilizer needs but also reduces nitrogen pollution, helping agriculture become more sustainable and environmentally friendly.

A number of companies are leveraging synthetic biology and biotechnology to develop biological solutions aimed at reducing nitrogen-based synthetic fertilizers. Here are some notable ones:

1. Pivot Bio develops nitrogen-fixing microbial products that can be applied directly to crops. Their microbial product lines, like Pivot Bio PROVEN, target major crops like corn, wheat, and rice, supplying nitrogen to plants throughout the growing season and reducing the need for synthetic fertilizers.
2. Gingko Bioworks, in partnership with companies like Bayer, focuses on engineering microorganisms that can improve nutrient availability, including nitrogen fixation, for plants. They work on synthetic biology innovations to create microbes that help crops access nitrogen more sustainably.
3. Corteva Agriscience offers various biological products for nutrient management, including nitrogen-fixing and nitrogen-utilizing microbes. The company has collaborated with startups to enhance biological solutions that reduce nitrogen-based fertilizer needs.
4. Kula Bio has developed a biological nitrogen fertilizer alternative that uses nitrogen-fixing bacteria to help plants access nitrogen in the soil. Their products aim to provide stable, on-demand nitrogen to crops, reducing the dependency on synthetic fertilizers.
5. Azotic Technologies produces a microbial product called Envita, which contains a nitrogen-fixing bacteria that colonizes plants' roots and leaves. This enables crops to access atmospheric nitrogen directly, offering a sustainable alternative to synthetic nitrogen fertilizers.
6. AgBiome uses microbial discovery and synthetic biology to create microbial products that improve soil health and plant nutrition. Although primarily focused on pest and disease control, they are exploring microbes that enhance nutrient uptake, potentially reducing the need for synthetic fertilizers.
7. Symborg specializes in biotechnology products that enhance plant nutrient uptake and growth. Their MycoUp product, for instance, includes beneficial mycorrhizal fungi that help plants access nitrogen and other nutrients more effectively.
8. Bayer (through its partnership with Joyn Bio) has partnered with Ginkgo Bioworks to form Joyn Bio, a company focused on engineering microbes that provide sustainable nitrogen to crops, reducing reliance on synthetic nitrogen fertilizers.
9. Indigo Ag provides microbial seed treatments that promote plant growth and improve nutrient availability. Their microbial products focus on improving nitrogen fixation, water use, and soil health to help farmers reduce synthetic fertilizer use.
10. Concentric Ag offers biological products that improve soil health and nutrient efficiency. They produce biofertilizers and microbial solutions that help crops access more nitrogen naturally.

These companies are at the forefront of synthetic biology and microbial engineering to reduce dependence on nitrogen-based fertilizers. Their products aim to provide nitrogen more sustainably, improving soil health and promoting a shift toward environmentally friendly farming practices.

About

Climate Systems Solutions (CSS)'s purpose and mission is focused on the complex climate impacts affecting local economies and the requisite solutions available to mitigate and adapt to changing conditions. Understanding and deploying regenerative practices effectively sequesters carbon back into the soil. This practice of Soil Carbon Capture Sequestration (#SCCS) at the same time produces low carbon intensity materials (Low CI Score) for food and industrial uses, while also improving water management and reducing fertilizer inputs. We work with stakeholders within businesses and communities to take ownership of the change process, providing access to the network of innovators hard at work bringing real solutions into practice. Our goal is to educate organizations about adapting a whole systems approach that will unite business operations to adopt climate solutions at every point in the supply chain. This education includes working with business leaders from across industries to support market-based solutions for climate restoration.