Lower greenhouse gas emissions from food production.

Engineering Biology for Climate & Sustainability

Lower greenhouse gas emissions from food production.

Current State-of-the-Art

Current food production and agricultural practices contribute significantly to global greenhouse gas (GHG) emissions. From 2000 to 2014, CO₂ emissions from food production increased from 1 to 1.28 gigatonnes amongst 14 of the world’s top 20 agricultural producers.¹ This production of GHGs includes nitrous oxide from synthetic fertilizer usage and agricultural production,²^, ³ and methane produced by livestock as part of their natural digestion process.⁴^, ⁵

The Haber–Bosch process for manufacturing fertilizers is a cornerstone of industrial agriculture. However, the Haber process is energy intensive and generates large amounts of N₂O, a potent and long-lived GHG with 300 times the warming potential of CO₂.⁶ Engineering biology is developing alternatives to decrease or eliminate the need for industrial fertilizers and chemical supplements. The rhizosphere, the soil zone where plant roots influence biological and chemical features of the soil, supports natural symbiosis with bacteria that help the plant with nitrogen fixation. This ability could be extended to more crops (i.e., non-legume plants) by engineering enhanced nitrogen fixation capabilities to crop plants and engineering bacteria associated with crops as fertilizers.⁷^, ⁸ Research is also underway to engineer microbial-plant interactions that enable lower use of phosphorus fertilization.⁹^, ¹⁰^, ¹¹ Some of this is already practiced commercially by companies such as Pivot Bio, though most technologies are still at an early stage of development. These new biobased fertilizers can help reduce the need for water, enable the use of currently non-arable land for plant growth, and prevent ecological disruption caused by run-off of water-soluble nitrates and the eutrophication of marine environments.

Advances in genetic engineering (e.g., CRISPR) and precision agriculture will lead to more efficient crop production that generates fewer greenhouse gases. Genetically engineered crops have been grown successfully since 1996 with important impacts on carbon emissions.¹² As an example of where engineering biology tools and technologies can impact the emissions from crop production, we can look at a world-wide staple crop: rice. Rice cultivation usually includes a period of time where fields are intentionally flooded, creating an environment where methanogens thrive. Methane from rice production accounts for approximately 11% of annual anthropogenic methane emission.¹³ Rice engineered to maintain high yields with minimal flood time, or an engineered microbiome that suppresses methanogen activity during flooding, could lower total methane emissions (see Kumar et al., 2014¹⁴; Scholz et al., 2020¹⁵). As a specific example, a recent Science publication details the overexpression of a transcriptional regulator in rice, induced by light and low-nitrogen, resulting in increased photosynthesis and nitrogen utilization and higher yield.¹⁶ In addition to this example, the engineering of plant-incorporated protectants (PIPs) into more crop varieties could reduce emissions by decreasing the total production, transportation, and application of pesticides. Emissions caused by Conventional Tillage techniques can be reduced by engineering crops that enable transitions to Reduced Tillage or No Tillage,¹⁷ for example by engineering enhanced crop allelochemical production (see Mahé et al., 2022¹⁸). Crops that do not typically benefit from symbioses with nitrogen-fixing microbes could be engineered to do so. Plant biosensors could communicate phosphorus or nitrogen needs to enable their precise use, reducing overuse and runoff. Expanding the approaches, engineering goals, targeted crop species and varieties, accessibility, and general education about crop engineering will increase the ability to reduce emissions.

Food production from livestock is the largest anthropogenic source in the global methane budget, mostly from enteric fermentation of domestic ruminants.¹⁹ Engineering biology could reduce methane in agriculture by producing more climate friendly diets for livestock. To prevent methane emissions, methanotrophs could be introduced through feed or inoculation to stably colonize the ruminant gut microbiome. Colonized microbes could be engineered to secrete small molecule inhibitors (see Duin et al., 2016²⁰ and Patra et al., 2017²¹, for examples) in ruminant guts to reduce methane formation or metabolize methane into non-gaseous compounds to enhance animal health (e.g., acetate, succinate, butyrate, amino acids, methanol).²² Engineering biology could also be used to pretreat animal feed and increase animal feed efficiency. For example, engineered microbes could synthesize animal nutrients (e.g., essential amino acids, micronutrients, vitamins) not naturally found in unprocessed feed or maintain specific moisture content in hay, haylage, or silage to increase feed production efficiency.

Further development and expansion of the “cellular agriculture” sector, including current cultured/cultivated meat and algae food products, to produce a broader variety of meat alternatives would reduce climate change by providing substitutes for animal and crop use (agricultural footprint), and support resilience in the wake of the effects of climate change. Meat and protein alternatives enabled by engineering microbial, fungal, or plant production of proteins, fats, and flavorings offer another means to continue feeding a growing global population.²³ These technologies can also help to reduce the consumption of resources, including land, water, fertilizers, and pesticides. For instance, the milk protein market relies on animals and plants as a source for dairy and dairy alternatives (e.g., oat and nut milks); a recent modeling study concluded that microbes could be cultured to scalably produce Bovine Alpha Lactalbumin, one of the most prevalent whey proteins in the market and used for human infant formula among other products.²⁴ Engineering biology to improve the taste, texture, and nutritional value of protein alternatives and lowering the cost of ingredients (e.g., flavorings, fatty acids, enzymes) will make these products more attractive and accessible to the global population. These proteins may ultimately be produced from CO₂ or methane using photo- and chemoautotrophic organisms, similar to previously demonstrated production of single cell protein (SCP) from methane.²⁵^, ²⁶

Finally, the conversion or recycling of food and agricultural wastes into value-added products will help to circularize the sector, reducing greenhouse gas emissions, not just from the wastes themselves (e.g., emissions from rotting foods), but also waste management practices.²⁷ Engineered enzymatic pathways can be used to transform waste biomass into feedstocks, such as nutrients for biofertilizers or biomass for biofuels.²⁸^, ²⁹ To do so sustainably means ensuring that these systems can be implemented where wastes are generated and where the value-added products can be used or consumed locally.

Breakthrough Capabilities & Milestones

Enable sustainable, climate-friendly biobased fertilizers.

Expand the toolbox for engineering rhizosphere microbes and communities (including isolation of tractable microbes, genetic parts).

Bottleneck/Challenge: Lack of effective, scaleable screening strategies for genetic parts from diverse organisms.

Potential Solution: Apply cell-free lysate system for high-throughput automated prototyping of regulatory and other genetic elements.

Bottleneck/Challenge: Competition between existing soil rhizobia communities and inoculants decreases the viability of the inoculant rhizobium in the soil and access to host tissue.

Potential Solution: Identify native soil and rhizobia microbes (like Azorhizobium caulinodans and Rhizobium sp.) that can be genetically engineered.

Develop bacteriophage-based tools for detecting and engineering rhizosphere microbes in situ to avoid the need to culture these in a lab.*

Bottleneck/Challenge: Phage engineering, currently mostly focused on killing microbes, needs to be technically adapted to engineer microbes to have new functions.³⁰

Potential Solution: Development of systems using temperate phages and other integrative and conjugative elements (e.g., Brophy et al., 2018³¹).

Bottleneck/Challenge: There is the potential for many different microbes and pathways to be used, but it is not clear where the best solutions are.

Potential Solution: Leverage current -omics data to identify effective targets for engineering (e.g., Mendes et al., 2011³²).

Improve understanding of gene expression dynamics in different bacterial growth phases under relevant soil conditions.

Engineer genes and enzymes that facilitate symbiotic relationships between plants and soil microbes to promote nutrient fixation and reduce runoff.

Bottleneck/Challenge: Lack of tools to non-disruptively study microbial behavior in complex, opaque environments like soils.

Potential Solution: Utilize interconnected fungal highways to study bacterial behavior via fluorescence expression.³³

Assess the fidelity and longevity of biobased fertilizers and fertilizer components and formulations under field conditions.

Test biocontainment strategies for engineered microbes in rhizospheres.

Engineer soil enzymes for nitrogen fixation, phosphorus assimilation, and other nutrients for improved activity.

Discover and engineer catabolic pathways for plant-specific root exudate compounds to control the persistence of microbiome members and to prevent their spread into off-target plant rhizospheres.

Engineer nitrogen-intensive crops to form symbiotic relationships with nitrogen-fixing microbes.

Establish obligate plant-microbiome ecosystems that provide containment of engineered microbes.

*Zurier, H. S., Duong, M. M., Goddard, J. M., & Nugen, S. R. (2020). Engineering Biorthogonal Phage-Based Nanobots for Ultrasensitive, In Situ Bacteria Detection. ACS Applied Bio Materials, 3(9), 5824–5831. https://doi.org/10.1021/acsabm.0c00546

Engineer agricultural crops that are less emission-intensive.

Engineer additional crop varieties with plant-incorporated protectants to decrease pesticide inputs.

Engineer additional common rice varieties with drought tolerance to reduce submergence time in irrigated rice paddies.

Engineer rice field microbiomes to minimize methane production by at least 50%.

Bottleneck/Challenge: Maintenance of engineered microbiome composition and balance over growing season or seasons.

Potential Solution: Engineer spatio-temporal control mechanisms for stimulating growth of desired microbiome community members.

Bottleneck/Challenge: Ensuring that engineered microbiome does not negatively impact crop yield or soil health over time.

Potential Solution: Longitudinal study of rice paddy mesocosm to investigate crop yield over seasons.

Engineer tunable and directed symbiosis between nutrient fixing bacteria (e.g., rhizobia) and non-legume plants (including engineering desired persistence time in the environment).

Bottleneck/Challenge: Symbioses are complex relationships with many genetic determinants in each organism.

Potential Solution: The diversity of existing nitrogen fixation symbioses provides many “blueprints” for engineering.³⁴

Potential Solution: Potential Solution: Comparative genomics and iterations of the DBTL cycle may enable identification of minimal genes needed for symbiosis.^(ibid)

Bottleneck/Challenge: Symbioses can involve trade-offs that may decrease crop yield.

Potential Solution: Engineer symbiosis to be active only when nitrogen availability is low and may already impact plant yield.

Engineer weed-suppressing allelopathic crops that decrease the need for tillage and herbicide application by at least 50%.

Bottleneck/Challenge: Engineering allelopathy with broad enough specificity to impact the variety of weeds found in fields across different regions.

Potential Solution: Engineer crops with the capability to inducibly synthesize weed-specific allelochemicals in response to weed presence.

Bottleneck/Challenge: Maintenance of suppression despite selective pressure for weeds to become insensitive to allelochemicals.

Potential Solution: Engineer crops with multiple allelochemicals and/or use in conjunction with other weed suppression approaches (e.g., engineered microbiomes).

Develop crops with phosphorus and nitrogen biosensing and reporting capabilities to enable targeted and precise application of supplements/fertilizers.

Engineer commodity crops that require less emissions-intensive field preparation and inputs each year, such as perennial varieties of annual crops.

Bottleneck/Challenge: The genetic determinants of annual vs. perennial growth are complex and not well-understood across crop species.

Potential Solution: Develop more robust genetic tools across commodity crops for understanding and engineering growth determinants.

Bottleneck/Challenge: Crops deplete soil nutrient composition.

Potential Solution: Engineer crops for seasonal rotations that maintain profits for farmers and preserve soil nutrient stability (e.g., improve our plant strain toolboxes so that crops can be mixed and matched based on demand but maintain or improve healthy soils).

Reduce methane production through livestock and manure management.

Engineer ruminant gut methanotrophs.

Bottleneck/Challenge: Colonization of methane-consuming methanotrophs in the ruminant gut microbiome.

Potential Solution: Develop fast-growing thermophilic anaerobic methanotroph organisms that can stably colonize the rumen.

Potential Solution: Engineer methanotrophs to synthesize beneficial metabolites and compounds not naturally found in unprocessed feed to support the ruminant gut microbiome.

Bottleneck/Challenge: Databases and other knowledge necessary to develop next-gen animal health probiotics.

Potential Solution: Collaborations between animal scientists and synthetic biologists to better characterize and understand the ruminant gut microbiome and impacts of feed.

Engineer ruminant gut microbiome to produce less hydrogen, to reduce methane production by methanogens.

Bottleneck/Challenge: Limited knowledge of physiology and metabolism of anaerobic and uncultured microbes in the rumen.

Potential Solution: Use new single-cell genomics, metabolomics, and physiology techniques alongside microbiome engineering and computational modeling to gain insight as to rumen microbiome dynamics.

Bottleneck/Challenge: Lack of genetic tools in keystone rumen microbes.

Potential Solution: Develop new culturing techniques and new methods of introducing DNA or mutations into non-model anaerobic microbes.

Bottleneck/Challenge: Expense of rumen studies, such as fistulated cattle and anaerobic culturing infrastructure, can be prohibitively expensive.

Potential Solution: Develop microscale rumen microcosm models to mimic rumen environment and enable experimental testing of hypotheses relating to microbiome interactions and rumen metabolism.

Implement manure management strategies using existing anaerobic digestion technology to capture methane.

Bottleneck/Challenge: Current range cattle manure management practices are not compatible with harvesting manure for anaerobic digestion.

Potential Solution: Study manure management strategies and their lifecycle impacts to understand the contributions of manure to rangeland soil quality and productivity versus methane emissions.

Potential Solution: Improve and incentivise anaerobic digestion and biogas recapture using engineered microbial consortia during cattle finishing.

Enable engineered methanotrophs to colonize the ruminant gut via feed or inoculation.

Bottleneck/Challenge: Introduction of novel microbes is likely to disrupt ruminant metabolism.

Potential Solution: Develop bacteriophage-based genetic engineering of ruminant gut microbes in situ (see Voorhees et al., 2020³⁵).

Develop enzymatic or microbial bioprocesses for manure management to produce biogas, bio-oil, biochar and recapture essential elements for fertilizer.

Develop forage crops for ruminant grazing that would result in lower methane production.

Enable sustainable production of alternative meats and proteins.

Enable precision fermentation for commercial-scale production of microbe-derived milk proteins.

Predict and model functional and sensory performance of plant-derived proteins.

Bottleneck/Challenge: Plant proteins currently exhibit high batch-to-batch variability and suppliers offer limited characterization data.

Potential Solution: Create industry-wide standards for analytical assays for characterizing plant protein ingredients to improve reproducibility.

Potential Solution: Refine and expand access to plant ingredient characterization techniques with established significance for predicting functional and sensory performance.

Potential Solution: Develop an open-access protein sequence, structure, and functionality database.

Potential Solution: Develop machine learning approaches to accelerate the designing process (protein sequence to texture and taste).

Improve chemoautotroph protein expression tools.

Bottleneck/Challenge: Chemoautotrophs are used for single cell protein production, but expression of specific target proteins often requires advanced expression and secretion tools only developed in traditional host organisms.

Potential Solution: Improve and adapt systems for extreme protein overexpression and secretion systems for a range of chemoautotrophic organisms to allow target protein production from CO2 or methane.

Potential Solution: Demonstrate production of alternative products (e.g., milk proteins) in chemoautotrophs and tailor protein content of chemotrophs.

Engineer microbes or plants with lipid-biosynthesis pathways that produce fats identical to animal-derived.

Engineer lower-cost and scalable growth media, specifically growth factors, for alternative meat production.*

Bottleneck/Challenge: Growth factors are currently too expensive to allow extensive alternative meat production at scale.

Potential Solution: Engineer yeast or other cost-effective hosts to produce growth factors and other small molecules useful in cell culture media.

Bottleneck/Challenge: Lack of clarity on best potential sources of low-cost feedstock, leading to uncertainty for rural producers about associated opportunities and challenges.³⁶^, ³⁷

Potential Solution: Partnerships with rural producers and other partners to test traditional crops and alternative forms of biomass; surveys to study how new production systems used to grow on these inputs would affect rural landscapes and feedstock costs.

Develop sustainable biological (vs. chemical or mechanical) processing methods for protein enrichment and extraction from crops.

Bottleneck/Challenge: Limited digestibility of protein from crops without extensive pre-treatment.

Potential Solution: Design novel proteins that incorporate important amino acids that can be expressed in seed or improve protein solubility.

Potential Solution: Edit plant protein sequences to increase digestibility through changes to structure and amino acid content or reduce expression of anti-nutritive factors.

Engineer crops for higher protein yields and functionality to decrease reliance on downstream processing steps.

Bottleneck/Challenge: Plant structure, lignin content, and anti-nutritive factors impede protein yield and bioavailability.

Potential Solution: Modulate seed-specific pathway genes to enhance protein accumulation in seed without impacting germination.

Potential Solution: Edit plant protein sequences to increase digestibility through changes to structure and amino acid content or reduce expression of anti-nutritive factors.

Engineer complete nutrition crops, optimized for downstream processing into specialized meat and protein foods.

* See for example https://multus.media/

Enable engineered biology to convert food and agricultural waste to value-added products.

Engineer efficient microbes, consortia, or cell-free systems for biogas and biofuel production from food and agriculture lignocellulose waste.

Bottleneck/Challenge: Food and agriculture wastes typically require pre-treatment to increase solubility and conversion.

Potential Solution: Engineer biosystems with increased expression of cellulase and hemicellulase that can work in concert with downstream anaerobic digestion.³⁸

Engineer inexpensive, multi-enzyme immobilized pathways for at-scale production of biodiesel from spent cooking oil and animal fats.

Engineer microbes or microbial consortia to produce commodity and high-value chemicals from biogas released from anaerobic digestion.

Bottleneck/Challenge: Biogas utilization organisms are usually slow growing, difficult to culture, or require mutualistic partners to work together as a consortia;³⁹ engineering these systems usually takes more effort compared to model bacteria.

Potential Solution: Engineer unique metabolic traits of biogas-utilizing organisms to well-known microbes to enable faster development and optimization (for example, see Yu et al., 2022⁴⁰).

Potential Solution: Engineer consortia designed for extensive synergistic co-digestion.⁴¹^, ⁴²

Diversify feedstock for food additive production (e.g., amino acids, vitamins, etc.) to lignocellulosic biomass, one-carbon molecules, and industrial agricultural wastes via metabolic engineering.

Enable protein and enzyme production from solid-phase fermentation of food processing byproducts or side-stream, such as spent grains.

Engineer microbes capable of stabilizing and detoxifying biomass, enabling a longer conservation without spoilage.

Engineer highly-efficient hydrolytic pathways into consortia for recovery of fatty-acids, sugars, amino acids, and phosphates from mixed-waste streams.

Bottleneck/Challenge: Microbial consortia population depends highly on feedstock and could be affected by the diverse compounds in mixed-waste streams.

Potential Solution: Develop regulatory systems in the (synthetic) consortia that help regulate the microbial population to tolerate environmental change and remain functional despite variations in mixed-waste streams.⁴³

Engineer consortia of microalgae that can grow on pure commercial food wastes for algal biomass/feedstock production.*

Enable bioprocessed recovery of nutrients from waste streams to reuse as fertilizer on industrial scales.**

*Pleissner, D., & Lin, C. S. K. (2013). Valorisation of food waste in biotechnological processes. Sustainable Chemical Processes, 1(1), 21. https://doi.org/10.1186/2043-7129-1-21

**Wang, J. Y., Stabnikova, O., Tay, S. T. L., Ivanov, V., & Tay, J. H. (2004). Biotechnology of intensive aerobic conversion of sewage sludge and food waste into fertilizer. Water Science and Technology: A Journal of the International Association on Water Pollution Research, 49(10), 147–154. Retrieved from https://pubmed.ncbi.nlm.nih.gov/15259949/

Footnotes

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