Scientists at the University of California, Davis (UC Davis) have developed a strain of wheat capable of producing its own nitrate fertiliser, thereby increasing yields and reducing the amount of artificial nitrate that needs to be applied to fields. They achieved this by harnessing the nitrogen-fixing abilities of common soil bacteria that convert atmospheric nitrogen into nitrates in a form plants can absorb. Their research is published, open access, in the Plant Biotechnology Journal.
We seem to have been here before, observing how a food crop or domesticated animal could have been far more productive or better suited to human needs had it been given a more efficient “design” to begin with. In fact, virtually all our cultivated plants and domesticated animals have been profoundly reshaped by human selection, using the same biological principles as natural selection: favouring advantageous genes and eliminating those that are less so.
The new wheat strain produces nutrients that support anaerobic bacteria similar to those found in the root nodules of legumes such as peas and beans. These bacteria thrive in the low-oxygen environment of specialised nodules, where they fix nitrogen for the host plant. Wheat, however, lacks such nodules, and attempts to transfer nodule-forming genes from legumes have so far been unsuccessful. Instead, this new approach encourages nitrogen-fixing bacteria to live in close association with the wheat root system, effectively bypassing the need for nodules altogether.
This raises an awkward question for Intelligent Design creationists who equate their designer deity with the allegedly omnibenevolent, omniscient, omnipotent god of the Bible, Torah, and Qur’an. Why didn’t this deity simply give crops like wheat and other staple foods the genes the bacteria use, or at least give them the genes required to host nitrogen-fixing bacteria directly, rather than devising an unnecessarily complex symbiosis only some plants can use? And if, for some reason, these were impossible, why didn’t it create a system resembling the one now designed by the UC Davis researchers?
As with so much in nature that ID proponents like to cite as evidence of complexity—and therefore design—closer inspection typically reveals solutions that are suboptimal, needlessly intricate, and often wasteful. As I point out in my book, The Unintelligent Designer: Refuting The Intelligent Design Hoax, these are not hallmarks of intelligent engineering, which should aim for minimal complexity and maximal efficiency. Instead, they are entirely consistent with an undirected evolutionary process that tinkers with what already exists, with no foresight and with success measured solely by reproductive output.
The simple fact is that humans, using intelligence, can and do devise more efficient, sensible solutions than those found in nature—as the UC Davis team has demonstrated. Such solutions ought to have been obvious to any genuinely omniscient designer.
This leaves creationists with a stark dilemma: must they conclude that their designer god is incompetent, unable to anticipate future needs, or malevolent in withholding solutions that would benefit humanity? Or is it more plausible that these biological systems arose through the natural evolutionary processes they insist “don’t work”?
How Nitrogen Fixation Works. Most plants can’t use nitrogen directly from the atmosphere, even though nitrogen gas (N₂) makes up about 78% of the air. To become biologically useful, nitrogen must first be converted into ammonia (NH₃) or related compounds. This transformation is carried out by specialised microorganisms—mainly bacteria and archaea—through a process called nitrogen fixation.The UC Davis team’s research is further explained in a news item by Trina Kleist.
- The Role of Nitrogenase
Nitrogen fixation depends on an enzyme complex called nitrogenase, one of the most energy-demanding enzymes known. It breaks apart the extremely strong triple bond in atmospheric nitrogen (N≡N) and reduces it to ammonia. This requires large amounts of ATP and functions only in low-oxygen conditions, because oxygen inactivates nitrogenase.- Symbiosis in Legumes
Leguminous plants such as peas, beans, and clover host nitrogen-fixing bacteria (usually Rhizobium species) inside specialised root nodules. These nodules maintain the low-oxygen environment needed for nitrogenase to work. The plant supplies the bacteria with sugars and energy; in return, the bacteria provide ammonia, which the plant converts into amino acids, nucleotides, and other nitrogen-rich molecules.- Free-Living Nitrogen Fixers
Some bacteria, such as Azotobacter and Clostridium, fix nitrogen independently in soil or sediments. They contribute to the natural fertility of ecosystems but tend to fix less nitrogen overall than symbiotic species.- Why It Matters
Fixed nitrogen is essential for building proteins and DNA, yet natural fixation is often too slow to meet the demands of modern agriculture. This limitation is why industrial nitrate fertilisers are widely used—and why engineering crops like wheat to support nitrogen-fixing microbes could significantly reduce environmental impact.
Wheat That Makes Its Own Fertilizer
Bacterial Work-Around Aims to Reduce Pollution, Lower Costs for Farmers
Scientists at the University of California, Davis, have developed wheat plants that stimulate the production of their own fertilizer, opening the path toward less air and water pollution worldwide and lower costs for farmers.
The technology was pioneered by a team led by Eduardo Blumwald, a distinguished professor in the Department of Plant Sciences. The team used the gene-editing tool CRISPR to get wheat plants to produce more of one of their own naturally occurring chemicals. When the plant releases the excess chemical into the soil, the chemical helps certain bacteria in the soil convert nitrogen from the air into a form the nearby plants can use to grow. That conversion process is called nitrogen fixation.
The study was published online in Plant Biotechnology Journal. In developing countries, the breakthrough could be a boon for food security.In Africa, people don't use fertilizers because they don’t have money, and farms are small, not larger than six to eight acres. Imagine, you are planting crops that stimulate bacteria in the soil to create the fertilizer that the crops need, naturally. Wow! That’s a big difference!
Professor Eduardo Blumwald, senior author
Department of Plant Sciences
University of California, Davis, USA.
The breakthrough in wheat builds on the team’s earlier work in rice. Research also is underway to extend this technology to other cereals.
Worldwide, wheat is the No. 2 cereal crop by yield and takes the biggest share of nitrogen fertilizer, using about 18% of the total. Globally, more than 800 million tons of fertilizer were produced in 2020 alone, according to figures from the United Nations Food and Agriculture Organization.
But plants take up only about 30 to 50% of the nitrogen in fertilizer. Much of what they don’t use flows into waterways, which can create “dead zones” that lack oxygen, suffocating fish and other aquatic life. Some excess nitrogen in the soil produces nitrous oxide, a potent climate-warming gas.
The work-around: Protect the fixer
Nitrogen-fixing bacteria produce an enzyme called nitrogenase, the “fixer” in nitrogen fixation. Nitrogenase is only located in the bacteria, and it can only work in environments with very little oxygen.
Legumes such as beans and peas have root structures, called nodules, that provide a cozy, low-oxygen home for nitrogen-fixing bacteria to live.
Unlike legumes, wheat and most other plants don’t have root nodules. This is why farmers use nitrogen-containing fertilizer.
For decades, scientists have been trying to develop cereal crops that produce active root nodules, or trying to colonize cereals with nitrogen-fixing bacteria, without much success. We used a different approach. We said the location of the nitrogen-fixing bacteria is not important, so long as the fixed nitrogen can reach the plant, and the plant can use it.
Professor Eduardo Blumwald.
To find a work-around, the team first looked at 2,800 chemicals the plants produce naturally. They found 20 that, among other jobs useful to the plant, also stimulate bacteria to produce biofilms. Biofilms are a sticky layer that surround the bacteria and create a low-oxygen environment, allowing nitrogenase to work. The scientists determined how the plant makes those chemicals and which genes control that process.
Then, the team used the gene-editing tool CRISPR to modify wheat plants to produce more of one of those chemicals, a flavone called apigenin. The wheat, now with more apigenin than it needs, releases the excess through its roots into the soil. In experiments they conducted, apigenin from the wheat stimulated bacteria in the soil to create the protective biofilms, allowing nitrogenase to fix nitrogen and the wheat plants to assimilate it.
The wheat also showed a higher yield than control plants when grown in a very low concentration of nitrogen fertilizer.
Farmers could save billions
Farmers in the United States spent nearly $36 billion on fertilizers in 2023, according to U.S. Department of Agriculture estimates. Blumwald calculates that nearly 500 million acres in the U.S. are planted with cereals.
Imagine, if you could save 10% of the amount of fertilizer being used on that land,” he pondered. “I’m calculating conservatively: That should be a savings of more than a billion dollars every year.
Professor Eduardo Blumwald.
Other authors include Hiromi Tajima, Akhilesh Yadav, Javier Hidalgo Castellanos, Dawei Yan, Benjamin P. Brookbank and Eiji Nambara.
Publication:
ABSTRACT
Nitrogen availability remains a principal constraint to crop productivity. Plants cannot directly assimilate the abundant nitrogen available in our atmosphere; instead, they rely on the uptake of inorganic forms of nitrogen, such as ammonium and nitrate from the soil. Nitrogen is a limiting nutrient in wheat production, and wheat yields are very responsive to nitrogen fertilisation. Only diazotrophic bacteria can convert atmospheric nitrogen to ammonia via biological nitrogen fixation (BNF), and although improving BNF in wheat has been a longstanding objective, there have been no descriptions of successful modification of wheat crops showing increased BNF in the literature. Here we describe the use of polycistronic multiplexed CRISPR to modify the flavone biosynthetic pathway of hexaploid wheat (Triticum aestivum) plants, generating DNA-edited plants with increased apigenin content. The apigenin-enriched plants exude apigenin into the soil, inducing the colonisation of the roots and subsequent formation of biofilms in soil by diazotrophic bacteria. The low permeability of the biofilm to oxygen protected the bacterial nitrogenase and stimulated BN. Under nitrogen-limiting conditions, apigenin-enriched wheat lines exhibited increased nitrogen content, improved photosynthetic performance, and higher grain yield relative to wild-type controls. This work demonstrates the feasibility of engineering associative BNF in cereals via metabolic reprogramming of root exudation, offering a sustainable route to reduce dependence on synthetic nitrogen fertilisers.
1 Introduction
Nitrogen is essential to plant growth and crop production. In contrast to legume crops which have evolved the capacity to associate with nitrogen-fixing bacteria (diazotrophs), lodged inside host plant root nodules (Udvardi and Poole 2013), cereal crops depend exclusively on the uptake of inorganic forms of nitrogen, such as nitrate and ammonium, from the soil.
Although cereal crops demand high N-fertiliser (Masclaux-Daubresse et al. 2010), their Nitrogen Use Efficiency (NUE) is relatively low and only 30%–35% of the N-fertiliser is taken up by the plant (Raun and Johnson 1999). The inefficient NUE of cereals greatly contributes to nitrate contamination of soils and ground water, leading to serious health challenges to the general population (Essien et al. 2020). In addition, leaching of N fertilisers from the soil to the underground water contributes to the eutrophication of water bodies (Withers et al. 2014), and inorganic N-fertilisers are volatilised to nitrous oxide that depletes the ozone layer in the stratosphere, contributing to global warming (Thompson et al. 2019).
The addition of N-fertilisers to cereal crops contributes to enhanced food production, and more inorganic N-fertiliser will be needed to support a further increased food production required to satisfy the needs of an increasing world population (Omara et al. 2019.1). These additional inputs of N-fertilisers would make grain production more expensive, with a considerable aggravation in environmental pollution. Thus, there is a growing need to develop sustainable alternative agricultural practices aimed at reducing the excessive use of inorganic N-fertilisers.
The conversion of atmospheric nitrogen to ammonia by soil diazotrophs can supplement crop' N needs, contributing to crop productivity of both legume and non-legume species, and reducing the amount of inorganic N-fertiliser used in agriculture (Herridge et al. 2008; Van Deynze et al. 2018). Diazotrophs produce nitrogenase, an enzymatic complex that catalyses the conversion of atmospheric N2 to NH3, a process called Biological Nitrogen Fixation (BNF). BNF is hindered by the presence of oxygen, which inhibits the enzyme nitrogenase irreversibly and represses its synthesis (Robson and Postgate 1980; Hill 1988; Dixon and Kahn 2004). Thus, BNF by free-living diazotrophs in aerated agronomical soils is limited by the presence of oxygen. The regulation of nitrogen fixation and ammonia assimilation, via Glutamine synthetase and GOGAT, is associated to maximise the use of fixed nitrogen by the bacteria (Colnaghi et al. 1997; Bueno Batista and Dixon 2019.2). Nevertheless, micromolar amounts of ammonia, converted to ammonium at physiological pH, can be excreted out of the bacteria cells (Ortiz-Marquez et al. 2012; Barney et al. 2015). The ammonium excreted can be readily transported into the plant by the action of highly efficient high-affinity transporters (AMTs, AKT1, and NSCC) localised at the root cells plasma membranes (Bloom et al. 2002; Hachiya and Sakakibara 2017).
Several strategies aimed at engineering BNF in cereals have been reported. Bacterial nitrogenase genes have been expressed in both yeast and in plants. The nifH gene was expressed in tobacco chloroplasts (Buren et al. 2017.1), while the nif operon from Klebsiella pneumoniae was introduced into tobacco mitochondria (Allen et al. 2017.2). Also, the nitrogenase co-factor maturase NifB was expressed in tobacco mitochondria and chloroplasts (He et al. 2022), as well as rice mitochondria (Jiang et al. 2022.1). Although expression was attained in all the above-mentioned cases, the expressed proteins were inactive. Research aimed at the induction of root organogenesis in cereals, like legume nodules, has also been reported. Expression of nodulation genes and the induction of nodule-like structures have been reported in rice roots (Shen and Feng 2024, and references therein), but functional nitrogen-fixing nodules have not yet been achieved. The overexpression of transcription factors that regulate root development and control stem cell definition in rice led to the formation of root nodule-like structures (Hiltenbrand et al. 2016), which resemble nodules morphologically but lack the complex features required for symbiotic establishment with rhizobia. While this suggests some potential for engineering nodule-like organs in cereals, these structures do not support key requirements for symbiosis, such as infection thread formation and appropriate vascularity. Moreover, the maintenance of microaerophilic conditions in these structures needed for nitrogenase function is still unresolved (Guo et al. 2023).
A synthetic biology approach was used to create a plant-bacteria signalling circuit to improve N-fixation activity of bacteria associated with the roots of a target plant. Barley was engineered to produce scyllo-inosamine (SI), a rhizopine signalling molecule, and the bacterium Azorhizobium caulinodans was transformed to express a SI-uptake system (Haskett et al. 2022.2). This system allowed a tight rhizopine-dependent control of factors driving the expression and activity of the nitrogenase from bacteria colonising the barley roots. This activation was specific to the genetically modified barley and supported the notion of generating plant-controlled symbiosis where the nitrogen-fixing bacteria could associate specifically with a particular target plant species (Haskett et al. 2022.2; Guo et al. 2023).
Recently, a strategy for the induction of BNF in cereals through the formation of biofilms by soil diazotrophic bacteria was postulated (Yan et al. 2022.3). Flavone biosynthetic pathways in rice were modified using CRISPR/Cas9, inducing the increase of apigenin content in rice plants growing under limiting N-conditions. The increase of apigenin content in CRISPR-modified plants, with the concomitant apigenin increase in root exudates, promoted biofilm formation in soil diazotrophs with the concomitant induction of BNF that resulted in a significant increase in grain yield as compared to the wild-type plants growing under similar N-limited conditions (Yan et al. 2022.3).
Here, we successfully used polycistronic multiplexed CRISPR to modify the flavone biosynthetic pathway of hexaploid wheat plants, generating CYP75B knockouts that resulted in increased apigenin contents. The apigenin-enriched wheat plants exuded apigenin into the rhizosphere, inducing the formation of bacterial biofilms that supported increased BNF, allowing significant yield increases in plants growing under limited N conditions.
Tajima, H., Yadav, A., Castellanos, J.H., Yan, D., Brookbank, B.P., Nambara, E. and Blumwald, E. (2025)
Increased Apigenin in DNA-Edited Hexaploid Wheat Promoted Soil Bacterial Nitrogen Fixation and Improved Grain Yield Under Limiting Nitrogen Fertiliser.
Plant Biotechnol. J, 23: 5146-5160. https://doi.org/10.1111/pbi.70289
Copyright: © 2025 The authors.
Published by John Wiley & Sons. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
What this research highlights once again is the troubling inconsistency at the heart of Intelligent Design claims. If an omniscient, omnibenevolent designer truly existed and played an active role in shaping life, then systems like nitrogen fixation in crops should already have been in place. A being with limitless foresight would have known that staple cereals such as wheat, rice, and maize would underpin human civilisation, and it could easily have equipped them with the means to harness atmospheric nitrogen directly. Instead, we see a patchwork system restricted to some plants but not others, dependent on delicate symbioses and easily disrupted conditions—precisely what we would expect from natural evolution, not conscious engineering.
The same logic applies to every cultivated plant and domesticated animal we rely on today. Their “designs” as we know them are overwhelmingly the result of human-guided selection: thousands of years of trial, error, and incremental improvement. If a perfect designer had created them, there would have been no need for humans to intervene, reshape, and refine them into viable crops or dependable livestock. The raw forms presented by nature were often barely usable until generations of selective breeding transformed them.
Creationists, of course, simply look past this evidence. They dismiss the clear signs of natural processes at work and instead attribute every clumsy, inefficient or incomplete biological system to a flawless intelligence. But the more closely we examine these systems, the harder that claim becomes to sustain. If an intelligence were responsible, it would have to be either incapable of designing robust solutions, indifferent to the suffering and waste created by its poor designs, or entirely unconcerned with human welfare. What it certainly cannot be is omniscient, omnipotent, and benevolent.
In contrast, evolution offers a straightforward explanation. Life is not shaped with purpose or foresight but by cumulative changes that favour immediate survival and reproduction. Inelegant, imperfect, wasteful systems are exactly what we expect from such a process—and exactly what we observe.
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