2023-12-29 10:30:14
Reduce synthetic fertilizers and improve yields? The microbiome revolution is coming to agriculture.
Henry I. Miller and Kathleen L. Hefferon, ACSH*
Image : Wikipedia Commons
Microbiomes are the collective and highly personal assortment of microorganisms that live in us, on us, and around us. If genetically engineered effectively, these ‘black boxes’ could help us cure cancer, understand how we can adapt to rising temperatures, play a role in mental health and improve children’s nutrition .
In recent years, there has been much discussion about the importance of the human microbiome, particularly regarding the gut microbiome and the importance of its microbial inhabitants for our health. From deciphering more information about the probiotics found in our food products to routinely performing previously unimaginable procedures such as fecal transplants, the possibilities for harnessing the mysteries of the microbiome seem endless.
A complex relationship like that between humans and microorganisms also exists between microorganisms and our soil. Like the impact of deciphering the microbiome on human health, could a better understanding of the soil microbiome allow us to better understand complex environmental problems and perhaps offer new solutions? Could learning more about the soil microbiome even provide us with new approaches to solving the formidable problem of climate change? Could this research lead to a significant reduction in the use of polluting synthetic fertilizers?
The use of fertilizer has long been recognized as essential but problematic. Without macro- and micro-fertilizers, nature struggles to replenish nutrients in the soil. Crops can grow without them, but they may be weak. Over time, nutrients in the soil decrease because when crops are harvested, essential nutrients are taken with them and end up on the dinner table. If the soil is not replenished with nutrients through fertilization, crop yields will decrease.
As always in agriculture, there are compromises to be made. Too much fertilizer can harm the environment. Microorganisms naturally present in the soil can be damaged by chemicals in fertilizers. These can destroy the soil fertility of an area and reduce the organic matter and humus content of the soil. They can also lead to the release of greenhouse gases.
Scientists have spent years studying the intricacies of the nutrient cycling mechanisms of the soil microbiome that affect our food crops and environment. Take the example of nitrogen, an essential element in the construction of all organisms. It is abundant in the air, but unfortunately in a form unusable by most plants. In soil, nitrogen can be scarce, but some plants, such as legumes, harbor a type of bacteria on their roots known as rhizobia, which forms nodules to fix atmospheric nitrogen into easily accessible ammonia.
This relationship is very specific and only exists between certain plants and soil microorganisms. This is why growing staple crops such as cereals requires the application of fertilizers. Artificial fertilizers have helped prevent widespread starvation, but because many of them are produced from petroleum products and for a variety of other reasons, they are not an environmentally friendly solution.
The production of synthetic ammonia (e.g., the Haber-Bosch nitrogen fixation process) and its application accounts for approximately 5% of global greenhouse gas emissions. If this process had not been invented, the number of people the planet can adequately feed would have reached capacity many years ago. As we rapidly move toward a global population of 10 billion, we need to double our agricultural productivity.
However, it is far from easy to achieve this. Excessive fertilizer use leads to excess fertilizer runoff into waterways, creating anoxic dead zones and releasing N2O, a greenhouse gas 300 times more potent than CO2 in global warming . It is therefore essential to understand the relationship between crops and the soil microbiome to ensure our food security and reduce agricultural greenhouse gas emissions. One way to do this is to get microorganisms to fix more nitrogen so crops can use it.
Genetic engineering of bacteria
Using the same tools that have enabled advances in human microbiome research, we can now harness the soil microbiome to solve some of the problems related to food security and environmental sustainability. A “pivotal” moment came a few years ago when scientists demonstrated that bacteria could be genetically engineered to fix nitrogen in the roots of non-legume crops, such as corn, in a way that dramatically reduced the use fertilizer. Partially replacing fertilizers with genetically modified bacteria would also reduce nitrogen runoff and N2O emissions.
The multi-year, multi-site study in the Corn Belt has paved the way for agricultural start-up Pivot Bio to commercialize and make widely available this exciting technology in the form of a soil-applied liquid or a powder coating the seeds. Recently, the company showed that its products could replace a quarter of synthetic nitrogen without reducing crop yield.
This discovery could be momentous. Pivot Bio’s products are already used on more than 1.2 million hectares of agricultural land in the United States, for various crops such as corn, wheat and sunflowers. This has already reduced the amount of synthetic fertilizer applied on American farms by 29,000 metric tons in 2022, which translates into an estimated reduction of 200,000 tons of CO2, the equivalent of burning 1,200 rail cars of coal. These savings come from the estimated reduction in emissions required for the production of synthetic fertilizers, combined with the prevention of the release of N2O from the soil.
Others have worked on grain plants that create their own fertilizer. At MIT’s Whitehead Institute, Jing-Ke Weng’s research group studied how plants and microorganisms signal each other to initiate the nitrogen fixation process in legumes, as a prelude to the introduction of an analogous signaling pathway in cereal crops.
Similarly, the team of Eduardo Blumwald, from the University of California, Davis, used gene editing to modify rice to increase the production of chemical compounds, by stimulating the activity of bacteria fixing nitrogen at the plant roots.
Professor Lisa Stein, a microbiologist at the University of Alberta, is exploring another aspect of the problem by creating nitrification inhibitors – chemical compounds that reduce nitrous oxide emissions by suppressing the conversion of nitrogen to nitrate by soil microorganisms. Combined with fertilizers, they prevent the production of N2O and its pollution of waterways.
Blue-green algae?
Cyanobacteria, sometimes called blue-green algae, can spread in freshwater lakes and ponds, diverting oxygen and nutrients. They can form biofilms on water or soil and cause disease.
Biofilms on water. Image: Genetic Literacy Project
Among the oldest organisms on Earth, they are ubiquitous, can be used as a food source, and are also a source of natural dyes and alternative fuels. They produce a wide range of antimicrobial metabolites. Cyanobacteria also represent a promising alternative to artificial fertilizers, because they too can fix nitrogen from the air and make it available to plants.
Not all species of cyanobacteria can form the strong symbiosis necessary with every type of crop, but when it does form, the cyanobacteria can attach to and even penetrate the intercellular spaces of plants, so that the bacteria and the host can both benefit from nutrient exchange. Cyanobacteria applied to the soil surrounding crop plants in the form of biofilms, which exist as surface-attached communities or suspended aggregates, may provide additional benefits. They can provide beneficial secondary metabolites to plants and increase soil water retention.
Cyanobacteria do not need to be grown on arable land and their cultivation is carbon negative, meaning that the amount of carbon captured through photosynthesis is greater than that which is released into the environment. Cyanobacteria can therefore produce fertilizer at a fraction of the cost and without using fossil fuels.
All of these products could revolutionize sustainable food production by reducing the need to use synthetic fertilizers used on a large scale today. This would address complex environmental issues such as nitrogen runoff and nitrous oxide emissions.
Like our rapidly improving knowledge of the human microbiome, advances in understanding the soil microbiome will significantly change our agricultural practices, improving crop yield while reducing dependence on soil microbiome. synthetic nitrogen and the damage it causes to the environment. Just as our growing understanding of the human microbiome is revolutionizing medicine, our increased knowledge of the soil microbiome will transform agriculture.
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Kathleen L. Hefferon is professor of microbiology at Cornell University. Find Kathleen on X @Khefferon.
Henry I. Miller, physician and molecular biologist, is the Glenn Swogger Distinguished Fellow of the American Council on Science and Health. He was the founding director of the FDA’s Office of Biotechnology. Find Henry on X @henryimiller.
Source : Reduce Synthetic Fertilizers and Improve Yields? The Microbiome Revolution Comes to Agriculture. | American Council on Science and Health (acsh.org)
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