A team of researchers from the Boyce Thompson Institute (BTI) has discovered a distinct group of bacteria that may help fungi and plants acquire soil nutrients. The findings could point the way to cost-effective and eco-friendly methods of enriching soil and improving crop yields, reducing farmers’ reliance on conventional fertilizers. Researchers know that arbuscular mycorrhizal (AM) fungi establish symbiotic relationships with the roots of 70 percent of all land plants. In this relationship, plants trade fatty acids for the fungi’s nitrogen and phosphorus. However, AM fungi lack the enzymes needed to free nitrogen and phosphorus from complex organic molecules. A trio of BTI scientists led by Maria Harrison, the William H. Crocker Professor at BTI, wondered whether other soil microbes might help the fungi access those nutrients. In a first step towards examining that possibility, the team investigated whether AM fungi associate with a specific community of bacteria. The research was described in a paper published in The ISME Journal. The team examined bacteria living on the surfaces of long filament-like structures called hyphae, which the fungi extend into the soil far from their host plant. On hyphae from two species of fungi, the team discovered highly similar bacterial communities whose composition was distinct from those in the surrounding soil. “This tells us that, just like the human gut or plant roots, the hyphae of AM fungi have their own unique microbiomes,” said Harrison, who is also an adjunct professor in Cornell University’s School of Integrative Plant Science. “We’re already testing a few interesting predictions as to what these bacteria might do, such as helping with phosphate acquisition. “If we’re right, then enriching the soil for some of these bacteria could increase crop yields and, ultimately, reduce the need for conventional fertilizers along with their associated costs and environmental impacts,” she added. Her co-researchers on the study were former BTI scientists Bryan Emmett and Véronique Lévesque-Tremblay. Among the fungi In the study, the team used two species of AM fungi, Glomus versiforme and Rhizophagus irregularis, and grew them in three different types of soil in symbiosis with Brachypodium distachyon, a grass species related to wheat. After
letting the fungus grow with the grass for up to 65 days, the researchers used gene sequencing to identify bacteria sticking to the hyphae surfaces. The team found remarkable consistency in the makeup of bacterial communities from the two fungal species. Those communities were similar in all three soil types, but very different from those found in soil away from the filaments. According to Harrison, the function of these bacteria is not yet clear, but their composition has already sparked some interesting possibilities. “We predict that some of these bacteria liberate phosphorus ions in the immediate vicinity of the filaments, giving the fungus the best chance to capture those ions,” she said. “Learning which bacteria have this function could be key to enhancing the fungi’s phosphate acquisition process to benefit plants.” Harrison’s group is investigating the factors that control which bacteria assemble on the filaments. Harrison thinks the AM fungi may secrete molecules that attract these bacteria, and in turn, the bacterial communities may influence which molecules the fungus secretes. Highway patrol Among the hyphae microbiomes were members of Myxococcales and other taxa that include “bacterial predators” that kill and eat other bacteria by causing them to burst and release their contents. These predators move by gliding along surfaces so “the fungal filaments could serve as linear feeding lanes,” said Emmett, who is currently a research microbiologist for the U.S. Department of Agriculture’s Agricultural Research Service in Ames, Iowa. “Many soil bacteria appear to travel along fungal hyphae in soil, and these predators may make it a more perilous journey.” While not every member of those taxa on the filaments may be predatory, Harrison’s group plans to investigate how and why those putative predators assemble there. “It’s possible that the actions of predatory bacteria make mineral nutrients available to everyone in the surrounding soil – predators and fungi alike,” she said. ●
Arbuscular mycorrhizal fungi extend long filament-like structures called hyphae far out into the soil. The hyphae, which are smaller than a human hair, can be seen here among the roots of a grass plant.
Photo: Maria Harrison
Leguminous plants, like peas, beans and various species of clover, obtain the organic nitrogen they need for their growth from symbiotic soil bacteria via specialized structures in their roots. Now, a team led by cell biologist Prof. Dr. Thomas Ott from Germany’s University of Freiburg's Faculty of Biology has detected a factor in the root cells that the plants need for the initial contact with these so-called root-associated bacteria, which live in the soil. They discovered a protein found only in legumes called symbiotic formin 1 (SYFO1) and demonstrated the essential role it plays in symbiosis. Together with molecular biologist Prof. Dr. Robert Grosse University of Freiburg's Faculty of Medicine and evolutionary biologist Dr. Pierre-Marc Delaux from the Laboratoire de Recherche en Sciences Végétales (LRSV) in Toulouse, France, the team published their results in the journal Current Biology. When a root nodule bacterium encounters the roots of a leguminous plant in the soil, the SYFO1 protein causes the tiny hairs of the root to change the direction of their growth. They thus wrap themselves around the potential symbiotic partner. Thanks to these
bacterial helpers, legumes do not need any nitrogenous fertilizer, in contrast to other plants.
"If we understood precisely how the symbiosis comes into being, we could give crop plants back this special property they have lost in the course of evolution," says Ott. Both he and Grosse are members of the Cluster of Excellence CIBSS—Center for Integrative Biological Signaling Studies. Ott's research at CIBSS involves studying the spatial organization of the signaling paths that enable the symbiotic relationship with symbiotic bacteria in the first place. Grosse, on the other hand, focuses in his work in Freiburg on the cytoskeleton of animal cells. "In our collaboration, which was made possible by CIBSS, we were able to contribute our expertise in different areas of specialization in the best possible way," says Ott. The team demonstrated in the legume Medicago truncatula (barrel medic) that the root hairs of plants in which the gene for SYFO1 has been switched off are practically no longer capable of wrapping themselves around the bacteria. In further studies, the researchers discovered that the protein binds to actin, a component of the cytoskeleton, and at the same time to the cell wall outside the cells, thus changing the direction of its growth. Instead of growing straight, the tiny hairs now change their direction and form a loop around the bacterium.
"SYFO1 constitutes a special innovative step in the evolution of the plants," explains Ott. "While formin proteins are present in many forms in cells and interact with actin, this special type only responds to symbiotic signals from the bacteria." ●
A root hair (blue) grows around the symbiotic bacteria (red).
Photo: Pengbo Liang/University of Freiburg
Bayer Crop Science and Biome Makers has teamed up to validate an automatized recommendation engine using soil microbiome and environmental data to determine the most suitable product application to optimize yield and soil health. Biome Makers has developed a software package that uses advanced machine learning to help farmers and agronomists pinpoint what their crops and soils need to boost yield in a sustainable way. The scientific teams of Bayer Crop Science and Biome Makers tested and disclosed the first application of this groundbreaking technology on bioRxiv, the preprint repository operated by Cold Spring Harbor Laboratory. The study and resulting scientific paper detail the analysis of the soil microbiome to assess effectiveness of Bayer´s biological fungicide Minuet. Specifically, machine learning software allowed Bayer CS to predict potato yield improvement before application of the input. The predicted result was a yield bump of up to 40 percent in one of the fields tested in Idaho, U.S. "It's a unique approach to utilize soil biology and optimize the use of crop inputs moving forward towards sustainable and economically favourable solutions to improve crop productivity," said Varghese Thomas the project leader at Bayer CS. The company maintains the technology is a giant leap forward for agronomists who, up until now, have lacked the data required to accurately determine biological solutions for their seasonal soil and crop decisions. With the availability of an AI virtual assistant to help predict the effect of different solutions is game-changing, and progress towards a more productive and sustainable agriculture system.
AI is an ever-evolving resource and, as such, is currently being "trained" to resolve other farming concerns as well, including questions about produce shelf-life, nutrient quality of the produce, and projected carbon credits based on the use of different products or management practices. Input manufacturers can add their own, custom solution to the AI recommendation system by testing it under the strict Gheom field trials protocol, a service Biome Makers offers. Gheom: microbial-based protocol for field trials Biome Makers said Gheom is designed to accurately gauge biological product efficacy by analyzing the most meaningful bioindicator in nature: the soil microbiome; today, international companies that produce biostimulants, soil amendments and biofertilizers are using Gheom to test solutions. For instance, Terravesco is a California manufacturer employing this protocol to analyze their organic worm-based soil amendment. Similarly, LIVENTIA is assessing how their microbial biostimulants based on microbial consortia impact the ecological balance of soils, promoting effects like root growth, nutrient uptake, and stress tolerance to boost yield and crop quality. Likewise, Fertile Ground is another company sourcing the program to validate their product performance. Other companies like Sustainable Growing Solutions or the European manufacturer, Bioiberica, are already using protocol results to confirm the functional claims of their products for different crops such as vineyards, lettuce or olive trees. "Combining this breakthrough technology with the entire toolbox of precision agriculture, such as self-driving tractors and precision spraying applications, allows us to imagine a bright, new future of secure and sustainable farming worldwide," said Alberto Acedo, chief scientific officer at Biome Makers. Currently, select growers in the U.S. and EU can test the recommendation system with complimentary functional soil analytics for their fields. ●
Inorganic fertilizer is still an important input required to achieve challenging yield targets in sugarcane farms. However, it is costly and known to deteriorate the environment when not managed properly. Not all nutrients from inorganic fertilizers could be assimilated by the crop. Some are lost due to runoff and leaching. With the application of nanotechnology in agriculture, these losses can be reduced. Hence, nanofertilizers are emerging as a promising alternative. FertiGroe N, P, and K are the new slow-release nanofertilizers. These are nano-sized (1-100nm) particle technology that increase surface area for nutrient adsorption. The products offer better economic yield and are safer for the environment through their strong potential of slowing down or controlling nutrient release to increase nutrient use efficiency. The Agricultural Systems Institute (ASI) and La Granja Research and Training Station (LGRTS) of the University of the Philippines Los Baños (UPLB) are currently testing the formulated FertiGroe N, P, and K nanofertilizers for sugarcane through the project, “Development of Application Protocol and Field Verification of FertiGroe N, P, and K Nanofertilizers in Sugarcane.” The project is one of the seven components of the program “Optimization of the Production and Use of FertiGroe N, P, and K Nanofertilizers in Selected Agricultural Crops,” funded by the Department of Science and Technology (DOST) and monitored by the Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRD). The program aims to optimize the production process and develop application protocols of FertiGroe N, P, and K nanofertilizers to increase yield of rice, corn, vegetables, sugarcane, coffee, cacao and banana. Initial results of the field evaluation trial show that FertiGroe nanofertilizers-treated sugarcane obtained as much as 218.76 50kg-per-hectare (Lkg/ha), which is higher than the average yield of 129.62 Lkg/ha in La Carlota Mill District, Negros Occidental. Use of FertiGroe nanofertilizers increased nutrient uptake, minimized nutrient losses, reduced fertilizer inputs by 50 percent, and reduced production costs. Efficacy trials are still ongoing and are expected to be completed soon. ●
MIT chemists have determined the structure of the complex that forms when gaseous dinitrogen, or N2, binds to an iron-sulphur cluster, offering clues as to how microbes (in yellow) use nitrogenases to break the nitrogen-nitrogen bond (in pink and green).
Nitrogen, an element that is essential for all living cells, makes up about 78 percent of Earth’s atmosphere. However, most organisms cannot make use of this nitrogen until it is converted into ammonia. Until humans invented industrial processes for ammonia synthesis, almost all ammonia on the planet was generated by microbes using nitrogenases, the only enzymes that can break the nitrogen-nitrogen bond found in gaseous dinitrogen, or N2. These enzymes contain clusters of metal and sulphur atoms that help perform this critical reaction, but the mechanism of how they do so is not well-understood. For the first time, MIT chemists have now determined the structure of a complex that forms when N2 binds to these clusters, and they discovered that the clusters are able to weaken the nitrogen-nitrogen bond to a surprising extent. “This study enables us to gain insights into the mechanism that allows you to activate this really inert molecule, which has a very strong bond that is difficult to break,” says Daniel Suess, the class of ’48 career development assistant professor of chemistry at MIT and the senior author of the study.
Alex McSkimming, a former MIT postdoc who is now an assistant professor at Tulane University, is the lead author of the paper, which appears in Nature Chemistry.
Nitrogen fixation Nitrogen is a critical component of proteins, DNA and other biological molecules. To extract nitrogen from the atmosphere, early microbes evolved nitrogenases, which convert nitrogen gas to ammonia (NH3) through a process called nitrogen fixation. Cells can then use this ammonia to build more complex nitrogen-containing compounds. “The ability to access fixed nitrogen on large scales has been instrumental in enabling the proliferation of life,” Suess says. “Dinitrogen has a really strong bond and is really unreactive, so chemists basically consider it an inert molecule. It’s a puzzle that life had to figure out: how to convert this inert molecule into useful chemical species.” All nitrogenases contain a cluster of iron and sulphur atoms, and some of them also include molybdenum. Dinitrogen is believed to bind to these clusters to initiate the conversion to ammonia. However, the nature of this interaction is unclear, and until now, scientists had not been able to characterize N2 binding to an iron-sulphur cluster. To shed light on how nitrogenases bind N2, chemists have designed simpler versions of iron-sulphur clusters that they can use to model the naturally occurring clusters. The most active nitrogenase uses an iron-sulphur cluster with seven iron atoms, nine sulphur atoms, a molybdenum atom and a carbon atom. For this study, the MIT team created one that has three iron atoms, four sulphur atoms, a molybdenum atom and no carbon. One challenge in trying to mimic the natural binding of dinitrogen to the iron-sulphur cluster is that when the clusters are in a solution, they can react with themselves instead of binding substrates such as dinitrogen. To overcome that, Suess and his students created a protective environment around the cluster by attaching chemical groups called ligands. The researchers attached one ligand to each of the metal atoms except for one iron atom, which is where N2 binds to the cluster. These ligands
prevent unwanted reactions and allow dinitrogen to enter the cluster and bind to one of the iron atoms. Once this binding occurred, the researchers were able to determine the structure of the complex using X-ray crystallography and other techniques. They also found that the triple bond between the two nitrogen atoms of N2 is weakened to a surprising extent. This weakening occurs when the iron atoms transfer much of their electron density to the nitrogen-nitrogen bond, which makes the bond much less stable. Cluster cooperation Another surprising finding was that all of the metal atoms in the cluster contribute to this electron transfer, not only the iron atom to which the dinitrogen is bound. “That suggests that these clusters can electronically cooperate to activate this inert bond,” Suess says. “The nitrogen-nitrogen bond can be weakened by iron atoms that wouldn’t otherwise weaken it. Because they’re in a cluster, they can do it cooperatively.” The findings represent “a significant milestone in iron-sulphur cluster chemistry,” says Theodore Betley, chair of the department of chemistry and chemical biology at Harvard University, who was not involved in the study. “Although the nitrogenase enzymes known to fix atmospheric nitrogen are composed of fused iron-sulphur clusters, synthetic chemists have never, until now, been able to demonstrate dinitrogen uptake using synthetic analogues,” Betley says. “This work is a major advance for the iron-sulphur cluster community and bioinorganic chemists at large. More than anything, this advance has shown that iron-sulphur clusters have a rich reaction chemistry yet to be discovered.” The researchers’ findings also confirmed that simpler versions of the iron-sulphur cluster, such as those they created for this study, can effectively weaken the nitrogen-nitrogen bond. The earliest microbes to develop the ability to fix nitrogen may have evolved similar types of simple clusters, Suess says. Suess and his students are now working on ways to study how the more complex, naturally occurring versions of iron-sulphur clusters interact with dinitrogen. ●
Photo: Jose-Luis Olivares, MIT
