Developing a new variety of crop inoculant: a bacteria known as methylotrophs

One of the major challenges in agriculture is increasing yield while minimizing inputs and environmental impacts. One exciting approach to this problem is developing commercial inoculants of plant growth promoting microorganisms. Many people will typically associate bacteria and fungi with disease, both in plants and in people. However, just as we have come to understand the importance of our whole microbiome in human health, scientists have begun to explore the role of the plant microbiome in agriculture. The human microbiome carries out lots of functions, from aiding our digestion to keeping our immune system functioning. The plant microbiome can do many similar things, including supplying hard-to-acquire nutrients, manipulating plant hormone levels to promote growth, and protecting plants from pathogens and abiotic stresses such as drought. Scientists have identified specific bacteria that provide these services to plants and developed inoculants that are well-adapted to surviving on the plant. Farmers can purchase treatments for seeds or for the soil that will get the bacteria to colonize the plant and provide these beneficial services. These treatments can then increase agricultural yield without the use of fertilizers or other environmentally damaging inputs.

I am part of a team that is working to develop a new variety of crop inoculant. We are working on a type of bacteria known as methylotrophs. Methylotrophs are able to grow on substances such as methanol (CH3OH) that have only a single carbon and no carbon-carbon bonds. Most methylotrophs also have the ability to grow on multi-carbon sources as well. This metabolic flexibility makes methylotrophs an exciting organism to study for microbiologists and biochemists who are interested in using the bacteria for industrial applications. Most importantly for us, these metabolic abilities mean that methylotrophs are extremely well-suited to live in the phyllosphere, or on the surface of the above-ground parts of plants. They are able to utilize the methanol that plants release from their stomata in the process of growing leaves, while other bacteria that can’t engage in one-carbon metabolism cannot access this carbon source. Methylotrophs have been shown to provide many important services for plants, ranging from nitrogen fixation to phosphate solubilization to protection from abiotic stress.

Methylobacterium grown on solid and liquid media

We are particularly interested in pairing methylotrophs with fertilization with rare earth elements (REEs). The name rare earth elements is misleading: these elements are not actually all that rare in the earth’s crust. Rather, they are generally found in low concentrations in forms that are very hard to solubilize. For this reason, they had long been considered to be biologically inert. However, farmers in some parts of the world have been fertilizing their crops with REEs and seeing increases in plant growth. However, no one knew how the REEs were increasing yield. Scientists have recently found that methylotrophs can use REEs in the cellular machinery they use to metabolize methanol. Methylotrophs can grow faster and use methanol more efficiently when they have REEs available. Thus, we think that plant growth promotion from REE fertilization is caused by the REEs stimulating the growth of methylotrophs on plant leaves. The larger population of methylotrophs on the plant leaves lets the bacteria provide more services to the plants, which allows the plants to grow faster.

Soybean at various growth stages

We are working to test this hypothesis currently. We have successfully confirmed that a dual treatment of REEs and methylotrophs increase plant growth more than treatment with methylotrophs or REEs alone. Now we are working to answer a number of questions about this interaction. We are exploring the genes that the bacteria expresses while it colonizes the plant, as well as the metabolites that they exchange with the plant. This will help us understand exactly what services the bacteria is providing to the plant, and how these services are affected by the presence of REEs. We are also testing out a range of REE concentrations so we can determine the optimal amount of REE to apply. Finally, we have collected a large number of methylotroph strains from the environment. We are testing how well these strains are able to colonize and persist on the plant, in addition to testing their metabolic abilities. This work will help us determine what characteristics the methylotrophs needs to have to survive on the plant and provide the maximum amount of services to the plant. Other members of the team are working on studying how methylotrophs are able to bind and transport REEs to get them into their cells. This ability is important for their growth on plant leaves, but also opens the possibility of using these bacteria to acquire REEs from natural sources for use in industry. Even more importantly, these bacteria may be able to recycle REEs from spent industrial materials such as used cell phone batteries. This makes it possible for REEs to be sustainably acquired.

Over the next few years, we aim to thoroughly characterize this interaction. We will also explore how REEs affect interactions between the plant and microbes that colonize the rhizosphere, or the belowground portion of the plant. This will allow us to extend our research to how REEs affect the benefits from rhizobia, well-established commercial inoculants that fix nitrogen in association with legumes. Our team is actively involved in translating this research out of the laboratory and into agricultural fields. We are currently testing whether it is possible to develop a broad-range inoculant that will stimulate growth in a variety of species, or whether crop-specific inoculants will be required. In the long run, we aim to have highly effective commercial inoculants available for use in agriculture, in addition to being able to recommend ideal REE levels for efficient plant growth promotion. I am particularly excited to work on this project because it combines my intellectual interests with my career goal of using microbiology to improve people’s livelihoods. I am fascinated by the amazing metabolic abilities microbes have developed to survive in and interact with organisms so much larger than themselves. I am driven to discover ways in which humans can utilize microbes to make our world a better place. This technology will have multiple stakeholders and beneficiaries: it will generate employment and economic development in the development and production of inoculants strains, it will benefit growers by increasing yields with relatively low inputs, and it will benefit consumers and society as a whole by increasing agricultural yields in a sustainable manner.

Colleen Friel, United States

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