Friday, 13 January 2017 13:11

Peanuts and Probiotics

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Published in Microbial Sciences

peanutsFigure 1. peanuts. Source

The world has a problem: an exploding human population, which will require crop yields to double by 2050 without increasing crop acreage. Solving this problem will necessitate help from some of the smallest members of Earth’s population using a concept that has both George Washington Carver and cutting edge startups in common.

Carver was a faculty member at the Tuskegee Institute in the early 1900s and reintroduced the concept of crop rotation with peanuts, soy, and other legumes to U.S. agriculture. By alternating corn and cotton crops with peanuts, farmers replenished the nutrients in the soil but continued harvesting a cash crop.

Legumes are an intriguing type of plant since they rely on bacteria, (e.g., Rhizobia) that grow in specialized nodules on their roots to provide them with nutrients, like nitrogen. In return, the plants supply the bacteria with sugars and oxygen for growth, a symbiotic exchange for nutrients the legumes cannot produce themselves. Most plants, however, rely on bacteria not in attached root nodules, but in their rhizospheres.

The rhizosphere, the soil around a plant’s roots, is packed with microbes like bacteria and fungi. In fact, there can be 100 billion microbial cells, the number of stars in the Milky Way galaxy, all packed into a teaspoon of rhizosphere dirt. And just as certain kinds of gut microbes benefit human health, certain kinds of bacteria (and fungi) in the rhizosphere benefit plant health.

Supplementing crops with beneficial bacteria every planting season is a growing industry (Indigo received $56 million in startup funding last year) and these “plant probiotics” are the foundation of biofertilizers — a mixture of fertilizer and bacteria helpful for plant growth.

Biofertilizer use is increasingly popular in agriculture, particularly organic farming, as it is less expensive, causes less pollution than industrial fertilizers, and makes industrial fertilizers more effective. Many different crops — including rice, coffee, rubber, and coconuts — can benefit from plant probiotics. The microbes contained in these biofertilizers benefit plant growth and increases crop yield by helping plants access important nutrients, encouraging root growth, and protecting plants from pathogens.

Helping plant nutrition

Like legumes, most plants have trouble acquiring certain nutrients from the soil, even when directly applied in fertilizer. Plants can only take up 10-40% of the minerals and nutrients in fertilizer on their own, so rainwater frequently washes away the remaining nutrients and minerals before plants can absorb them. If a mixture of fertilizer and plant probiotics is given to plants, however, they receive the same health benefits from lower nutrient or mineral concentrations.

Figure 2. Tomato speck--a plant disease caused by a serovar of Pseudomonas syringae. Source

The microbes in biofertilizers confer these benefits because they have a number of nutrient-gathering tricks up their sleeves. Plants need to absorb nitrite and nitrate from the soil to help build proteins and replicate DNA. Some bacteria convert, or fix, atmospheric nitrogen to forms that a plant can use. By adding nitrogen-fixing bacteria in a biofertilizer, farmers both use less fertilizer and populate the soil with probiotics for future crops. Like nitrogen, phosphorus is difficult for plants to access. Required for DNA and RNA synthesis, phosphorus cannot be accessed by plants without a slightly acidic soil pH. Some inhabitants of the rhizosphere (like the fungi mycorrhiza) can help lower the pH, thus solubilizing phosphorus and making it easier for the plant roots to absorb. These are only two examples of many; some rhizosphere bacteria even help plants access more complex compounds like vitamins.

Enhancing plant root growth

In order for a plant to gather nutrients like nitrogen, phosphorus, and even water, it needs extensive, healthy roots. This is where plant growth-promoting rhizobacteria (PGPR) come in handy by encouraging plants to invest in strong root systems. PGPRs secrete chemicals that mimic plant hormones or stimulate seeds to germinate and grow. In both cases, plants respond by making more roots or increasing the number of root hairs on each root. This increases the surface area for plants to access water and nutrients, and (most importantly to the microbe) provide more sugar for the helpful microbes. Consider two radishes: one, “a,” was grown with the PGPR Pseudomonas corrugata but the second radish, “b,” was not. Over a 17-day period, the PGPR enabled radish “a” to take up more nutrients resulting in a budding radish and a stronger root system that looks healthier and more developed than radish “b.”

Protection from plant pathogens

Another way plant probiotics help plants is by stopping phytopathogens — microbes that attack and damage plants like the fungi that cause tomato blights. In addition to sugars, plants secrete chemicals like amino acids, fatty acids, and vitamins that promote bacterial growth — probiotics and pathogens alike. Probiotics prevent phytopathogen infections by staking claim to the resources provided by the plant and secreting chemicals to inhibit or kill competing microbes. Some species of Bacillus (a genus of bacteria often found in the rhizosphere) can produce antibiotics to help control phytopathogens. B. thuringiensis prevents the phytopathogen Erwinia carotovora from degrading plant cell walls by producing an enzyme that interrupts E. carotovora’s chemical communication. Plant probiotics can also activate the plant’s immune response to make the plant better able to fight off invaders. In one example, simply by virtue of its presence in the carnation rhizosphere a particular strain of Pseudomonas prevents Fusarium wilt.

Improving biofertilizers

While research and experience have revealed much about plant probiotics, a lot of progress is still left to be made. For instance, many available biofertilizers don’t work well in mountainous regions, partially because the probiotic bacteria they contain grow poorly at the colder temperatures associated with higher elevations. To help address this need, researchers isolated bacteria from glaciers(!), looking for new PGRPs that could stand the cold. The authors found several bacteria that could grow in a range of low temperatures from 4°C (your refrigerator’s temperature) to 30°C (about the temperature of a climate-controlled room) plus perform important probiotic activities like solubilize phosphorous, enhance root growth, and block phytopathogens. They hope these bacteria can be used to generate “cold-active biofertilizers” as an environmentally friendly option for agriculture.

A similar concept is already hitting the U.S. agricultural market place. Last year, Indigo tested cotton seeds coated in select microbes and this week released data indicating an average yield improvement of 11% over conventionally grown cotton, despite water shortages. According to Indigo CEO David Perry, “The plant microbiome… evolved with the plant over millions of years until modern technology has sort of systematically but unconditionally decimated them.” Like the double-edge sword of antibiotics on the gut microbiome, they were “tremendous breakthroughs… but they also had unintended negative consequences”.  

Using biofertilizers to improve crop health and yield is an exciting idea. But there are many unanswered questions before biofertilizers reach their full potential, particularly regarding the factors involved in plant/biofertilizer interactions. What types of soil and environments are optimal for a given probiotic? Which crops will they benefit the most? Are there certain combinations of probiotics that yield more, or less, effective biofertilizers? Perhaps rice and wheat have different probiotic needs. What are the components of a naturally protective soil? Are there ethical considerations to biofertilizer use? The list goes on.

George Washington Carver’s insight about legumes gave us some of the first agricultural techniques to harness the power of microbes. But that was only the beginning; there’s much more to learn about designing effective biofertilizers, and their promise for both increasing crop yields and decreasing fertilizer pollution is one worth digging into.

*Post adapted with permission from

Last modified on Friday, 13 January 2017 16:42
Ada Hagan

Senior Contributor Dr. Ada Hagan is an ASM Journals Fellow working with the ASM Journals Chair Dr. Pat Schloss in the Department of Microbiology and Immunology at the University of Michigan. Her post-doctoral research analyzing scientific publishing in the field of microbiology. Ada's graduate research at UM focused on the methods that the bacterial pathogen Bacillus anthracis uses to gather iron during infections. Ada is also an advocate for science communication by scientists. She was a co-founder of the graduate student science writing blog You can find more on her projects on LinkedIn and by following her on Twitter (@adahagan).