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Microbes for Sustainable Agriculture

We need to revisit the potential of microbes to help us sustain humanity
by Dr. Samina Mehnaz

In 2016, when the United Nations established Sustainable Development Goals (SDGs), a key objective was to focus on attaining environmental, social, and economic growth through green and clear production techniques. The goals were established keeping in mind the fact that, despite global advances in technology, a significant portion of the human population continues to be denied basic necessities such as food, clothes, and healthcare.  In view of the SDG goals, it would not be wrong to say that scientists worldwide are working on solving the problems facing humankind in these testing times.

As a researcher, my work focuses on microbial ecology. I study microbes, tiny organisms that cannot be seen without a microscope. These organisms exist everywhere in nature, including soil and plants. If we go back to the inception of human life, microbes were vital to the maintenance of life on earth and, given the current environment in which researchers globally are attempting to  find better alternatives to the use of chemicals in agricultural farming, perhaps microbes have the answer, after all. We, therefore, need to revisit the potential of microbes to help us sustain humanity.

Plants need nitrogen, phosphorus, potassium, and zinc for healthy growth. When the soil is deficient in these nutrients, crops do not reach their full potential and grain and fruit production decreases. In the 1960s, as technology transfer initiatives gained momentum, this deficiency was addressed by the Green Revolution. The introduction of high-yielding varieties of seeds and better management practices resulted in high-productivity crops, controlled plant diseases through the use of pesticides, and fulfilled the nutrient deficiencies of soil through the use of fertilizers.

Functions of plant growth-promoting rhizobacteria

However, for the last two decades, it has become increasingly obvious that excessive use of chemicals is responsible for environmental insecurity, since this practice requires the use of non-sustainable agricultural methods. It also has a negative impact on soil fertility, ground water, the atmosphere, and human health. Fertilizers have ingredients which penetrate the soil and contaminate groundwater. Some ingredients stay in the soil but are unavailable to the plants, making soil infertile. Others convert into gas and escape, contaminating the air.

Take the example of pesticides. Pesticides are applied to shoots, leaves, flowers, fruits and grains, mostly in the form of sprays. In the process, some particles mix with the air, some fall on the soil, and some penetrate fruit and grains, causing harm to the environment as well as to the humans who consume the crops.

We know the problems caused by these chemicals but what can be done about it? One solution is to go back to organic farming—a technique that avoids the use of synthetic substances–but, realistically, it cannot provide food to seven billion people. Another way around is to minimize the use of these chemicals by introducing bioformulations.

Bacteria, fungi and protozoa have the ability to serve as fertilizers and pesticides. Formulations containing these organisms–known as bioformulations–can reduce the use of agro-chemicals, increase soil fertility, improve crop production in saline and water-deficient areas, and protect plants from diseases and pest attacks. Bioformulations are cost-effective, as well as harmless to farmers, consumers, and the environment.

Bioformulations contain living microorganisms that have been suspended in liquid or mixed with some other material in which they can survive, allowing farmers to easily apply them to crops. These bioformulations can be divided into two categories, biofertilizers and biopesticides.

Biofertilizers have the ability to promote plant growth in a natural way. They contain beneficial bacteria (known as plant growth-promoting rhizobacteria, i.e. PGPR), fungi, or single cell organisms (known as protozoa), living naturally in close association with plants.These microorganisms can be found in the soil around the roots as well as inside the roots, stem, and the leaves of plants.

Pure culture of Pseudomonas aurantiaca

PGPRs take nitrogen from the air, convert it into ammonium and provide it to the plant to fulfill their nitrogen requirements, in much the same manner as nitrogen fertilizers (urea, ammonium nitrate, etc.). Interestingly, PGPRs only do this when the soil is deficient in nitrogen. If enough nitrogen is available, they switch off their mechanism.

PGPRs and fungi help to break down insoluble phosphorus present in soil that would otherwise not be available to the plants. This is done by producing certain acids and enzymes to dissolve insoluble compounds and convert them into a form which can be absorbed by the roots. This process helps to reduce the amount of phosphorus fertilizers required by the plants as well as to improve soil fertility.

On the other hand, biopesticides use living microorganisms or chemicals naturally produced by plants to protect them without harming the environment. Microbes produce a variety of natural chemicals, known as metabolites, and release them outside. These chemicals employ various mechanisms to protect the plants by killing insects and harmful pathogens, such as fungi and bacteria. Some metabolites boost plants’ immune systems by stimulating the production of jasmonic and salicylic acid, which play a role in a plant’s defense system and enable survival under stress.

Microbes can also also help us fight problems such as water stress and salinity, which adversely affect agriculture in several ways, including through the reduction of crop productivity. One approach to handle this problem is to develop salt-tolerant and drought-resistant plants. At present, researchers are attempting to develop new crop varieties and improve existing ones to tackle this issue. However, this is a time-consuming process and it will be a long while before these new varieties emerge.

Another option could be to use microbes from drought- and salt-tolerant plants. Microbes living in close proximity to such plants as para and kallar grass that grow in saline areas have the ability to survive well in saline lands and can also contribute to the reclamation of the soil. Similarly, plants such as the cactus, which grow under water stress, have microbes around their roots that help them to survive drought. These microbes can then be used to develop formulations that can improve the soil condition and crop productivity in saline and water-deficient soils.

An ideal bioformulation will contain microbes that can serve as biofertilizers as well as biopesticides. In 2006, after coming back from Canada, I started working on such bioformulations. My team and I isolated PGPRs from sugarcane and we were able to find a bacterium which showed aggressive antifungal activity against more than 40 fungal pathogens, while at the same time increasing zinc and potassium solubility and promoting phytohormone production. Eventually, in 2012, with the help of a group established at Forman Christian College University, Lahore, we discovered a further eight bacterial candidates for biopesticides.

All of these were identified as Pseudomonas chlororaphis subsp. aurantiaca, a well-known PGPR that can simultaneously act as a biofertilizer as well as a biopesticide. It promotes plant growth through phytohormone production and improves the solubility of zinc and potassium. At the same time, it also acts as a biopesticide by producing a large number of metabolites, including phenazines, HCN, siderophores, bacteriocins and lahorenoic acids, that kill pathogenic fungi, bacteria and worms.  Our group has used it as a PGPR for corn, wheat, and tomato.

After completion of lab experiments at our institute, we handed over these strains to our collaborators at Yediteppe University Istanbul, Turkey, for further research and commercialization. At present, multiple international companies are selling bioformulations based on this single organism. Two examples are Cedomon by BioAgriAB, Italy, and Howler by AgBiome Innovations, USA. Other universities, such as University of Hertfordshire, UK and Universidad Nacional de Rio Cuardo, Argentina, are also developing bioformulations based on Pseudomonas aurantiaca.

One may ask that if these microbes are naturally present in plants’ environments, why do we need such bioformulations, or even fertilizers? To answer this question, we need to look at the formulation of soil. Each kind of soil contains both good and bad microbes, whose population is controlled by many factors, including nutrients, weather, and water availability. Bioformulations contain a large population of plant-beneficial microbes which, when applied to the soil, start multiplying. When a plant is surrounded by a large number of beneficial microbes, it has more nutrients and hormones available to it, resulting in an improved immune system. Thus, microbes can be considered probiotics for the plants and soil.

The use of bioformulations is not a new idea; researchers have been working on it for over a century. In the USA alone, bioformulations based on Rhizobium (bacteria) have long been used for legume plants (such as chickpeas, peas, and lentils). Then, why did it take so long to introduce this concept globally? One major reason was lack of public awareness about the hazards of agricultural chemicals. Another was the consistent and quick results of fertilizers and pesticides, which are not possible with bioformulations, due to which farmers could not be convinced to adopt the alternative.

Over time, researchers continued to improve bioformulations by using various combinations of microorganisms, making them multipurpose (nitrogen, phosphorus, potassium, zinc), better carrier materials to increase shelf life, allowing different methods of application (on seeds, in the soil, or on the plants), and making them available in both liquid and powder forms. As a result, commercial bioformulations are far better than those that were available a decade ago, giving farmers several options to choose from.

Pseudomonas aurantiaca reduces fungal growth

Another benefit of bioformulations is that they have the potential to greatly boost the economies of developing countries. Many of these countries currently import expensive fertilizers to meet their needs. Due to the high cost, most farmers apply nitrogen and phosphorus fertilizers and skip the potassium and zinc ones. Bioformulations allow plants to get all the required nutrients at a much lower cost.

Campaigns by environmentalists have served to increase public awareness about the hazardous effects of chemical fertilizers and pesticides, helping to boost global demand for bioformulations. In 2018, the size of the global biofertilizer market stood at USD 1.57 billion and a compound annual growth rate of 10.1% is expected between 2020-2025.

The future of sustainable agriculture lies with minimum use of chemical fertilizers and pesticides, and the maximum use of bioformulations in conjunction with organic farming. To feed the world and keep the environment safe through the use of sustainable agriculture, none of these can be used in isolation. It goes without saying that microbes can contribute to achieving all 17 of the UN’s Sustainable Development Goals. The products and processes associated with microbes also have immense potential to reduce the harm to the environment, while simultaneously creating opportunities for economic and social growth. To ensure cost-effective production as well as a sustainable ecosystem, one must look towards creating global partnerships that can harness the full potential of microbes for sustainable development.

Dr. Samina Mehnaz is a professor at School of Life Sciences at Forman Christian College University, Lahore.

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