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Microbial Biotechnology

Microbes (or microorganisms) are organisms that are too small to be seen by the unaided eye. They include bacteria, fungi, protozoa, microalgae, and viruses.

Microbes live in familiar settings such as soil, water, food, and animal intestines, as well as in more extreme settings such as rocks, glaciers, hot springs, and deep-sea vents. The wide variety of microbial habitats reflects an enormous diversity of biochemical and metabolic traits that have arisen by genetic variation and natural selection in microbial populations.

Historically, humans have exploited some of this microbial diversity in the production of fermented foods such as bread, yogurt, and cheese. Some soil microbes release nitrogen that plants need for growth and emit gases that maintain the critical composition of the Earth's atmosphere.

Other microbes challenge the food supply by causing yield-reducing diseases in food-producing plants and animals. In our bodies, different microbes help to digest food, ward off invasive organisms, and engage in skirmishes and pitched battles with the human immune system in the give-and-take of the natural disease process.

A genome is the totality of genetic material in the DNA of a particular organism. Genomes differ greatly in size and sequence across different organisms. Obtaining the complete genome sequence of a microbe provides crucial information about its biology, but it is only the first step toward understanding a microbe's biological capabilities and modifying them, if needed, for agricultural purposes.

Microbial biotechnology, enabled by genome studies, will lead to breakthroughs such as improved vaccines and better disease-diagnostic tools, improved microbial agents for biological control of plant and animal pests, modifications of plant and animal pathogens for reduced virulence, development of new industrial catalysts and fermentation organisms, and development of new microbial agents for bioremediation of soil and water contaminated by agricultural runoff.

Microbial genomics and microbial biotechnology research is critical for advances in food safety, food security, biotechnology, value-added products, human nutrition and functional foods, plant and animal protection, and furthering fundamental research in the agricultural sciences.

CSREES has identified four major related research objectives:

Assure that the complete nucleic acid sequences of high priority beneficial and detrimental agricultural microorganisms are available in public databases.

Assure that the agricultural research community has adequate resources and facilities available for the functional analysis of agricultural microbes (for example, expression array technologies, proteomics, relational databases, and other bioinformatics tools) so that practical benefits are not delayed.

Support training and extension for microbial genomics and its evolving technologies. Foster U.S. interests through national and international public and private partnerships in microbial genomics, and, through such partnerships, facilitate capacity development in the United States and abroad that ensures public access and appropriate use of intellectual property.

Microbial biotechnology has a variety of useful applications in agriculture

Assessing and managing environmental risks from transgenic microorganisms is an important issue for which scientists have developed research needs and priorities.

The mapping of microbial genomes is a key technology to understanding microorganisms and devising ways to improve their use in agricultural production, food safety, and bio-based chemicals. For more, see the Microbial Genomics program page.

Microbial Fermentation

For many years, man has been taking advantage of the activities of millions of microorganisms found in the soil to improve agricultural productivity. With the large scale cultivation of microbes or other single cells, occurring with or without air - known as microbial fermentation -man has used naturally occurring organisms to develop biofertilizers and biopesticides to assist plant growth and control weeds, pests, and diseases, respectively.

Many of the microorganisms that live in the soil actually help plants absorb more nutrients than they would by themselves. Plants and these friendly microbes are involved in "nutrient recycling". The microbes help the plant to "take up" essential energy sources. In return, plants donate their waste byproducts for the microbes to use for food. Because the microbes have helped plants digest more nutrients, plants develop stronger and bigger root systems. The larger the plants' roots, the more living space and food there is for the microbes to enjoy.

Scientists use these friendly microorganisms to develop biofertilizers.


Phosphate and nitrogen are important for plant growth. These compounds exist naturally in the environment but plants have a limited ability to extract them. Phosphate is abundant in the soil but remains mostly bound, and nitrogen is abundant in the air. Phosphate plays an important role in crop stress tolerance, maturity, quality and directly or indirectly, in nitrogen fixation. If phosphate is not quickly used by the plant, it becomes locked into the soil through chemical reactions. This leaves only a small amount of this vital nutrient available to the plant. The plant cannot unlock phosphate by itself.

A fungus called Penicillium bilaii is the roots' key to unlock phosphate from the soil. It makes an organic acid which dissolves the phosphate in the soil so that the roots can use it. A biofertilizer made from this organism is applied either by coating seeds with the fungus (called inoculation), or putting it directly into the ground where the plant's roots will live.

The friendly fungus can wrap itself around the root, and prevent other less helpful organisms from living there. It has the first chance to use the plant's byproducts. This will make the microbe stronger, and able to convert more phosphate for the roots to use. With additional phosphate, the plants will be stronger and more productive.

Another example of an organism that is used to make biofertilizers is the bacterium Rhizobium. This bacterium lives on the plant's roots in cell collections called nodules. The nodules are biological factories that can take nitrogen out of the air and convert it into an organic form that the plant can use. Because the bacteria live within the roots, it transfers the nutrient directly into the plant.

This fertilization method has been designed by nature. With a large population of the friendly bacteria on its roots, the legume can use naturally-occurring nitrogen instead of the expensive traditional nitrogen fertilizer.

Biofertilizers help plants use all of the food available in the soil and air thus allowing farmers to reduce the amount of chemical fertilizers they use. This helps preserve the environment for the generations to come.

NitroPlus, Bio-N and BIO-Fix are some Philippine examples of bio fertilizers that utilize the ability of microorganisms like rhizobia to fix free nitrogen. Other products like Mycogroe and Mykovam help plants absorb water and phosphorus from the soil. The mycorrhizal fungi that colonizes the roots of plants prevent further infections by pathogens and make plants more tolerant to drought and heavy metals. BIO-Quick, a composting inoculum, helps hasten the decomposition of farm and agro-industrial wastes by as much as 80%.


As we all know, there are also microorganisms found in the soil that are not so friendly to plants. These pathogens can cause extreme disease or damage to the plant. As with friendly microorganisms, scientists have developed biological "tools" which use these disease-causing microbes to control weeds and pests naturally.


Weeds are a constant problem for farmers. They not only compete with crops for water, nutrients, sunlight, and space but also harbor insect and disease pests; clog irrigation and drainage systems; undermine crop quality; and deposit weed seeds into crop harvests. If left uncontrolled, weeds can reduce crop yields significantly.

Farmers fight weeds with tillage, hand weeding, synthetic herbicides, or typically a combination of all techniques. Unfortunately, tillage leaves valuable topsoil exposed to wind and water erosion, a serious long-term consequence for the environment. For this reason, more and more farmers prefer reduced or no-till methods of farming.

Similarly, many have argued that the heavy use of synthetic herbicides has led to groundwater contaminations, death of several wildlife species and has also been attributed to various human and animal illnesses.

The use of bioherbicides is another way of controlling weeds without environmental hazards posed by synthetic herbicides. Bioherbicides are made up of microorganisms (e.g. bacteria, viruses, fungi) and certain insects (e.g. parasitic wasps, painted lady butterfly) that can target very specific weeds. The microbes possess invasive genes that can attack the defense genes of the weeds, thereby killing it.

The better understanding of the genes of both microorganisms and plants has allowed scientists to isolate microbes (pathogens) whose genes match particular weeds and are effective in causing a fatal disease in those weeds. Bioherbicides deliver more of these pathogens to the fields. They are sent when the weeds are most susceptible to illness.

The genes of disease-causing pathogens are very specific. The microbe's genes give it particular techniques to overcome the unique defenses of one type of plant. They instruct the microbe to attack only the one plant species it can successfully infect. The invasion genes of the pathogen have to match the defense genes of the plant. Then the microbe knows it can successfully begin its attack on this one particular type of plant. The matching gene requirement means that a pathogen is harmless to all plants except the one weed identified by the microbe's genetic code.

This selective response makes bioherbicides very useful because they kill only certain weed plants that interfere with crop productivity without damaging the crop itself. Bioherbicides can target one weed and leave the rest of the environment unharmed.

The benefit of using bioherbicides is that it can survive in the environment long enough for the next growing season where there will be more weeds to infect. It is cheaper compared to synthetic pesticides thus could essentially reduce farming expenses if managed properly. It is not harmful to the environment compared to conventional herbicides and will not affect non-target organisms.

With the advances of genetic engineering, new generation bioherbicides are being developed that are more effective against weeds. Microorganisms are designed to effectively overcome the weed's defenses. Weeds have a waxy outer tissue coating the leaves that microorganisms have to penetrate in order to fully infect the weeds. Through biotechnology, these microorganisms will be able to produce the appropriate type and amount of enzymes to cut through the outer defenses. Streamlining of the microbe's plant host specificity will ensure that the weeds are taken out and not the crops. On the other hand, microbes can also be made to be effective against several host weeds and not only to one type of weed as this can be too expensive to produce for commercial use.


The science of biotechnology can also help in developing alternative controls to synthetic insecticides to fight against insect pests. Research has found microorganisms in the soil that will attack fungi, viruses or bacteria which cause root diseases. Formulas for coatings on the seed (inoculants) which carry these beneficial organisms can be developed to protect the plant during the critical seedling stage.

While synthetic pesticides are an invaluable tool for agricultural productivity, some of them also have their drawbacks: they are expensive, they are often not foolproof; they can accumulate in our environment and pollute our water systems; and they are not species specific as they can also kill non-target organisms.

Bioinsecticides, on the other hand, do not persist long in the environment and have shorter shelf lives; they are effective in small quantities, safer to humans and animals compared to synthetic insecticides; they are very specific, often affecting only a single species of insect and have a very specific mode of action; slow in action and the timing of their application is relatively critical.

Some of these characteristics however, are seen by critics as a disadvantage. For example, because most of these bioinsecticide agents are living organisms, their success is affected by several factors like temperature, pH, moisture, UV, soil conditions, and other microbial competitors present in the environment. Slow in action means much longer time for it to eradicate pathogens compared to synthetic pesticides.

Fungi-based bioinsecticides

Fungi that cause disease in some 200 different insects are gaining prominence as bioinsecticides. One of the earliest to be discovered in the 1880s is Beauveria bassiana (Bb), a fungus found worldwide in soils and plants. Another half a dozen fungi are also known to have characteristics valuable for insect control. In China, over two million hectares are sprayed with Bb annually to control forestry pests. Since 1993, six new fungal bioinsecticides have become available in North America and Europe.

Inexpensive fermentation technology is used to mass produce fungi. Spores are harvested and packaged so they can be applied to insect-ridden fields. When the spores are applied, they use enzymes to break through the outer surface of the insects' bodies. Once inside, they begin to grow and eventually cause death.

Bioinsecticides based on Bb have many advantages. The fungus does not grow in warm-blooded organisms (such as people), nor does it survive long in water reservoirs or rivers. However, its spores can withstand long periods of dryness and other harsh environmental conditions. Studies to date have shown that the fungus also does not hurt plants and becomes inactivated by the sun's ultraviolet rays in one to eight weeks.

Fungal agents are viewed by some researchers as having the best potential for long-term insect control. This is because these bioinsecticides attack in a variety of ways at once, making it very difficult for insects to develop resistance.

Virus-Based Bioinsecticides

A group of virus-based insecticides that scientists are testing are the rod-shaped baculoviruses. Baculoviruses affect insect pests like corn borers, potato beetles, flea beetles and aphids. One particular strain is being used as a control agent for bertha army worms, which attack canola, flax, and vegetable crops. During the worst years of the infestation in the early 1980's in Canada, they cleaned out over one million hectares of prairie crops. In the past, farmers used chemical insecticides to control these pests. But Bertha army worms attack crops while in the larval (caterpillar) stage. Traditional insecticides do not affect the worm until after it has reached this stage and by then much of the damage has been done.

Source: http://www.csrees.usda.gov/nea/biotech/in_focus/biotechnology_if_microbial.html

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