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Economic Importance of Bacteria | Microbiology

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In this article we will discuss about the beneficial and harmful activities of bacteria.

A. Beneficial Activities of Bacteria:

There are many kinds of bacteria without which we could not live. They are absolutely essential to the presence of life on earth. They make possible the continued existence of green plants and therefore of animals because the plants are the only source of food for animals.

Following is a brief account of the more important activities of the bacteria:

1. Role in Agriculture:

(i) Decay and decomposition:

Soil bacteria play an important role in brining about decomposition of organic matter. They serve a double purpose. In the first instance they act as scavengers removing harmful waste from the earth.

Secondly, they return it to the soil as plant food. The dead bodies and wastes of organisms (both plants and animals) are decomposed by the activities of the saprophytic bacteria.

In consequence a variety of elements of minerals of the earth such as carbon, oxygen, hydrogen, sulphur and phosphorus which make up their bodies are reduced to simple compounds such as carbon monoxide, water, nitrates, sulphates and phosphates.

Some of these go back to the soil and the rest to the air. From the soil they can be absorbed as plant food. This activity of the bacteria is used in sewage disposal system of cities. The bacterial action on the city’s sewage promotes decay.

As a result water is finally purified and changed into an odourless and valuable fertiliser instead of a dangerous and expensive waste product.

(ii) Soil fertility:

Some bacteria play an important role in maintaining and others in increasing soil fertility. The fertility of soil is proportional to its nitrogen content. Nitrogen is an essential ingredient of all living protoplasm. All growing plants, therefore, require it in their metabolism.

Atmosphere, no doubt, is four-fifths (80%) nitrogen, green plants generally are unable to use it. They mostly absorb it as nitrates and to some extent as ammonia from the soil.

Continuous absorption of these salts results in their exhaustion in the soil. Nearly all fertilisers for the soil include a large proportion of such soluble nitrogen compounds to promote plant growth.

In nature the presence of a regular supply of these salts is ensured by bacteria of certain types. These bacteria which function as Nature’s farmers belong to three categories, namely, ammonifying bacteria, nitrifying bacteria and nitrogen-fixing bacteria.

They are the agents of maintaining a continual circulation of nitrogen in nature between the plant world, in soil and the atmosphere. The series of changes through which the nitrogen passes due to the activities of these organisms constitute the nitrogen cycle (Fig. 18.18).

Nitrosomonas oxidizes ammonium carbonate to nitrous acid liberating energy. The nitrous acid then combines with bases in the soil forming potassium nitrite. Nitrobacter oxidizes nitrites to nitrates again liberating energy.

Neither the ammonifying nor the nitrifying bacteria add to the total quantity of combined nitrogen in the soil. The ammonifying bacteria convert amino acids into ammonia. The process is called ammonification.

The nitrifying bacteria convert nitrogen from the unavailable form of ammonium salts to the available nitrates. This process converting unavailable ammonium salts into available nitrates is called nitrification.

(c) Nitrogen-fixing Bacteria:

A considerable amount of nitrogen is lost by denitrification and through drainage. The loss must be made good by equal gains if the soil fertility is to be maintained.

The electric discharges in the atmosphere bring about the formation of traces of nitrogen compounds which are washed to the soil by rain water. The largest additions, however, come from a biological fixation process through the activity of two types of nitrogen-fixing bacteria.

Some of them live free in the soil and others in the root nodules of leguminous plants. They are able to make use of the atmospheric nitrogen and change it into nitrogenous compounds.

The nitrogen-fixing bacteria are thus unique in tapping a source of nitrogen not available to most other plants. This process of nitrogen transformation is called nitrogen fixation.

(i) Azotohacter heijerinckia (aerobic forms) and Clostridium (anaerobic) live free in the soil:

They take gaseous nitrogen from the air present between the soil particles. The nitrogen combines with other elements forming organic nitrogenous compounds. These compounds are assimilated by the bacteria.

In due course these bacteria die and their dead bodies containing nitrogenous compounds are decomposed by another type of bacteria called the bacteria of decomposition. During decomposition ammonia is produced.

The nitrifying bacteria convert this ammonia first into nitrites and finally into nitrates. Nitrates constitute the form of nitrogen needed by the green plants.

(ii) Rhizobium leguminosarum (syn. Bacillus radicicola) is another nitrogen-fixing bacterium:

It lives in the roots of such plants as Pea (Fig. 18.19A), Bean, Medicago and others. All these belong to the Pea family (Leguminoseae). Besides the legumes, the nodules are found on the roots of Alnus glutinosa, Casuarina, species of Coriaria and a few others.

The symbiont in non- leguminous plants is a member of Plasmodiophorales. The presence of bacteria in the roots causes the formation of little nodules (Fig. 18.19A). In Pavetta indica the bacterial nodules are formed on the leaves.

These nodules or the tubercles are the homes of millions of these bacteria. They have the ability to take up free nitrogen of the air and convert it into nitrogen compounds.

A part of the fixed nitrogen passes into the tissues of legume plant and a part diffuses into the surrounding soil. These bacteria enter into a mutually beneficial partnership with the host plant.

They give to the host the nitrogen compounds and receive in return carbohydrates manufactured by the host plant. This association is an excellent example of symbiosis. The legumes are very rich in nitrogen because of this association.

Some of our best protein plant foods come from the legume family of plants. The legume plants can flourish on land that has been depleted of its nitrogen by other plants. They are sometimes grown and ploughed under by the farmer when a foot or so in height.

The decaying bodies of these legume plants enrich the soil. They furnish a rich supply of nitrogen to the future crop. This is called green manuring. The soil on which repeated crops of cereals are grown becomes impoverished.

It can be enriched again by growing on it a crop of some plants of Pea family. This practice of alternating cereals with leguminous crop is known as rotation of crops. The leguminous plants contain more of nitrogen than they get from the soil salts.

The additional quantity is obtained from the air by Rhizobium. Neither Rhizobium nor the legume root alone can fix nitrogen.

Rhizobium lives in the soil where it has the form of coccus. The legume roots secrete substances which attract bacteria on to their surface. The bacteria, in turn, secrete a growth hormone which causes the root hairs to curl.

The cocci enter the curled root hairs. They grow in the root hair in the form of a continuous thread-like mass which finally reaches the root cortex. In this way many of the cortical cells become filled with a dense mass of these bacteroids.

Their presence in the cortical cell serves as a stimulus causing abnormal growth. The cortical cells around the infection divide and redivide and grow to form a nodule. A nodule comprises a central mass of cells full of bacteroids.

Around this zone of infection are a few cell layers thick of bacterial free cortical zone. At the apex of the nodule is the meristematic region and a vascular strand at its base (Fig. 18.19 B).

Within the host cells the cocci feed on the carbohydrates and other foods and undergo a change in their form (Fig. 18.19 C). They become V, T or Y shaped. The core of the nodule is red owing to the formation of red respiratory pigment haemoglobin.

2. Role of Bacteria in Industries:

Man has utilised the activities of bacteria for various industrial processes. The butter and cheese industries entirely depend upon the activities of the lactic acid bacteria.

The souring and curding of milk by lactic acid bacteria is another common example of application in everyday life. It takes place in two steps. In the first step the lactose sugar of milk is fermented into glucose by an enzyme lactose secreted by the lactic acid bacteria.

In the second step there is transformation of glucose into lactic acid. The latter sours the milk and coagulates the milk proteins (casein) forming curds and whey. Oxidation of alcohol into vinegar (acetic acid) is brought about by the acetic acid bacteria.

The curing of tea, tobacco and manufacture of indigo are other examples of useful chemical activities of bacteria which have been controlled for the benefit of mankind. The process of tanning hides in leather making and preparing sponges also involve the use of bacteria.

The production of linen is impossible without bacterial activity. The tough fibres, which are left behind, are separated. These fibres are spun and woven into linen cloth, ropes, etc.

The preparation of coffee and cocoa is also dependent upon bacterial action. The cocoa beans are white in colour and quite bitter in taste. The bacteria digest the bitter coverings of seeds and give the characteristic colour, flavour and aroma.

Many saprophytic bacteria in their metabolic activities excrete waste products of great commercial importance.

Some of these are:

(i) Lactic acid:

It is useful in tanning industries.

(ii) Citric acid:

It is used to give aroma and flavour to beverages, sweets and other foodstuffs.

(iii) Vitamins:

Vitamin B is the product of fermentation of sugars and starch by Clostridium acetobutilicum. The vitamins are used in medicinal preparations.

(iv) Butyl alcohol:

Butyl alcohol, acetone and ethyl alcohol are produced in one fermentation operation when a certain bacterium is allowed to act on cooked com starch. These products are important commercial solvents.

(v) Acetone:

It is an important ingredient of explosives and is also used in the manufacture of photographic films.

3. Role of Bacteria in Medicine:

1. Source of Antibiotics:

The milder antibiotics of bacterial origin are tyrothricin, subtilin, polymyxin B, and bacitracin. Bacillius subtilis is the source of subtilin. Bacitracin is obtained from a stain very much like B. subtilis.

The actionomycetes which are filamentous, bacteria-like organisms produce more powerful antibiotics such as streptomycin, aureomycin and terramycin.

2. Preparation of Serums and Vaccines:

These are substances which are used to develop immunity to various diseases in man. Serums are used in advance as a therapeutic measure. They are also used when a person actually suffers from a disease.

Diphtheria, lockjaw, pneumonia, etc. are the diseases in which the serums are effective. Vaccines are commonly used to make people immune to diseases like typhoid, small-pox, cholera, scarlet fever, etc.

In the preparation of serums, small doses of bacterial toxins (poisons) are injected into the blood of animals such as horses. To combat or neutralize the bacterial poisons, the body of the animal produces antibodies.

The blood of the animal is then withdrawn. Impurities such as blood corpuscles and other solid matter are removed from the blood. The clear blood liquid containing the antibodies is the serum. It is used as weapon to combat diseases caused by these bacteria.

To produce vaccines dead or weakened disease producing bacteria or their diluted poisons (antigens) are directly injected into a man to cause a disease in a mild form. As a reaction the host is stimulated to form antibodies.

The latter may remain for years in the body of the host imparting immunity against the same type of bacteria which may later enter his body.

This is an incomplete account of the beneficial activities of bacteria. Anyhow it indicated their extreme importance in everyday life. Because of these beneficial activities the bacteria are called the friends of mankind.

B. Harmful Activities of Bacteria:

1. food poisoning:.

Of course, all activities of bacteria are not beneficial. Some saprophytic bacteria cause decay of our food and make it unpalatable. The activities of certain bacteria produce powerful toxins such as ptomains in the food.

These toxins are powerful enough to cause food poisoning which results in serious illness and even death. Some species of Staphylococcus are the common offenders.

There is another dangerous food poisoning bacterium known as Clostridium botulinium. It causes botulism—a fatal form of food-poisoning.

2. Disease:

Many parasitic bacteria are the causative agents of bacterial diseases. They cause diseases of our economic plants, domesticated animals and man. T.J. Burrill in 1878 first gave the information that bacteria cause plant diseases.

There are more than 170 species of bacteria which cause plant diseases. Usually they are rod-like and non-spore forming. Many of them have flagella.

The bacteria gain entry into the host through wounds or natural openings such as stomata, lenticels, hydathodes or through the thin epidermis.

The bacterial diseases of plants belong to the following categories:

(i) Wilt diseases caused by blocking of the vessels of host plant by masses of bacteria. The common example of this category are the wilt diseases of potato, cucumber, water melon and eggplant.

(ii) Crown gall and Hairy root diseases. These are due to overgrowth or hyperplasia. The crown gall of beets and hairy root of apple are the examples.

(iii) Narcotic blights, leaf spots and rots caused by killing of parenchyma cells. Fire blight of apple, and pear and soft rot of carrot and turnip are the common examples. The following Table 3 gives a list of some important disease-causing bacteria, host plants and diseases.

3. Denitrification:

There are, sometimes, a group of bacteria in the soil which reverse the nitrifying process. They injure the soil by causing the loss of a part of its combined nitrogen.

This they do by breaking down nitrates into nitrites and nitrites into ammonia compounds or to free nitrogen.

NO 3 → NO 2 → NH 3 → N gas ↑

The free nitrogen passes into the atmosphere and is lost to the soil. The result is the lowering of soil fertility. This process is called denitrification. The bacteria which bring about denitrification are called the denitrifying bacteria.

They are most active in the soil containing excess of nitrogen compounds such as the heavily manured soils. Soils deficient in oxygen are also favourable for the activity of this type of bacteria.

Denitrification is checked if the soil is well aerated by ploughing or digging and well drained. It is uneconomic to use natural and artificial nitrate manures simultaneously.

The denitrifying bacteria found in the faeces contained in the manures tend to destroy the nitrates.

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Economic Importance of Bacteria: Beneficial Uses & Functions

Economic Importance of Bacteria: The human relationship with bacteria is quite fascinating. Many bacteria are considered to be hazardous. A specific type of bacteria causes diseases like typhoid, cholera, diphtheria, pneumonia, and numerous infections in open wounds. However, life on Earth would be impossible without the work of some species of bacteria. Certain bacteria are cultivated by humans since they are required for biological processes. Bacteria are one of the most common life forms on the planet. They are also among the tiniest of all living creatures.

The Economic Importance of Bacteria comes from the fact that bacteria may be used by humans in a variety of useful ways. Despite the fact that some bacteria cells play harmful roles, such as causing disease and spoiling food, the economic importance of bacteria includes both their useful and harmful aspects. This article will study more about the Economic Importance of Bacteria and their roles.

What are Bacteria Cells?

Bacteria are the members of a large group of unicellular microorganisms which may have cell walls but lack organelles and an organized nucleus, including some that can cause disease. Bacteria (singular bacterium) are the members of the kingdom Monera, the only prokaryotic kingdom. They comprise a large domain of prokaryotic microorganisms. They may be saprophytes, deriving their food from dead and decaying matter, or parasites, living on or inside the body of other organisms. Some of them also have an autotrophic mode of nutrition. Some forms, like  Nostoc , contain chlorophyll.

Fig: Bacteria

Are Bacteria Plants or Animals?

Bacteria are prokaryotic. They do not have a true nucleus and no membrane-bound organelles. Scientists have never entirely agreed on how to classify bacteria. They show heterotrophic nutrition like animals, and some have autotrophic nutrition, like plants. But they cannot be grouped in either of these groups. They are neither plants nor animals.

What is the Economic Importance of Bacteria?

Bacteria have widespread economic importance as they are used in various processes, as discussed below. The Economic Importance of Bacteria examples will help understand the significance of bacteria.

1. Dairy products

Quite a few genera of bacteria are used in food preparation, directly or indirectly.

a.  Formation of Curd:  Milk is converted into curd by bacterial action. The milk’s lactose is converted into lactic acid, which gives the characteristic sour taste of the curd. Lactic acid bacteria (LAB) like  Lactobacillus  are added to milk. Indian curd is prepared by inoculating milk with  Lactobacillus acidophilus .

b.  Yoghurt preparation:  It is produced by curdling milk with  Streptococcus thermophilus  and  Lactobacillus bulgaricus .

c.  Cheese  production starts with milk coagulated with lactic acid bacteria and the curd formed is filtered to separate the whey. The solid mass is then ripened with the growth of mould that develops flavour in it.  Propionibacterium shermanii  is used to make cheese.

2. In Industry A large number of products are obtained due to bacterial activity, directly proportional to the economic importance of Bacteria.

3. In Medicine Some bacteria have been exploited to produce antibiotics. Antibiotics like Terramycin, Streptomycin, Tetracycline, Aureomycin, Neomycin are obtained from different bacterial species.

a. Vaccines:  Several vaccines have been developed from either killed or attenuated (living but multiplying at low rates) bacteria. For example, tuberculosis vaccine, whooping cough vaccine, plague vaccine, DTP (Diphtheria, Tetanus, Pertussis) vaccine, pneumonia vaccine are all prepared with the help of bacteria.

4. In Maintenance of Environmental Balance and Agriculture:  Bacteria act as decomposers. They make the nutrient available for plants. Specific genera of bacteria are used as biocontrol agents in agriculture.  Bacillus thuringiensis  (Bt) yields protein-based toxins used to kill insects.

5.   Nitrogen fixation and soil fertility:  Certain bacteria are helpful in the fixation of atmospheric nitrogen.  Azotobacter  and  Clostridium  are present in the soil and help in nitrogen fixation. Species of  Rhizobium  bacteria are present in the root nodules of leguminous plants, and they increase the soil’s nitrogen content by fixing up atmospheric nitrogen. The process is known as symbiotic nitrogen fixation.

Several cyanobacteria also help in nitrogen fixation.  Nostoc ,  Anabaena , etc., possess heterocysts with nitrogenase enzymes and fix atmospheric nitrogen in symbiotic conditions.  Nostoc  is associated with the coralloid roots of  Cycas  and helps in this process.  Anabaena azollae  is associated with water fern,  Azolla , and helps in nitrogen fixation in paddy fields.

6.   Role in Nitrogen Cycling:  Nitrification is one of the most critical steps in the nitrogen cycle, performed by nitrifying bacteria. Nitrifying bacteria are chemolithotrophic organisms that include the genera  Nitrosomonas, Nitrococcus, Nitrobacter, Nitrobacillus , etc. These bacteria get their energy by the oxidation of inorganic nitrogen compounds.

The denitrifying bacteria, like  Pseudomonas denitrificans ,  Thiobacillus denitrificans,  transform the nitrates to atmospheric nitrogen.

7.  Biogas Production:  Biogas is a standard domestic and industrial fuel, which contains \(50-60\%\) methane, \(30-40\%\) carbon dioxide, \(0-3\%\) Sulphur compounds, and traces of other gases like hydrogen CO, nitrogen, etc.

1. In a biogas digester, cattle dung is used to obtain gas (gobar gas) in the following steps:

a. Hydrolysis is the initial step that needs anaerobic bacteria like  Clostridium ,  Pseudomonas , etc. b. Acidogenesis is the second step, in which the facultatively anaerobic, acidogenic bacteria and obligate anaerobic organisms help convert the simple organic material into acids like formic acid, acetic acid, etc. c. Methanogenesis is the last step, in which anaerobic Methanogenic bacteria like  Methanobacterium ,  Methanococcus , etc., convert organic acids into Methane.

8.   Sewage Treatment:  Sewage is agricultural and domestic waste products that pollute the water. The treatment to remove such waste is partially chemical, biological treatment. a. Secondary treatment is the biological treatment, which reduces the BOD significantly. Aerobic bacteria are used in this process. b. Tertiary treatment is done once there is a reduction of BOD in the settling tank. Mainly Methanogens grow anaerobically and produce biogas.

Formation of Curd with Bacteria

Curd formation from milk is performed by mixing LAB (Lactic Acid Bacteria), like Lactobacillus, with warm milk. These bacteria convert the milk sugar (lactose) into lactic acid resulting in the formation of curd. Once the curd is made, it is transferred to a cooler place to reduce the further growth of bacteria. Otherwise, the bacteria would make it sour by excessive production of lactic acid.

How are Bacteria Harmful to us?

1. Spoilage of Foodstuff: Cooked food, fruits, vegetables, butter, fish and meat are spoiled by bacteria, particularly during summer months, by causing putrefaction of food materials.

Fig: Food Poisoning Bacteria

Certain bacteria like Salmonella typhimurium and Clostridium botulinum cause a severe type of food poisoning when bacteria-contaminated food is consumed. Clostridium botulinum causes food poisoning, commonly known as botulism. 2. Reduction of Soil Fertility – Denitrification: Certain species of anaerobic bacteria inhabit soils that are either waterlogged or have high organic matter content. These bacteria reduce soil fertility by depleting the soil’s nitrogen content. They break down nitrates present in the soil and release nitrogen, which escapes into the air, thereby reducing soil fertility (denitrification). 3. Animal Diseases: Bacteria cause tuberculosis in cattle, anthrax in sheep, cholera in chickens and pneumonia in horses, sheep and goats. 4. Human Diseases: Many serious diseases are caused by bacteria in human beings. Some of these are as follows:

5. Plant Diseases: Several plant diseases are induced by bacteria. They cause leaf spots, soft rots, vascular diseases, and bacterial galls. Xanthomonas citri causes citrus canker. 6. Bioweapons : A bioweapon or biological weapon is a device that carries and delivers a disease-causing biological agent (like bacteria, viruses, genetically altered organisms) or a toxin derived from it to the target organism. The biological agent or toxin is called a bioweapon agent. Biological agents are used against humans, crops and animals. Such use of bioweapons is termed BioWare or biological war. Some of the bioweapons can cause anthrax, smallpox, plague and gastroenteritis. Bacillus anthracis is the causative agent of anthrax, Vibrio cholera of gastroenteritis and Yersinia pestis of plague. Botulinum toxin from Clostridium botulinum is used to cause fatal food poisoning. Some of these agents have already been used. For example, anthrax bacterium was sent through letters in \(2001.\) Bioweapons are low-cost weapons and cause far more casualties than conventional weapons.

In this article, we studied that bacteria are the members of the kingdom Monera. They are the most diverse organisms with wide distribution, modes of nutrition, reproduction, etc. They are saprobiotic, parasitis, and autotrophic in their nutrition. Some forms are helpful for human beings, while most others are pathogenic and cause harm to animals and plants. We also looked at the economic importance of bacteria processes through some examples.

Q.1. What is Koch’s postulate on bacteria? Ans: The bacteria must be present in every case of the disease. The bacteria must be isolated from the host with the disease and grown in pure culture. The specific disease must be reproduced when a pure culture of the bacteria is inoculated into a healthy susceptible host.

Q.2. What are the three important uses of bacteria? Ans: Bacteria are used in Biogas production, Cheese production, improving soil’s health and productivity, and sewage treatment.

Q.3. Which bacteria are responsible for the formation of curd from milk? Ans: Lactobacillus species bacteria are responsible for the formation of curd from milk.

Q.4. What is the major function of an Economic Importance of Bacteria? Ans: Some of the primary functions of the economic importance of Bacteria are Curing of Cheese, In Maintenance of Environmental Balance and Agriculture, Nitrogen fixation and soil fertility,  In Medicine, Sewage treatment, Biogas production, etc.

Q.5. Which bacteria are responsible for causing Leprosy disease in human beings? Ans: Mycobacterium leprae bacteria are responsible for causing Leprosy disease in human beings.

Q.6. List a few harmful roles of bacteria. Ans: Spoilage of Foodstuffs, Reduction of Soil fertility Denitrification, Animal Diseases, Human Diseases, Plant Diseases, etc., are a few harmful roles of bacteria.

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Economic Importance of Bacteria

Animesh sahoo.

• March 31, 2024

Bacteria exert both deleterious and benefical effects on human life. Beneficial species liberate fertilizer elements for growing crops, destroy sewage and other wastes, and produce valuable chemicals.

Some species are harmful for animals as well as humans.

Beneficial and harmful aspects of bacteria are briefly discussed below:

Table of Contents

Beneficial Activities

1. to increase soil fertility.

• Both symbiotic bacteria (Rhizobium, Pseudomonas) forming nodules and asymbiotic bacteria (Clotridium, Azotobacter) living in the soil are capable of fixing inorganic nitrogen into organic form and helping to increase soil fertility.
• Increase soil fertility by decomposing proteins of dead organic remains of plants and animals.
• Clostridium, Pseudomonas, Bacillus, etc. help in ammonification, and Nitrosomonas and Nitrobacter help in nitrification. 

2. Putrefaction and Decay

• Putrefaction to the anaerobic decomposition of organic remains with the product of malodorous substances.
• The most important role of bacteria is in the decomposition of organic matter.

3. Retting of Fibres

• Bacteria help in the retting and separation of fibres of jute, hemp, flax, etc.
• Genus Clostridium hydrolyzes the pectic substance that binds the fibres together.
• These are used in the making of ropes and sacks.

4. Preparation of Dairy Products

• The dairy industry uses bacteria in the manufacture of dairy products like curd, butter, ghee, cheese, etc.
• E.g., Streptococcus, Leuconostoc, and Lactobacillus.

5. Lactic Acid Production

• Lactobacilli (L. bulgaricus) are used in the manufacture of lactic acid.
• The sugar present in the whey is converted into lactic acid by the enzyme lactase produced by the bacilli.

6. Vinegar Production

• Vinegar, or acetic acid, is produced from alcohol by bacteria.
• E.g., Acetobacter, Gluconobacter and Gluconacetobacter.

7. Alcohol and Acetone Production

• Various bacteria, including Clostridium, Eubacterium, and Bacillus, are used in the production of acetone and alcohol.

8. Amino Acid Production

• Many amino acids are produced on a commercial basis with bacterial fermentation.
• Lysin is produced by E. coli and Enterobacter aerogenes. Glutamic acid is produced by Corynebacterium glutamicum.

9. Production of Fermented Foods

• Important food items are produced by microbial fermentation.
• Pickles are produced with the help of Lactobacillus and Streptococcus.

10. Protein Food

• Bacteria produced in massive quantities are an attractive source of food.
• These, when cultivated, yield a large cell crop that is rich in protein (single cell protein).
• Dried cells of Pseudomonas that grow on petroleum products have 69% protein.

11. Production of Silage

• Production of silage, a food of high nutritive value for cattle.
• E.g., Streptococcus, Lactobacillus

12. Curing and Repering of Tobago and Tea

• Bacillus megaterium is used for the curing process.
• The ripening or fermentation takes place due to the action of Micrococcus condisans.

13. In Paper and Textile Industry

• The enzyme amylase, excreted from Bacillus subtilis, is used in sizing paper and desizing textiles.

14. In Leather Industry

• Bacillus subtilis is used in tanning leather.

15. In Sewage Disposal

• Enterobacter, Alcaligenes, Pseudomonas, etc. are used in the various processes associated with sewage treatment and disposal.

16. Enzymes Production

• Enzymes secreted by bacteria inhabiting the stomach and intestines of cattle, horses, etc. help digest the carbohydrate cellulose.
• Enzyme amylase is produced by Bacillus subtilis, Streptococcus.

17. Vitamin Production

• Many vitamins are produced by bacteria.
• Vitamin B – Streptomyces olivaceus, Vitamin K – Streptococcus haemolyticus, and Vitamin C – Gluconobacter suboxydans

18. Antibiotic Production

• Antibiotics are produced by several species of bacteria.
• Example: polymyxin, subtilin, bacteriocin, gramicidin, etc.
• Antibiotics produced by higher bacteria are amphatercin, carbomycin, tetracycline, etc.

19. As Human Symbionts

• The bacteria E. coli living in the intestine of human beings are symbionts and synthesis vitamin B.

20. Other Medicine

• The substance dextran produced by Leuconostoc mesenteroides is used as a blood plasma substitute.
• The enzymes streptokinase and streptodornase, produced by Streptococcus haemolyticus, are used in dissolving blood clots.

21. Pigments Production

• Pseudomonas sp. produces greenish to dark brown pigments.
• Chromobacterium sp. produces a violet pigment.
• Serratia sp. produces a red pigment.

Harmful Activities

1. reducing soil fertility.

• The bacteria Thiobacillus, Serratia, Micrococcus, and Pseudomonas are capable of transforming nitrogen in the soil into nitrogen gas by denitrification.
• This change leads to a net loss of nitrogen from the soil, i.e., a reduction in soil fertility.

2. Food Spoilage

• Bacteria generally decompose food and render it unfit for human consumption.
• E.g., Bread: Bacillus subtilis, Syrup: Enterobacter, Fruits and Vegetables: Micrococcus, Meat: Clostridium, Pseudomonas, Fish: Pseudomonas, Flavobacterium, Egg: Psudomonas, etc.
• Staphylococcus occurs, from which exotoxin is liberated, which results in poisoning.
• Botulism is a fatal food poisoning of humans and animals caused by the toxins produced by Clostridium botulinum.

3. Paper and Cotton Deterioration

• Some bacillus are responsible for degrading the cellulose of paper and cotton.

4. Bacteria and Diseases

• Pathogenic bacteria cause various diseases in humans, animals, and cultivated plants.

Disease of Humans:

Disease of Animals:

Disease of Plants:

Animesh Sahoo is a scientific blogger who is passionate about biology, nature, and living organisms. He enjoys sharing his knowledge through his writings. During his free time, Animesh likes to try new activities, go on adventures, experiment with different biological aspects, and learn about various organisms.

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Bacteria in food

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The importance of bacteria to humans

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Milk from a healthy cow initially contains very few bacteria, which primarily come from the skin of the cow and the procedures for handling the milk. Milk is an excellent growth medium for numerous bacteria, and the bacteria can increase rapidly in numbers unless the milk is properly processed. Bacterial growth can spoil the milk or even pose a serious health hazard if pathogenic bacteria are present. Diseases that can be transmitted from an infected cow include tuberculosis ( Mycobacterium tuberculosis ), undulant fever ( Brucella abortus ), and Q fever ( Coxiella burnetii ). In addition, typhoid fever ( Salmonella typhi ) can be transmitted through milk from an infected milk handler. Pasteurization procedures increase the temperature of the milk to 63 °C (145 °F) for 30 minutes or to 71 °C (160 °F) for 15 seconds, which kills any of the pathogenic bacteria that might be present, although these procedures do not kill all microorganisms.

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Certain bacteria convert milk into useful dairy products, such as buttermilk , yogurt , and cheese . Commercially cultured buttermilk is prepared from milk inoculated with a starter culture of Lactococcus (usually L. lactis or L. lactis cremoris ). Yogurt and other fermented milk products are produced in a similar manner using different cultures of bacteria. Many cheeses are likewise made through the action of bacteria. Growth in milk of an acid-producing bacterium such as L. lactis causes the casein to precipitate as curd. Following the removal of moisture and the addition of salt, the curd is allowed to ripen through the action of other microorganisms. Different bacteria impart different flavors and characteristics to foods; for example, the mixture of Lactobacillus casei , Streptococcus thermophilus , and Propionibacterium shermanii is responsible for the ripening of Swiss cheese and the production of its characteristic taste and large gas bubbles. In addition, Brevibacterium linens is responsible for the flavor of Limburger cheese, and molds ( Penicillium species) are used in the manufacture of Roquefort and Camembert cheeses . Other types of bacteria have long been used in the preparation and preservation of various foods produced through bacterial fermentation, including pickled products, sauerkraut , and olives .

The toxins of many pathogenic bacteria that are transmitted in foods can cause food poisoning when ingested. These include a toxin produced by Staphylococcus aureus , which causes a rapid, severe, but limited gastrointestinal distress, or the toxin of Clostridium botulinum , which is often lethal. Production of botulism toxin can occur in canned nonacidic foods that have been incompletely cooked before sealing. C. botulinum forms heat-resistant spores that can germinate into vegetative bacterial cells that thrive in the anaerobic environment , which is conducive to the production of their extremely potent toxin. Other food-borne infections are actually transmitted from an infected food handler, including typhoid fever, salmonellosis ( Salmonella species), and shigellosis ( Shigella dysenteriae ).

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Bacteria in industry

Often, the first thing that comes to mind when we think about microbes in the built environment are damage, decay, discolouration and staining to building materials and their surfaces. What we don’t consider is their ability to act as bioengineers. Apart from the production of important compounds, bacteria are also useful in the breakdown of environmental contaminants such as pesticides, petroleum additives and plasticisers. The successful use of bacteria on an industrial scale has prompted expansion into more diverse areas. A recent addition to the résumé of these tiny organisms is the utilisation of biomineralizing bacteria in self-healing construction materials.  

It is becoming the norm to exploit bacteria in industrial processes for their ability to act as ‘cell factories’ that can produce important speciality products such as detergents, plastics, fuels and essential oils.

How can bacteria impact industry?

Bacteria can have a huge impact on industry and national and financial interests. The usefulness of microbial biomineralization in construction materials has been established in principle in the laboratory and in several field trials. However, several challenges still have to be overcome. For example, methods for optimising the survival of the bacteria within concrete are currently being developed.

In geotechnical applications, bacteria are now being used as part of the engineering toolbox for the consolidation and stabilisation of soils to counteract erosion, enhance bearing capacity, and enable excavation and tunnelling. This is due to the intrinsic ability of a wide range of bacteria to promote the precipitation of mineral carbonate, such as calcium carbonate, as a by-product of their metabolism.  

Read more about how and why the use of bacteria in industry matters to our members and the wider microbiology community, access our additional resources and find out a bit more about the next field of microbiology that matters to our community, as we explore 'Vaccines: the global challenge for microbiology.'

Microbiologists working in this area

To celebrate our 75th anniversary in 2020, we invited microbiologists to nominate the discovery or event that best showcases why microbiology matters and helps us demonstrate the impact of microbiologists past, present and future. Learn more about microbiologists working to understand bacteria in industry.

Resources and further reading

Discover how and why bacteria are being exploited in industrial processes, the biotechnological applications scientists are using to make use of bacteria and how research has led some microbiologists to use antimicrobial stewardship ward rounds in hospitals to improve patient care.

Vaccines: the global challenge for microbiology

Vaccines are made from microbes that are dead or inactive so that they are unable to cause disease. Not only do vaccines protect individuals, they can also provide herd immunity. We will explore four key areas of vaccination, including how vaccines work, are produced, more about herd immunity and eradicating disease.

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Bacteria and Their Industrial Importance

• First Online: 08 March 2022

Cite this chapter

• Nirmala Akoijam 2 ,
• Debajit Kalita 2 , 3 &
• S. R. Joshi 2  

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Bacteria have been of immense importance to man and the environment. Apart from their role in geochemical cycling and eco-restoration of the environment, bacteria are widely used in industries to synthesize products beneficial to humans. The ever-increasing utility of bacteria in industrial applications has impelled the expansion of the microbial industries into more varied and valuable horizons. Microbial cells function as mini biofactories and synthesize novel, economically important products like enzymes, organic acids, vitamins, antibiotics, antibodies, hormones, carotenoids, steroids, alkaloids, alcoholic beverages, interferons, and vaccines. Apart from the synthesis of these products, bacteria are also involved in wastewater treatment, bioremediation, biomineralization, biorecovery of precious metals and metalloids, biocontrol agents, production of prebiotics and probiotics, biogas, and eco-friendly nanomaterial production. In this chapter, we present a summary of the wide range of industrial applications of bacteria ranging from beneficial products to rehabilitation of the environment.

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Akoijam, N., Kalita, D., Joshi, S.R. (2022). Bacteria and Their Industrial Importance. In: Verma, P. (eds) Industrial Microbiology and Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-16-5214-1_2

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Economic Importance Of Bacteria

Bacteria play a key role in many essential biological processes, including nutrient cycling, soil formation, food production (such as curd or yogurt, cheese, ghee, and vinegar), digestion, and the breakdown of organic matter in nature.

They are also essential for human health, providing essential nutrients, nitrogen cycles, bioweapons, producing antibiotics and other drugs, and protecting us from disease-causing organisms. Bacteria also play an important role in biotechnology, providing enzymes and other proteins for industrial applications, such as the production of biofuels and other chemicals.

Bacteria are also important in agriculture because they help compost and produce fertilizer by natural means. Bacteria are used in genetic engineering where specific genes are introduced into bacteria for the production of desired products.

Economic importance contains both useful and harmful activities related to the topic, here we will discuss the benefits and harm caused by bacteria.

Beneficial Activities of Bacteria

Industrial uses of bacteria in

• Biotechnology – It’s a technology that involves the biological systems, living organisms, or parts of this to develop or create different products. For example, the use of microorganisms including bacteria in the manufacturing industries. The chemical manufacturing of acetone, enzymes, alcohol (ethanol), organic acids, and perfumes is carried out through this process.
• Making dietary supplements and pharmaceuticals – Some vitamins are used as external food supplements. E. coli bacteria are used to produce D-amino acids such as D-p-hydroxyphenylglycine, which is an important intermediate for the synthesis of the antibiotic amoxicillin.
• Pest control – Some bacteria can be used in place of pesticides under biological pest control. This process commonly uses Bacillus thuringiensis (Bt.) and soil-dwelling bacterium.
• Acetobacter aceti is used to make vinegar (Acetic acid) – In this process, ethanol is converted into acetic acid (CH3COOH).
• Clostridium butylicum is used in the commercial preparation of Riboflavin (vitamin B12) and Butyric acid
• E. coli (Escherichia coli) or coliform bacteria produces vitamin E, vitamin K, etc.
• E. coli bacteria are present in human and other herbivores’ intestines which helps the body digest the food we eat and produces vitamins B1, B2, and K. Bacteria living in the gut are called gut microbiota in cattle, horses, and other herbivores, for example, Ruminococcus spp., helps in the digestion of cellulose by secreting the enzyme cellulase. This is how herbivores are able to fulfill the body’s energy demand they need from grass and other plants.
• Bacillus and Propionibacterium produces vitamin B12.
• Retting of fibers – Separation of fibers from plants with the help of bacteria.
• In Ganga river water bacteria named Bdellovibrio bacteriovorus and Bacteriophage are present where they kill the other polluting bacteria and make the water fit.
• In degrading oil in seawater, in it, a bacteria named Alcanivorax borkumensis used to remove oil from the water’s surface.
• Pollution indicator – Water in which E. coli bacteria are present is called polluted water and is an indicator of fecal contamination in water. The quality of water depends on the number of E. coli. If E. coli are very much in number, the water will be highly polluted. So, E. coli is known as a pollution indicator.
• Genetic engineering – Genetic engineering is also called genetic modification or genetic manipulation. In this process, direct manipulation of an organism’s genes is done using biotechnology. Mainly E. coli and Agrobacterium bacteria are used in genetic engineering.
• Curing or flavoring of tea and processing of tobacco leaves – For this process Bacillus megatherium and Micrococcus conscience are used.

Bacteria are essential for the production of many medicines such as manufacturing antibiotics, which are used to treat infections caused by other bacteria. Bacteria can also be used to produce hormones such as insulin, which is used to treat diabetes and anti-cancer drugs.

Bacteria are also used to produce vaccines, which protect people from diseases. Finally, bacteria are used in bioremediation, which is the use of bacteria to clean up environmental pollutants.

Making Antibiotics

Bacteria are the source of many of the antibiotics that are used to fight infections. Antibiotics are made from compounds produced by bacteria, fungi, and other microorganisms. These compounds inhibit the growth of other microorganisms or kill them outright.

Antibiotics are used to treat bacterial infections such as urinary tract infections, skin infections, and pneumonia. Antibiotics can also be used to prevent infections and treat certain conditions. The use of antibiotics has saved countless lives and has contributed to improved health and quality of life.

What is an antibiotic?

Anti means against and biotic means life, so any substances against an organism’s life are called antibiotics . Some substances produced by microorganisms that inhibit the growth of other microorganisms are called antibiotic substances. Many antibiotic medicines are obtained from bacteria.

1st antibiotic used in the 2 nd world War by American soldiers is Streptomycin which is obtained from Streptomyces griseus (It is an actinomycete).

• Streptomyces venezuelae – Chloramphenicol (Chloromycetin)
• Streptomyces rimosus – Terramycin
• Streptomyces fradiae – Neomycin
• Streptomyces aureofaciens – Aureomycin
• Bacillus polymyxa – Polymyxin
• Bacillus subtilis – Antibiotics produced are three ribosomal antibiotics (TasA, Subtilosin, and Sublancin), four nonribosomal antibiotics (Bacitracin, Bacilysin, Plipastatin, and Surfactin), Bacilysocin, and Neotrehalosadiamine (NTD)
• Streptomyces strains – Tetracycline

Dairy Products

Food products made from lactic acid bacterial species are Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, and Weissella in which species of lactobacillus bacteria are more commonly used in the fermentation of dairy products are:

• Streptococcus lactis
• Lactobacillus lactis

Lactobacillus lactis increases vitamin B 12 in curd, Lactic Acid Bacteria (LAB) also help in the disease-causing microbes in the stomach.

Nitrogen Fixation or diazotrophy

Nitrogen fixation (N 2 → NH 3 ) is both a biological as well as a chemical process through which covalent bonded atmospheric nitrogen (N2), is converted into ammonia (NH3) or any nitrogenous compounds like amino acids, nitrate, and ammonium salts. Where nitrogen has a nonzero oxidation state, this is done typically in soil or aquatic systems and also artificially in industry.

Nitrogen fixation is done by two processes :

• Azorhizobium – In the stem nodules of Sesbania
• Azospirillium – Found on the root surface of cereals that is, superficial symbiosis. For example Rice, Maize, Wheat
• Bradyrhizobium
• Frankia – In the root nodules of non-legumes. For example Casuarina, Alnus
• Rhizobium – In the root nodules of legumes
• Sinorhizobium
• Azospirillum
• Azotobacter
• Beijernickia
• Clostridium
• Rhodomicrobium
• Rhodopseudomonas
• Rhodospirillum

Ammonification

The process of formation of ammonia is called ammonification. Ammonifying bacteria help in the process of ammonification (Protein → NH 3 ). It is a biological process, these bacteria convert protein (present in decaying plants and animals) into ammonia (NH 3 ).

• Bacillus Vulgaris
• Bacillus Romosus
• Bacillus Mycoids

Nitrification

Nitrification is done by nitrifying bacteria which are chemoautotrophs, in which bacteria convert ammonia (NH 3 ) into nitrite (NO 2 – ) and further nitrate (NO 3 – ) and it is a biological process.

• Nitrosomonas (2NH 3 + 3O 2 → 2NO 2 – + 2H + + 2H 2 O + Energy)
• Nitrococcus (2NH 3 + 3O 2 → 2NO 2 – + 2H + + 2H 2 O + Energy)
• Nitrobacter (2NO 2 + O 2 → 2NO 3 – + Energy)
• Nitrocystis (2NO 2 + O 2 → 2NO 3 – + Energy)

Harmful Activities of Bacteria

Diseases caused by bacteria in human beings

Disease caused by bacteria in animals

Disease caused by bacteria in plants

Denitrifying bacteria

Denitrifying bacteria help in the process of denitrification (NO 3- → N 2 ) which is both a biological as well as abiological process, in which some bacteria convert soil nitrates (NO 3 – ) into nitrites (NO 2 – ) and then nitrogen (N 2 ) this process is called denitrification. These bacteria reduce the fertility of the soil.

• Thiobacillus denitrificans
• Pseudomonas denitrificans
• Micrococcus denitrificans

Food poisoning or Foodborne illness

Botulism is caused by Clostridium botulinum and sometimes Clostridium butyricum and Clostridium baratii – It is an obligate anaerobe. It can not survive in our body because of the presence of oxygen (aerobic environment). It is a rare and the most lethal type of food poisoning .

These bacteria only survive in the absence of oxygen. These bacteria multiply in canned food. Their toxins attack the parasympathetic nervous system, which leads to paralysis of both smooth and striped muscles that results in difficulty in breathing which causes asphyxia and leads to immediate death .

Biological Weapons

Some bacteria are used as bioweapons such as :

• Bacillus anthracis (rod-shaped, gram-positive bacteria)— Causes Anthrax , a serious infectious disease. It can be found naturally in soil and commonly affects domestic and wild animals all around the world.
• Clostridium botulinum , Clostridium butyricum , Clostridium baratii — Causing food poisoning .
• Vibrio cholerae — Causes Cholera by infecting the intestine. It is an acute diarrheal illness in which people can get sick when they take food or water contaminated by cholera bacteria. The infection is often mild or without symptoms, but can sometimes be severe and becomes life-threatening.

Water Pollution

Several bacterial forms cause water pollution. These bacteria spoil the water and make it unfit for living organisms.

• Salmonella typhi
• Vibrio Cholerae

Nutrient cycling

Bacteria are essential for life on Earth, playing important roles in the cycle of nutrients and energy. They break down organic matter, such as dead plants and animals, into nutrients that can be used by other organisms. Additionally, bacteria can help to form healthy soil, which is important for plant growth.

Q: What is the economic importance of bacteria? A: Bacteria are important economically, as they are used in a wide range of industries and applications. For example, bacteria are used in the production of food, medicines, and bioremediation. Bacteria are also used to make bioplastics, biofuels, and other bioproducts. Bacterial enzymes are used in the production of detergents, enzymes, and other industrial products. Additionally, bacteria are used in the treatment of wastewater and sewage and are also used to produce biogas.

Q: What economic benefits do bacteria provide? A: Bacteria can have a range of economic benefits, including providing food sources, generating bioproducts, aiding in bioremediation, and aiding in the production of biofuels. Bacteria can also be used in the production of certain medicines and in biotechnology.

Q: How are bacteria used in bioremediation? A: Bacteria are used in bioremediation as they are able to break down and remove pollutants in the environment, such as oil and other hazardous chemicals. This process helps to clean up contaminated sites, making them safe for people and animals.

Q: How are bacteria used in the production of medicines? A: Bacteria are used in the production of certain medicines, such as antibiotics, which are used to treat bacterial infections. Bacteria can also be used in the production of vaccines, which help to protect people from certain illnesses.

Q: How do bacteria aid in the production of biofuels? A: Bacteria can be used in the production of biofuels, such as ethanol and biodiesel. Bacteria can break down organic matter, such as corn and other plants, and convert them into usable forms of energy.

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• Can Understand Concepts: The first step to master in the Economic Importance of Bacteria and Fungi chapter is to understand the concepts; for that students can take the help of Class 9 ICSE Biology notes and improve their preparation process. 
• Can Memorise Key Concepts: In the chapter Economic Importance of Bacteria and Fungi, there are many key concepts so to memorise those concepts, students can refer to Class 9 Biology Economic Importance of Bacteria and Fungi notes and improve their preparation level.
• Can Have a Quick Revision: Revision helps students to recall all the key topics and concepts; to have a quick revision, students can refer to Economic Importance of Bacteria and Fungi Class 9 ICSE notes and improve the learning process. 
• Can Practise Previous Papers: Practising Economic Importance of Bacteria and Fungi questions from the previous year papers is an excellent way to be prepared. To solve questions in a proper way students can refer to ICSE Biology Class 9 notes as in it concepts are explained which will help students answer the previously asked questions. 
• Can Collaborate With Peers: In order to give a boost to the preparation, students can collaborate with their friends or classmates to have a discussion on the Economic Importance of Bacteria and Fungi topic. Collaborating with peers helps students talk about new concepts too which enables them to deepen the understanding level.
• To Use Visual Presentation: The ICSE Biology Class 9 Economic Importance of Bacteria and Fungi notes involves flow charts, diagrams, mind maps; if students utilise it then they can understand the concepts in creative ways. 

Strategies to Cover the Chapter Economic Importance of Bacteria and Fungi With the Help of Economic Importance of Bacteria and Fungi ICSE Class 9 Notes

Strategies are considered as action of planning to achieve a given task; the same is implemented to cover the chapter Economic Importance of Bacteria and Fungi with the help of ICSE Class 9 notes, some are discussed below: 

• Focus on Core Topics: Students are advised to focus on the core topics of the chapter Economic Importance of Bacteria and Fungi; they can identify the core topics with the help of ICSE Class 9 Biology Notes . 
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• Try to Solve Practice Questions: Students are advised to solve a lot of questions related to the chapter Economic Importance of Bacteria and Fungi; to solve the questions in an accurate way, they can take the help of Class 9 Biology notes. 
• Maintain a Good Sleep Routine: While completing ICSE Biology Class 9 Economic Importance of Bacteria and Fungi notes, students need to maintain a good sleep routine of 7 to 8 hours; then they can improve their memorisation skills. 

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Microbes Role in the Economic Development of a World

19 Pages Posted: 26 Dec 2019 Last revised: 5 Feb 2020

Naushad Khan

University of Agriculture, Peshawar - Institute of Development Studies; Institute of Development Studies

Date Written: December 25, 2019

Microbes are microorganism and with the help of microscope these are seen. It consists of bacteria, archaea, viruses, fungi, protists, protozoa and algae etc. Some microorganisms are beneficial while some are non beneficial for human beings. These all live on the earth in different forms. Seeing to its importance the present study was arranged in December, 2019 to examine the role of microbes in the development of a world. Secondary data was used for this study. Total 15 articles were downloaded from the web and 20 times were reviewed critically to fully know what role microbes play in world development. The analysis indicates that microbes are the permanent member of this world and in different form give benefits to humanity and keep the balance of ecosystem for the survival of human being while some are very dangerous which kill human and other living organism of this world. Microbiologists have discovered so many microbes, some make the yogurts but some make the cheese and beer for humanity. Similarly some add nitrogen to the soil for the growth of plant while few microbes convert the soil structure and make it favorable for the growth of plant. Some microbes release the methane gases in the air and create the heat in the environment which makes the problem of global warming. Some microbes spread different disease in the world and make the world polluted but some clean the pollution of the world. Vaccine of virus help in smallpox controlling, while some play great role in insulin manufacturing for the control of diabetes. The story of microbe is very long and some bacteria help in digestion process in ruminant animal while some spread the cancer and T.B in the arena of this world. Some microbes help in conversion of carbon dioxide into starch and glucose. Few scientists think that to remove the microbes from this world but majority stress that without microbes this world running is impossible and they told that microbes are very important and useful organism of this world because they play great role in different sector of economic development of the world. It is indicated from the mentioned discussion that without microbes this world business is impossible, so on the basis of this importance it is necessary for every government of the world to include this debate in the national policy at world level and keep a proper budget for implementation of the project for discoveries of new microbes for the beneficiary of society. Government of every country should be focused on microbes what microbes are beneficial and what are non beneficial and further also link this study with the world for advancement of the country.

Keywords: Microbes, Role, Economic, Development, World

Suggested Citation: Suggested Citation

Naushad Khan (Contact Author)

University of agriculture, peshawar - institute of development studies ( email ).

Institute of Development Studies Professor Colony Agriculture Peshawar Peshawar, khyber Pakhtunkhwa 25000 Pakistan

Institute of Development Studies ( email )

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The Importance of Microorganisms for Sustainable Agriculture—A Review

In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant–microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant–microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant–microorganism interactions, the functioning of the plant’s immune system during the plant–microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma . Our review aims to summarize the existing knowledge about plant–microorganism interactions and to highlight molecular pathways that need further investigation.

1. Introduction

Traditional agricultural techniques, such as chemical fertilizers, pesticides, fungicides, and herbicides, enable the protection of crop plants against pathogens and ensure better yield. Chemical compounds present in agricultural chemicals are harmful to the environment and cause soil, atmosphere, and water pollution [ 1 ]. These compounds are the reason for the extinction of fish [ 2 ], bees [ 3 ], and plants [ 4 , 5 ], and pose a threat to the biodiversity of soil bacterial [ 6 , 7 , 8 ] and fungal communities [ 9 ]. Chemical plant protection products negatively affect agricultural soils, i.e., they change soil physical properties, (e.g., texture, permeability, porosity), they disturb the cycle of the elements, such as phosphorus and nitrogen, and they decrease the complexity of soil microbiome [ 10 ]. In the face of a growing world population and increased demand for food both in terms of food quantity and food quality, the usage of bioinoculants, i.e., biofertilizers to increase the yield and biopesticides to protect plants, is the future of agriculture. Bioinoculants comprised of living or dormant microbes that are able to promote plant growth and development are called PGPM (plant growth-promoting microorganisms) and have great potential not only for enhancing plant yield but also for remediation of degraded soils [ 11 , 12 , 13 ]. Bioinoculants are cost-effective and environmental-friendly approaches in agriculture [ 14 ]. The first step in a bioinoculant formulation is the isolation and identification of a microbe. The further potential of a particular microorganism for plant growth promotion needs to be verified, and this ability should be confirmed in laboratory and field conditions. Moreover, potential risks to other organisms, such as animals and natural soil microbiomes, should be also determined [ 15 ]. The best-known examples of PGPM are mycorrhizal fungi and bacteria belonging to Rhizobium; however, plant growth-promoting microorganisms are found among varied taxa of bacteria, fungi, and algae [ 16 ]. In Table 1 , several examples of PGPM are shown.

Examples of plant growth-promoting microorganisms. The effect of PGPM on plants and, if known, the mode of action of microorganisms is also included.

One of the major drawbacks of the application of bioinoculants is the fact that the number of bioinoculants tested in laboratory/greenhouse conditions fail in the field trials. This is mostly because microbes introduced to the environment have to compete for a niche with native microorganisms in order to attain sufficient abundance. The ability of introduced microbes to survive and thrive is variable and significantly depends on environmental conditions including temperature, rainfall, and soil type, as well as on interactions with the host plant and other organisms. A good example of this dependence is the field trial that showed that the promotion of plant growth by subtropical strains of Azotobacter chroococcum and Azospirillum brasilense was observed only when used in the same type of climate and not in the alpine region with a temperate climate [ 80 ]. Moreover, it was demonstrated that the high biodiversity of the native soil microbiome has a negative impact on the survivability of applied bioinoculants, i.e., there is a negative correlation between the diversity of the soil microbes and the survival rate of the introduced strain [ 81 ]. Therefore, when the native microbiome biodiversity is low, the chance for a new strain to thrive is higher which corresponds with better availability of nutrients and reduced competition among microorganisms for niche [ 82 , 83 , 84 ]. Moreover, several studies showed that PGPM that promotes the growth of a particular plant species might not be beneficial for other species of plants. For example, fungi belonging to Penicillium sp. and Trichoderma sp. showed diversified effectiveness in enhancing the growth of varied wheat ( Triticum aestivum L.) cultivars [ 85 ]. Similarly, the effect of inoculation of winter and spring varieties of oilseed rape ( Brassica napus L.) with different strains of PGPM on the germination rate and growth of seedlings depended on the plant variety [ 86 ]. On the other hand, different strains of the same microbial species might differ significantly in their ability to promote plant growth and development. For example, Znajewska et al. [ 59 ] showed that seven Trichoderma viride isolates had various effects on winter rapeseed germination and growth promotion depending on the used strain.

Microorganisms colonize not only roots but also other plant tissues and organs including stems, leaves, flowers, seeds, and fruits. The aerial part of plants colonized by microbes is called the phyllosphere, whereas the rhizosphere is the soil adjacent to the root [ 87 ]. In contrast to the rhizosphere, the above-ground parts of plants are scarce in water and nutrients. Only a small number of microorganisms that reach the surface of the plant will land on beneficial spots and will have conditions to survive [ 88 ]. As a consequence, the number of microorganisms living in the rhizosphere is much higher than in the phyllosphere. Microbes are present at every stage of plant development, from seed to fully developed plant producing a new generation of seeds [ 89 ]. Some microorganisms live on the surfaces of plant organs, i.e., epiphytes whereas others are able to colonize the internal tissues of plants, i.e., endophytes [ 90 , 91 ].

Plant growth-promoting microorganisms stimulate plant growth and development through various direct and indirect mechanisms ( Figure 1 , Table 1 ). Production of phytohormones [ 92 , 93 ], nitrogen assimilation [ 94 ], solubilization, and mineralization of macro- and micro-elements [ 95 , 96 ], and modulation of the endogenous level of ethylene in plants tissues [ 97 ] are examples of direct mechanisms. Examples of indirect mechanisms are inhibition of pathogens growth through antibiosis [ 98 ], secretion of lytic enzymes [ 99 ], and competition, e.g., via siderophores production [ 100 ], induction/inhibition of plant genes expression [ 101 ], induction of plant immune response [ 102 ], and manipulation of plant microbiome composition [ 103 ]. This work aims to summarize the current knowledge about the interactions of plants with beneficial microbes, and how those interactions affect the overall health of the plant. For further development of environmental-friendly methods of plant cultivation, is it crucial to deeply understand the molecular mechanisms underneath (i) the recruitment of useful microbes by plants, (ii) the interactions among microorganisms, and (iii) the plant-microorganism interplay. The interactions between plants and microorganisms can be divided into three types, i.e., interactions are either neutral, negative, or positive in their effects on the host plant. This review focuses exclusively on positive interactions and mechanisms underneath those interactions. In this work, we also discuss the role of stringent responses in interactions between plants and microorganisms.

Multidimensional network of interactions between plants and PGPM, between plants and pathogens, and between PGPM and pathogens.

2. Rhizosphere and Root Exudates

The rhizosphere is defined as “the field of action or influence of a root”, i.e., it is soil adjacent to the roots which are influenced by root exudates that are the mixture of several compounds produced and secreted by roots [ 104 ]. The main components of root exudates are water, enzymes, amino acids, nucleotides, vitamins, organic acids, fatty acids, sugars, phenolic compounds, anions, volatile organic compounds (VOCs), polysaccharides, and proteins [ 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 ]. The composition of exudates varies depending on the plant species, and even phenotype; it changes during plant development [ 107 , 113 ] and it is dependent on environmental conditions, such as temperature [ 114 ], light [ 115 ], the amount of nutrients [ 116 , 117 , 118 , 119 ], and stress factors [ 120 , 121 , 122 ]. Moreover, the type and composition of soil can also affect the composition of root exudates [ 123 ]. For instance, plants that grow in soil deprived of nitrogen probably do not secrete extra amino acids or proteins to the rhizosphere [ 119 ]. Root exudates are also an important source of elements present in the soil. It was estimated that about 10–44% of carbon compounds [ 124 ] and about 10–16% of nitrogen compounds [ 125 ] synthetized by the plant is secreted to the rhizosphere. In legumes, the rhizodeposition of nitrogen is estimated between 4% and 70%, depending on the plant species [ 126 ].

The rhizosphere is the hotspot of plant–microorganism interactions. Interactions between those organisms have a direct influence on the availability of soil nutrients for plants [ 95 , 127 , 128 , 129 , 130 ] and on plant tolerance toward biotic and abiotic stresses [ 131 , 132 , 133 , 134 , 135 ]. Exudates are a rich source of carbon and other nutrients and, therefore, the abundance of microorganisms in the rhizosphere can be up to a hundred times greater than in the bulk soil [ 136 ]. Moreover, root exudates allow plants to communicate with rhizosphere microorganisms and affect their behavior through the secretion of various signaling molecules [ 137 , 138 , 139 , 140 ]. For instance, barley ( Hordeum vulgare L.) in response to infection by the fungus Pythium ultimum, secretes increased amounts of organic and phenolic acids, which activates the expression of the phlA gene in the endophytic bacterium Pseudomonas fluorescens CHA0. Hydroxymethylglutaryl-CoA synthase encoded by the phlA gene is involved in the synthesis of DAPG (1,4-diacetylphloroglucinol) that has antifungal activity [ 98 ]. Zhang et al. [ 141 ] demonstrated the role of organic acids in root exudates of cucumber ( Cucumis sativus L.) and banana ( Musa acuminata Colla). The citric acid present in cucumber root exudates attracted Bacillus amyloliquefaciens (isolated from cucumber rhizosphere) and B. subtilis (isolated from banana rhizosphere). Moreover, it induced the formation of the B. amyloliquefaciens biofilm. Fumaric acid present in banana root exudates promoted biofilm formation of both tested strains. Biofilm is a coherent multicellular structure embedded in a self-produced extracellular matrix that can be formed on the surface of plant organs. Members of biofilm are better protected from environmental factors; their nutritional status is enhanced and, therefore, the survival rate of members of biofilm is much higher than that of single bacteria cells, as reviewed in [ 142 ]. Another example of a molecule allowing plant–PGPM communication is polyamines present in root exudates, which inform rhizospheric microorganisms about the presence of a potential host plant [ 143 ]. For instance, putrescine and its precursor arginine attract Pseudomonas sp. and trigger a lifestyle change, promoting attachment to the root and formation of biofilm [ 144 ]. However, the best-known example is the mechanism of communication between Rhizobium and legumes. Flavonoids secreted by plants activate bacterial nod genes lead to secretion by bacteria of the nod factor. The nod factor promotes the formation of nitrogen-fixing nodules in roots [ 145 , 146 ].

Root exudates serve as a chemoattractant, by which plants “recruit” microorganisms ( Figure 1 ). Several studies showed that the composition of root exudates has an enormous effect on the composition of plant microbiome [ 147 , 148 , 149 , 150 , 151 , 152 ]. The composition of root exudates is specific for each plant species, which enables plants to attract a particular set of microbes [ 153 ]. Moreover, plants can secrete substrates that are available only for selected microbial groups or compounds that are toxic for certain groups of microorganisms in order to inhibit their growth [ 154 ]. A prominent example is the amino acid canavanine, which is present in seeds and root exudates of legumes. Canavanine is toxic to a number of soil bacteria excluding rhizobia which possess the msiA gene encoding canavanine exporter that warrants canavanine resistance [ 155 ]. Mardani-Korrani et al. [ 156 ] demonstrated that canavanine is secreted by Vicia villosa Roth, significantly decreased the diversity and changed the composition of microbial communities in soil. The presence of canavanine caused an increase in the abundance of Firmicutes and Actinobacteria and decreased the number of Proteobacteria and Acidobacteria. Another example of the selective action of compounds present in root exudates is coumarin secreted by Arabidopsis thaliana (L.) Heynh. Coumarin selectively inhibits the proliferation of some pathogenic fungi, stimulates the growth of some Pseudomonas spp. and other microbes that belong to the PGPM group, and increases the bioavailability of iron by ferric ions reduction [ 157 ]. Coumarins are used by plants to increase the bioavailability of iron. Coumarins, such as scopoletin and esculetin, enable the mobilization of Fe from minerals in acidic and alkalic soil [ 158 ]. Moreover, the depletion of Fe in soils enhances the biosynthesis and secretion of coumarins in A. thaliana [ 157 ]. It is also worth noting that fungi also produce and secrete exudates that might affect other rhizosphere microorganisms. An interesting observation was made by Toljander et al. [ 159 ], who showed that arbuscular mycorrhizal fungi (AMF) affect the composition of bacterial community through mycelia exudates. Analysis of exudates produced by Glomus sp. showed that the main components are water, low molecular weight sugars, and organic acids. Moreover, it was shown that Glomus exudates inhibited the growth of several bacterial strains including opportunistic pathogens Flavobacterium spp. and increased the abundance of bacteria belonging to Gammaproteobacteria.

Root exudates are usually secreted without energy, mostly through diffusion, ionic channel, and vesicle transport. Among several transporters involved in the secretion of exudates by roots are ABC (ATP-binding cassette) transporters which transport lipids and flavonoids [ 160 ], and anion channels are involved in secreting carbohydrates [ 161 ]. Moreover, for the secretion of root exudates transmembrane proteins aquaporins (AQPs) that are related to the membrane reflection coefficient and root hydraulic conductivity seem to be of great importance, as reviewed in [ 162 ]. Aquaporins are present in endogenous and exogenous membranes of eukaryotes and prokaryotes and are responsible for symplastic transport of not only water but also low molecular weight compounds and non-charged molecules including urea, glycerol, hydrogen peroxide, ammonium ions, and some elements, e.g., silicon and boron, as reviewed in [ 163 ]. Interestingly, it was demonstrated that during ectomycorrhiza formation the expression of fungi Laccaria bicolor aquaporins significantly increased. Moreover, fungal aquaporins exhibit high permeability for NH 3 and, therefore, it was suggested that they are involved in the transfer of this compound from fungal cytoplasm to plant [ 164 ]. Glycine max L. noduline 26 aquaglyceroporin (GmNod26) is located in the symbiosome membrane in N 2 -fixing nodules and is a transporter of ammonia. The C-terminal domain of GmNod26 interacts with the main ammonia assimilatory enzyme, i.e., glutamine synthetase, and this probably supports the effective assimilation of fixed nitrogen [ 165 , 166 ]. The potential of root exudates to determine the composition of the rhizosphere microbiome is also important for the biodegradation of various soil pollutants. Environmental pollution is a serious global challenge and needs urgent development of effective methods of remediation. An interesting observation was presented by Janczak et al. [ 167 , 168 ] who showed that the presence of plants had a positive effect on bacterial, (i.e., Arthrobacter sulfonivorans, and Serratia plymuthica ), and fungal, (i.e., Clitocybe sp. and Laccaria laccata ), ability to degrade polymers including polylactide (PLA) and poly(ethylene terephthalate) (PET). The effectiveness of biodegradation also significantly depended on the species, i.e., the presence of Salix viminalis L. (willow) enhanced the level of biodegradation more significantly that the presence of B. napus and Miscanthus x giganteus J.M.Greef, Deuter ex Hodk., Renvoize (giant miscanthus). It was suggested that root exudates probably support the growth of microorganisms and/or root exudates can activate microbial genes involved in the biodegradation of plastics, such as intra- and extra-cellular depolymerases. The breakdown of long polymers into oligo-, di-, and mono-mers enables uptake of those molecules by a bacterial cell which can be then utilized as a carbon and/or energy source [ 169 ]. Afzal et al. [ 170 ] reported that inoculation of Italian ryegrass ( Lolium multiflorum Lam.) and birdsfoot trefoil ( Lotus corniculatus L.) with alkane-degrading bacteria Pantoea ssp. and Pseudomonas sp. separately or in consortium resulted in higher biomass production by plants and bacterial consortium showed higher degradation ratio in comparison to single strain inoculants. The ability of these bacteria to degrade alkane was linked to the presence of genes encoding cytochrome p450 alkane hydroxylase (CYP153) and alkane monooxygenase ( alkB ). Enterobacter ludwigii possessing the CYP153 gene was able to degrade diesel fuel [ 171 ]. On the other hand, it was shown that the level of degradation of polycyclic aromatic hydrocarbon was reduced in the presence of ryegrass ( Lolium perenne L.) root exudates [ 172 ] which suggest that plants might differ in their potential to enhance bioremediation potential of soil microorganisms. The PGPM are able to degrade various other compounds of different origins as a means for the promotion of plant growth and development. Allelochemical compounds secreted by plants can hinder the cultivation of other plant species in cropping systems. Trichoderma harzianum SQR-T037 was shown to degrade allelochemicals secreted by cucumber roots (4-hydroxybenzoic acid, vanillic acid, ferulic acid, benzoic acid, 3-phenylpropionic acid, and cinnamic acid). The use of strains able to biodegrade allelochemicals can ameliorate allelopathic stress in continuous cropping systems [ 173 ]. Among common soil contaminants, plant protection agents are of special interest since their persistence in the agricultural soil is high, and their concentration may increase with each application. Diuron, a phenylurea herbicide, has a mean half-life of 330 days. Inoculation of soil containing diuron with fungal endophyte Neurospora intermedia leads to degradation of 99% of diuron in the soil after 3 days. Moreover, the authors reported that this strain is able to degrade other phenylurea herbicides, e.g., fenuron, monuron, isoproturon, chlorbromuron, and chlortoluron [ 174 ]. Although organophosphorus pesticides are perceived as non-persistent, they are highly toxic for a wide variety of non-target organisms, including mammals and rhizospheric microbes. Tested strains of T. harzianum and Metarhizium anisopliae showed an ability to degrade a number of organophosphorus pesticides such as diazinon, profenofos, and malathion in a temperature range of 20–45 °C [ 175 ].

3. Microbiome and Holobiont

Plants provide a multitude of ecological niches for various organisms to thrive. All these organisms including bacteria, fungi, protists, and nematodes that live on the surface and inside tissues/organs of a certain plant form the plant microbiome [ 176 ]. Although each member of the microbiome might contain genes related to the promotion of plant growth and development, the expression of those genes is dependent on the composition of the whole microbiome, on the population dynamics of potential pathogens, and on environmental conditions [ 177 ]. For example, the consortium of six bacteria ( Arthrobacter nitroguajacolicus , Bacillus cereus , Bacillus megaterium , Bacillus mojavensis , Pseudomonas azotoformans , and Pseudomonas frederiksbergensis ) was much more effective in the protection of Nicotiana attenuata Torr. ex S.Watson (coyote tobacco) against fungal pathogens Fusarium sp. and Alternaria sp. than individual members of the consortium [ 178 ]. Analysis of P. fluorescens transcriptome in response to the presence of bacteria belonging to three different genera revealed significant differences in the transcription response of P. fluorescens to different competitors [ 179 ]. Moreover, another layer of microbiome complexity is added by the presence of microbial symbionts of the members of the plant microbiome. For example, plant-associated fungi are in symbiosis with bacteria, i.e., endofungal/endohyphal bacteria [ 180 ]. Interestingly, it was shown that endohyphal bacteria Luteibacter sp. significantly increases the production of indole-3-acetic acid (IAA) in fungi Pestalotiopsis sp. However, Luteibacter sp. is not able to synthesize IAA [ 181 ]. Viruses can also interact with the plant microbiome. Dichanthelium lanuginosum (Elliott) Gould (panic grass) grows in geothermal areas in consortium with its endophytic fungus Curvularia protuberata . When the fungus is infected with Curvularia thermal tolerance virus (CThTV), soil temperature tolerance of panic grass increases from 40 °C to 65 °C [ 182 , 183 ]. Those results clearly show that other microorganisms present in soil strongly affect the PGPM potential to promote plant growth and development.

Although plants recruit a number of diverse microorganisms, they show preferences toward specific bacteria species. Analysis of seeds of medicinal plant red sage ( Salvia miltiorrhiza Bunge) collected at different locations revealed that there are no significant differences in the composition of the microbiome, whereas different plant species collected at the same location had significantly different microbiomes. This indicates that different species of plants exhibit a preference for specific groups of microorganisms [ 184 ]. Redford et al. [ 185 ] demonstrated the structure of microbial communities present on Pinus ponderosa Dougl. Ex C. Lawson needles are very similar regardless of geographic location. However, there are also examples of substantial differences in the microbiome of different cultivars of one plant species described in the literature. For example, Germida et al. [ 186 ] showed that root microbiomes of modern and older wheat cultivars were significantly different. Moreover, some microorganisms interact only with single plant species. For instance, a number of ectomycorrhizal fungi form mycorrhiza only with one species of a tree, e.g., Suillus grevillei and larch ( Larix sp.) (as reviewed in [ 187 ]). Species of Pinaceae are the only hosts for the fungal genus Rhizopogon [ 188 ]. The most known example is the highly specialized relationship between legumes and rhizobia [ 189 ]. Wicaksono et al. [ 190 ], by studying bog ecosystems, found that microbiomes of vascular plants are less diversified than those of non-vascular plants including bryophytes. Specificity between host and microbes seems to be a plastic trait modulated by the environment [ 191 ]. The mechanisms underneath the preferences of the host plant toward a specific set of microorganisms are not well understood, but recently Salas-González et al. [ 192 ] showed that mechanisms involved in the maintenance of plant mineral nutrient homeostasis also contribute to microbiome assembly.

The composition of the plant microbiome is largely dependent on the phase of plant growth and development. The mature seed is colonized by microorganisms that were associated with the mother plant, (i.e., microbes were transferred vertically), and those microorganisms are the first members of the microbiome of a newly emerging plant [ 193 ]. During germination, microbes transferred vertically have an advantage in plant colonization over the microorganisms present in the soil. During plant development, new symbiotic microorganisms transferred horizontally, (i.e., from the soil), appear [ 136 , 194 ]. Interestingly, it was demonstrated that microbes transferred vertically usually inhabit the phyllosphere, while the rhizosphere and root are colonized by the microorganisms from the soil. A study on oak ( Quercus robur L.) microbial inheritance showed that microbial composition of the phyllosphere was very similar to the composition of the embryo [ 195 ]. Sánchez-López et al. [ 196 ] showed that seed endophyte Methylobacterium sp. Cp3 was transferred via seeds across three generations of the plant Crotalaria pumila Ortega. Moreover, when Methylobacterium sp. Cp3 was inoculated to the soil at the time of C. pumila , flowering migration of bacteria from soil to seeds was observed. Moreover, the microbiome strongly differs among plant organs and tissues, i.e., the surface of the leaf is colonized by different microorganisms in comparison to the rhizosphere microbes [ 177 ]. A study on native and cultivated Agave species showed differences in bacterial taxa colonizing the rhizosphere, the phyllosphere, and the leaf and root endosphere. Interestingly, a composition of the fungal microbiome was affected mainly by the host plant biogeography [ 197 ]. Zarraonaindia et al. [ 198 ] demonstrated that below- and above-ground microbial communities of grapevine ( Vitis vinifera L.) were significantly different. Moreover, the composition of microbiomes of leaves, grapes, and flowers was more similar to the composition of soil microbiomes than to each other. Similarly, in sugarcane ( Saccharum sp.), clear differences in microbial taxa between organ types were observed. Interestingly, the microbiome composition of the young shoots formed from the underground ratoon was very similar to the microbiome of roots [ 199 ]. The phyllosphere is a hostile and dynamic environment. Microbes present on plant above-ground surfaces are subjected to irregular nutrient availability and changeable environmental conditions. The phyllosphere microbiome seems to be even more dependent on environmental conditions than the root microbiome [ 88 , 185 ]. It should be pointed out that the data regarding phyllosphere microbiomes other than leaf microbiomes is still rather limited. A study on the microbiome of apple ( Malus domestica Borkh.) flowers showed that the most popular are bacteria belonging to the extremophilic phylum Deinococcus - Thermus . Moreover, the composition of the flower microbiome was dependent on the phase of apple flower development [ 200 ].

The composition of the plant microbiome is also strongly influenced by various environmental factors, such as climate, soil properties [ 201 , 202 , 203 ], water [ 204 ], and nutrient availability [ 205 , 206 ]. The adaptation of plant metabolism to environmental change is strongly supported by rapidly changing microbial communities [ 204 ]. Analysis of the lettuce ( Lactuca sativa L.) microbiome showed that the composition of the phyllosphere microbiome is strongly dependent on the time of the year [ 207 ]. Drought is one of the most important stress factors significantly affecting not only plant growth and the yield of crops [ 208 ], but also the plant microbiome. Drought affects the microbiome directly because a low level of soil moisture inhibits the growth of several microorganisms. In drought conditions, plants recruit stress microbiomes, i.e., the most beneficial group of microbes allowing the plant to adapt to a particular set of environmental conditions. For instance, the abundance of Actinobacteria increased in drought-treated roots and the rhizosphere of 18 species belonging to Poaceae . The results suggest that although the microbiome is species-specific, drought caused a relatively conserved response in different hosts [ 209 ]. In drought stress conditions, an increase in the abundance of the rhizospheric drought stress-resistant bacteria in Oryza sativa L. was observed, mainly members of Actinobacteria and Chloroflexi, whereas the abundance of Acidobacteria and Deltaproteobacteria decreased [ 210 ]. Nelson et al. [ 211 ] reported enormous changes in microbial composition in forest soils after wildfires which occur more often due to climate change. As expected, an overall decrease in the abundance and biodiversity of bacterial and fungal communities was observed one year after the fire. Both the carbon and nitrogen cycle were found to be impaired not only by the loss of microbial taxa involved in geochemical cycles, (e.g., no expression of nifA genes in tested soils was detected), but also by the activity of viruses. The presence of plant pathogens has also a substantial effect on the microbiome ( Figure 1 ). In Gossypium hirsutum L. (cotton) infected with the pathogenic fungus Verticillium, the abundance of arbuscular mycorrhiza fungi and plant growth-promoting bacteria (PGPB) was lowered [ 212 ]. A study on strawberries ( Fragaria x ananassa Duchesne) infected with Verticillium dahliae and Macrophomina phaseolina showed that plants without symptoms of infection had a higher abundance of PGPB than plants with visible symptoms of infection. The microbiome of healthy plants includes more bacteria antagonistic or competitive towards pathogens [ 213 ]. Moreover, herbivores can shape the plant microbiome. Kong et al. [ 214 ] showed that whitefly infestation of Capsicum annuum L. (pepper) changed the overall microbiome composition. Pseudomonas spp. that are recruited by the plant to the rhizosphere microbiome increased the mortality of whitefly.

A particular part of the microbiome is the core microbiome which consists of those species of microbes that regularly and ubiquitously appear in the microbiomes of particular plant species. The concept of the core microbiome was first coined by a scientist involved in the Human Microbiome Project, with the goal to identify microbial taxa and/or genes that are shared by all or most humans [ 215 ]. Microbial taxa that are commonly found in a number of environments or host types can be assigned to a core microbiome. The most common approach to verifying whether a species belong to the core microbiome is to determine microbial groups that are shared among two or more microbiomes of a particular host in various environments [ 216 ]. For example, analysis of the B. napus rhizosphere microbiome grown in different conditions, i.e., the level of fertilization and the level of plant density, revealed that the core root microbiome of this plant is composed of microbes belonging to genera Streptomyces , Cryocola , Arthrobacter , Flavobacterium , Janthinobacterium , Serratia , Kaistobacter , Pseudomonas , Pedobacter , Agrobacterium , Burkholderia , Acidovorax, Erwinia , and Stentrophomonas [ 217 ]. Analysis of the composition of the microbiome of various plant species including A. thaliana , rice, sugarcane, grapevine, barley, and soybean has revealed that the core microbiome included microbes belonging to Pseudomonas , Agrobacterium , Methylobacterium , Sphingomonas , Erwinia , Cladosporium , Conithyrium , Resinicium , and Fusarium [ 177 ]. A special part of the core microbiome is a group of microorganisms called “hub microorganisms”. Those microorganisms strongly shape the composition of the microbiome through biotic interactions with host plants and other microbes. Microorganisms belonging to the hub species are called keystone species since they serve as mediators between the plant and members of the plant microbiome. Through the hub species, the host plant can selectively affect the composition of the associated microbiome. Removal of keystone species can result in the loss of interaction and a disturbance in the whole microbiome [ 218 ]. The analysis of the phyllosphere microbiome of A. thaliana showed that plant-parasitic oomycetes Albugo laibachii is a hub species that strongly affects the whole microbial community. As a consequence of infection with A. laibachii, high divergence between the composition of the microbiome of control and of infected plants was observed. Moreover, less variability among microbiomes of infected plants was shown [ 219 ]. In a study on corn ( Zea mays L.) hub species, the elimination of Enterobacter cloaceae from inoculum containing seven microbes resulted in a loss of a few other microbes from the microbiome. Removal of other bacteria from this system did not significantly change the microbial community which suggests that E. cloaceae functions as a keystone species [ 220 ].

A far wider concept than microbiome is the concept of holobiont which was introduced in 1991 [ 221 ]. Currently, a holobiont is defined as an organism composed of the plant host and of all the microorganisms that are associated with that particular plant. Natural selection between the plant and microbes supports the system and its stability throughout the evolution of a holobiont. In a holobiont, intricate networks of interactions between microorganisms and plant host are observed (as reviewed in [ 177 , 218 , 222 , 223 ]). All the genes present in the holobiont, i.e., plant genes and genes in the microbiome, constitute the hologenome [ 224 , 225 ]. The concept of a hologenome suggests that plants’ adaptability to the environment is determined not only by plant genes but also by genes of microorganisms. Hologenomes are responsible for shaping the phenotype of holobionts in response to a particular set of environmental conditions [ 226 ].

4. Plant Immune System in Plant–PGPM Interactions

The plant immune system plays a key role in plant–microorganism interactions. It is crucial not only for controlling pathogenic microorganisms but also for balancing the homeostasis of the microbiome and for overseeing commensal microbes [ 227 ]. The prominent role in plant–PGPM interactions play patterns recognizing receptors (PRRs), which recognize conserved microorganisms-specific molecules referred to as pathogen-/microbe-associated molecular patterns (P/MAMPs), such as flagellin, lipopolysaccharides, antibiotics, and VOCs [ 228 ]. PRRs are transmembrane multimeric protein complexes located at the plasma membranes present in all plant organs and tissues. Plant PRRs are either surface-localized receptor kinases that contain ligand-binding ectodomain and intracellular kinase domain or receptor-like proteins that do not have any intracellular signaling domain. PRRs contain various ligand-binding ectodomains that allow for the recognition of a wide range of P/MAMPs [ 228 ] and activate pattern-triggered immunity (PTI) [ 229 ]. Activation of PTI via MAMPs inhibits intensive proliferation of most microorganisms via synthesis and secretion of low-molecular-weight compounds, e.g., phytoanticipins and proteins, e.g., defensins. Moreover, plants synthesize cuticles which lead to the thickening of the cell wall [ 227 ]. Some pathogens secrete effector molecules, which disturb PTI functioning and thus allow for the infection of the plant [ 222 ]. Effector-triggered immunity (ETI) is activated by recognition of pathogen effector proteins via intracellular receptors R proteins encoded by resistance genes (R genes) [ 230 , 231 ] and via nucleotide-binding leucine-rich repeat receptors (NLR) located in the cytoplasm [ 229 ]. ETI leads to the overproduction of reactive oxygen species (ROS) and ion fluxes. As a consequence, hypersensitive response (HR) is activated which leads to apoptosis of infected plant cells that restrict the spread of infection [ 232 ].

Much less is known about the action of the plant immune system in the context of commensal microorganisms; however, there is some evidence that the plant immune system is crucial for microbiome assembly. Some strains of bacteria are able to modulate plant receptors, transcription factors, and molecules involved in the functioning of an immune system which allows for the colonization of plant tissues by other symbiotic microbes [ 233 ]. Moreover, some mechanisms used by the members of the microbiome to evade or suppress the plant immune system were also described. For example, in some symbiotic microorganisms, MAMP variants that do not activate plant immune response via PRRs have evolved. In addition, some commensal fungi are able to convert chitin into chitosan via deacetylation which induces a weaker immune response. MAMPs could be also degraded or sequestered by microbial proteases and other enzymes in order to evade recognition by PRR, as reviewed in [ 222 ]. It was also suggested that plants are able to actively ignore the presence of microbial commensals [ 234 ]. In A. thaliana, outer layers of roots low expression of PRRs and a lack of immune response in presence of pathogen- and commensal-derived MAMPs were reported. Neighboring cells harbor a high number of PRRs and show a rapid MAMP-triggered response [ 235 ].

5. Mechanisms Underneath PGPM–Plant Interactions

Plant growth-promoting microorganisms affect various aspects of plant growth and development. PGPM enhances the germination ratio [ 18 , 23 , 236 ], increases the elongation growth of the shoot and root [ 46 , 48 , 237 ], increases the biomass production [ 20 , 26 , 37 ], accelerates flowering [ 56 , 73 ], and increases the photosynthesis rate [ 27 , 42 ]. The examples of the mechanisms of action of plant growth-promoting fungi (PGPF) and bacteria (PGPB) are presented in Table 2 and Table 3 , respectively.

Examples of mechanisms of plant growth promotion by PGPF.

Examples of mechanisms of plant growth promotion by PGPB.

Several mechanisms underneath the promotion of plant growth and development by microorganisms are employed by both bacteria and fungi for example degradation of ethylene via ACC deaminase, production of phytohormones, and solubilization of various soil compounds to increase the bioavailability of nutrients ( Table 2 and Table 3 ). For sure the mechanism of greatest importance is the fixation of atmospheric nitrogen via nitrogenase, a mechanism that is specific to some specialized groups of prokaryotes (as reviewed in [ 271 , 272 ]). On the other hand, the fungi-specific mechanisms that allow for the promotion of plant growth and development includes the production of hydrophobins, swollenins, and peptaibols (please see the section Trichoderma -plant interaction—a case study, for details).

5.1. Plant Antioxidant Defence System

One of the best-known mechanisms to improve plant growth and development by PGPM is the modification of the level of antioxidants including antioxidative enzymes, e.g., superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase (POD), catalase (CAT), glutathione reductase (GR), and non-enzymatic antioxidants, e.g., proline, glutathione (GSH), ascorbic acid, carotenoids, and phenolics [ 25 , 273 , 274 , 275 , 276 , 277 ]. Islam et al. [ 278 ] demonstrated that inoculation of Vigna radiata (L.) R. Wilczek with Bacillus cereus Pb25 increased dry biomass and yield in salt stress conditions. Salt-induced oxidative damage was reduced by enhancing the activity of plant POD, SOD, and CAT and by increasing proline content in plants. Inoculation of O. sativa with Bacillus pumilus increased the activity of rice catalase and superoxide dismutase in salt stress conditions. Moreover, inoculation of rice with B. pumilus promoted the synthesis of photosynthetic pigments and proline [ 275 ]. Accumulation of phenols and proline was observed in cucumber inoculated with arbuscular mycorrhizal fungi in salt conditions [ 279 ]. A potato co-inoculated with T. viride and plant pathogen Alternaria solani showed improved redox homeostasis via increased activity of CAT and SOD, and enhanced concentration of free phenolics. Moreover, co-inoculation with T. viride and A. solani resulted in increased H 2 O 2 production which induced the expression of plant defense genes [ 274 ]. Chen et al. [ 25 ] reported increased salt stress tolerance in maize after inoculation with B. amyloliquefaciens SQR9. Inoculated plants showed a reduced level of Na + , a higher glutathione content, a higher concentration of soluble sugars, and enhanced activities of peroxidase and catalase. B. amyloliquefaciens enhanced chlorophyll content and promoted the overall growth of inoculated plants in comparison to control plants. In addition to the well-known elements of the antioxidant system, there are also other proteins exhibiting antioxidant activity, including small cysteine-rich proteins metallothioneins (MTs). MTs act as direct antioxidants since the reduced thiol groups (-SH) can be oxidized by ROS. MTs also serve as a donor of zinc and copper to other antioxidative enzymes [ 280 , 281 ]. Inoculation of rapeseed with fungal strains isolated from forest soil showed varied expressions of B. napus metallothioneins ( BnMT1 - BnMT3 ). L. laccata inoculated plants showed significant upregulation of BnMT2 expression with a decrease in BnMT3 transcripts [ 43 ].

5.2. Phytohormones

Some bacteria are able to synthesize and secrete phytohormones and thus regulate plant growth and development. For example, B. subtills synthesizes auxins and gibberellins [ 282 ], and A. brasilense [ 283 , 284 ], Peanibacillus polymyxa [ 285 ], and P. fluorescens [ 286 ] produce cytokinins. Inoculation of S. tuberosum damaged by insect attack (beetle Leptinotarsa decemlineata ) with B. subtilis 26D led to increased concentration of zeatin-riboside but not of abscisic acid (ABA) and indole acetic acid (IAA). The inoculation of potatoes with B. subtilis increased the mass of roots [ 287 ]. In the culture of Bacillus aryabhattai abscisic acid, indole acetic acid, cytokinins, and gibberellic acids were detected. Soybean inoculated with these bacteria produced more IAA, jasmonic acid, and some gibberellic acids. Moreover, inoculated plants displayed increased tolerance to heat stress possibly due to the ABA-induced closure of stomata [ 288 ].

Although different stressors affect plant organisms in various ways, most of them lead to increased ethylene production in plants. Weak stress factors can cause small overproduction of ethylene which leads to the activation of plant stress-related genes. Long periods of stress and severe stressors cause a high level of ethylene production, which might lead to senescence, chlorosis, and organ abscission [ 136 ]. Some PGPM are able to lower the level of ethylene through secretion of ACC deaminase, i.e., the enzyme that breaks down ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Inoculation of plants with microbes producing ACC deaminase effectively increased the plant resistance to stress caused by fungal pathogens [ 289 ], nematodes [ 290 ], and several abiotic stresses such as flooding [ 291 ], drought [ 135 ], salination [ 133 ], heavy metals [ 292 ], and toxic contaminates [ 134 ]. For example, inoculation of pearl millet seed with ACC deaminase-producing B. amyloliquefaciens increased plant growth in drought stress via increasing the level of enzymatic and non-enzymatic antioxidants [ 272 ]. Isolated from Brassica rapa L. rhizosphere bacteria belonging to Pseudomonas sp. improved biomass and yield of B. rapa . The positive effect of analyzed strains on B. rapa is possibly due to the production of IAA, ACC deaminase, and siderophores [ 95 ].

5.3. Availability of Micro- and Macronutrients

In most terrestrial ecosystems, nitrogen is the major nutrient limiting plant growth. PGPMs might increase the pool of nitrogen available for plants thorough various mechanisms. It is estimated that in nature more than 60% of fixed nitrogen is a result of biological nitrogen fixation [ 272 ]. A well-known example is the Rhizobia present in root and stem nodules of legumes that is able to reduce N 2 to ammonia. There are also other symbiotic, plant-endophytic, and free-living bacteria able to fix molecular nitrogen, including bacteria belonging to Frankia , Cyanobacteria , Azotobacter , Bacillus , and Azospirillum, as reviewed in [ 293 ]. The Co-inoculation of beans with Rhizobium phaseoli and bacteria belonging to Bacillus and Pseudomonas improved plant growth by enhancing the total content of nitrogen in plant tissues more efficiently than inoculation with R. phaseoli. Only [ 127 ]. Hungria et al. [ 130 ] reported that the co-inoculation of soybean seeds with Azospirillum and Bradyrhizobium significantly enhances the yield without any input of nitrogen fertilizers. Several lines of evidence showed that rhizobia are susceptible to drought-stress and the efficiency of N 2 -fixation dramatically declines in low-water conditions [ 294 ]. For example, co-inoculation of a common bean with Rhizobium tropici and two strains of P. polymyxa more effectively increased nitrogen content and promoted plant growth than inoculation with Rhizobium only especially in drought conditions [ 295 ].

Phosphorus is also considered as element limiting plant growth in most ecosystems. Although phosphorus is an abundant element in ecosystems, most of it is not bioavailable [ 296 ]. There is a group of microbes, phosphate solubilizing microorganisms (PSM), that are able to increase the available fraction of phosphorus for plants via solubilization and mineralization mediated by secretion of organic acids, phosphatases, protons, and exopolysaccharides [ 297 ]. Red clover ( Trifolium pratense L.) inoculated with phosphate solubilizing fungi Penicillium albidum showed a significant increase in root biomass. In soil inoculated with fungi, the phosphatase activity was 1.5-fold higher than in the non-inoculated soil [ 129 ]. In soil inoculated with Burkholderia sp., Gluconobacter sp., and Pseudomonas striata, higher activity of dehydrogenase and phosphatase and a higher level of available P were detected. Vigna unguiculata (L.) Walp. grown in inoculated soil had noticeably higher biomass and yield than plants grown in non-inoculated soil. Moreover, tested microorganisms enhance uptake not only of phosphorus but also of nitrogen [ 298 ]. Inoculation of T. aestivum with Serratia marcescens enhanced plant growth and nutrient uptake (P, N, and K) in low temperatures. The ability of tested bacteria to solubilize P decreased at low temperatures [ 299 ].

Soil minerals, such as feldspars and micas, are the most common form of potassium in soils. Up to 90–98% of soil potassium is present in a form unavailable for plants [ 300 ]. By secretion of organic acids and capsular polysaccharides, some PGPM are able to solubilize potassium rocks, e.g., bacteria belonging to Acidothiobacillus , Bacillus , Pseudomonas , Burkholderia , and Peanibacillus [ 301 ]. Ali et al. [ 302 ] reported that inoculation of potatoes with K-solubilizing B. cereus resulted in significantly improved plant growth and yield. Moreover, the content of K in potato tubers and the content of N, P, and K in leaves was higher in comparison to control plants. Inoculation of ryegrass with Mesorhizobium sp., Peanibacillus sp., and Arthrobacter sp. isolated from canola rhizosphere improved biomass and yield. The content of available K in soil was much higher and resulted in increased K content in plants [ 303 ]. Basak and Biswas [ 304 ] demonstrated that treatment of waste mica with Bacillus mucilaginosus led to the transformation of K forms into water-soluble forms. This had a positive effect on K uptake and biomass of sudan grass ( Sorghum vulgare Pers.). Similar effects were observed by Raji and Thangavelu [ 305 ], who analyzed the effect of inoculation of tomato ( Lycopersicon esculentum L.) grown in Alfisol and Vertisol soils with B. subtilis , B. cereus , Bacillus licheniformis, and Burkholderia cenocepacia . Inoculated plants showed higher K content in tissues and improved growth.

The deficiency of microelements, including copper (Cu), iron (Fe), zinc (Zn), and manganese (Mn), is also a prominent factor that negatively affects plant health. In calcareous soils (widespread in arid and semiarid regions of the world), the high content of calcium carbonate which acts as a buffer and maintains a pH above 7.5, is correlated with decreased bioavailability of Fe, Zn, and Mn [ 306 ]. Plants possess mechanisms allowing them to increase amounts of bioavailable microelements in soils. For example, to facilitate Fe acquisition, plants secrete siderophores, organic acids, and flavonoids [ 307 ], whereas the amount of bioavailable Zn is increased by the secretion of organic acids, such as propionic acid, formic acid, lactic acid, citric acid, succinic acid, malic acid, oxalic acid, and gluconic acid as well as by secretion of siderophores, as reviewed in [ 308 ]. A tomato grown in hydroponic culture with the addition of soil minerals in Cu-deficient conditions showed increased biomass and Cu uptake after inoculation with Trichoderma harzianum SQR-T037 in comparison to non-inoculated plants. Interestingly, inoculation of a tomato with T. harzianum SQR-T037 grown in an Fe-deficient hydroponic culture with the addition of solid mineral increased the Fe content in plant tissue, but the biomass of seedling was unaffected. In addition, inoculation of tomatoes grown in Zn-deficient hydroponic conditions did not increase the biomass and the concentration of Zn in plant tissues was decreased. Those observations suggest that in element-deficient conditions fungi compete with plants for nutrients [ 309 ]. Rana et al. [ 128 ] showed enhanced yield and increased concentrations of Fe, Zn, Cu, and Mn by 13–16% in rice grains after inoculation with Brevundimonas diminuta , Ochrobactrum anthropic , and Providencia sp. Wheat inoculation with Providencia sp. significantly increased yield and the content of Fe and Cu in grains was 45% higher than in control plants. Singh et al. [ 310 ] reported that endophytic bacteria isolated from wheat, such as B. subtilis , Arthrobacter sp., A. sulfonivorans , and Enterobacter hirae exhibiting plant growth-promoting traits, enhanced Fe and Zn fortification as well as yield and dry/fresh weight in pot experiment and field conditions. Moreover, a decrease in phytic acid was observed in grains of wheat plants inoculated with endophytes. A field study on common bean and wheat fortification showed that inoculation with A. brasilense and T. harzianum significantly enhanced micronutrients, i.e., Fe, Mn, and Zn content in both tested plants [ 311 ]. Enhanced content of selenium was observed in lettuce inoculated with bacteria Bacillus sp., Klebsiella sp., Acinetobacter sp., and with fungus Rhizophagus intraradices in drought stress conditions. Results showed that plants inoculated with bacteria showed higher biomass production in comparison to plants inoculated with fungus, and Klebsiella sp. was the most effective in the induction of Se accumulation in lettuce. Moreover, tested microbes increased drought stress resistance, the chlorophyll and carotenoid content, and enhanced the level of antioxidant enzymes [ 312 ]. The ability of some PGPM to increase the content of macro- and micro-elements in different parts of plants is also important for human nutrition. Microelements deficiency (especially zinc and iron) is widespread all over the world. Biofortification, i.e., approaches to enhance the nutritional value of crops, with microelements in edible parts of plants, is the most promising approach to fight against microelements deficiency, as reviewed in [ 313 , 314 , 315 ]. Therefore, PGPM seems to be of crucial importance for both food quantity, i.e., enhanced plant yield and food quality, i.e., edible parts of plants with high content of minerals.

5.4. Direct Interactions of PGPM with Plant Pathogens

PGPM might directly interact with various plant pathogens. Through various mechanisms, including the production and secretion of antimicrobial metabolites, antagonisms, mycoparasitisms, and competing for niche PGPM can enhance plant biotic stress resistance. Cabrefiga et al. [ 316 ] reported an antagonistic interaction between P. fluorescens EPS62e and Erwinia amylovora , bacteria causing fire blight disease on pear trees ( Pyrus sp.). P. fluorescens EPS62e did not produce antibiotics and required cell-to-cell contact with the pathogen in order to inhibit their growth on pear flowers and fruits. Interestingly, antagonistic activity was not shown when bacteria were grown in an Fe-rich medium, which suggested that the production of siderophores is responsible for the P. fluorescens EPS62e ability to inhibit the growth of E. amylovora . Inoculation of plants with antibiotic-producing microorganisms might lead to the suppression of various plant diseases. From the roots and rhizosphere soil of cucumber grown in soil inoculated with biocontrol agent B. subtilis, antibiotics surfactin and iturin A were extracted [ 317 ]. Bais et al. [ 318 ] showed that the biocontrol ability of B. subtilis against Pseudomonas syringae is tightly linked with the production of surfactin involved in biofilm formation on A. thaliana roots. B. subtilis mutant with a deletion in the surfactin synthase gene was unable to form biofilm and was ineffective in protection against P. syringae attack. Rhizospheric S. plymuthica HRO-C48 isolated from the rhizosphere of rapeseed produces antibiotic pyrrolnitrin and can protect plants against Verticillium wilt [ 319 ]. Kurze et al. [ 320 ] demonstrated that S. plymuthica HRO-C48 protects strawberries against fungal pathogens V. dahliae and Phytophtora cactorum . Moreover, the inoculation of strawberries with S. plymuthica promoted plant growth and improved yield. Inoculation of wheat seedlings with Trichoderma sp. resulted in an increase in plant resistance markers when plants were infected with Fusarium spp. Moreover, a decrease in IAA was observed. Biocontrol activity of Trichoderma was connected with the secretion of lytic enzymes and fungal elicitors as well as mycoparasitism [ 49 ]. An interesting observation was made by Chen et al. [ 321 ] who showed that Pseudomonas piscium isolated from wheat is able to alter histone acetylation in pathogenic Fusarium gramineareum and, therefore, reduce the fungus level of virulence and mycotoxin production by the fungus. An identified compound secreted by P. piscium, i.e., phenazine-1-carboxamide, disturbs the activity of fungal histone acetyltransferase FgGcn5, responsible for the regulation of gene expression involved not only in virulence and the growth of the mycelium, but also in asexual and sexual reproduction and stress response.

5.5. Induction of the Plant Resistance by Microbial Elicitors

Although the use of living microorganisms is a potent tool in the development of sustainable agriculture, it has also numerous constraints due to legal regulations [ 322 ]. As an alternative to the living microbes and cell wall polymers (CWP) of bacteria, fungi can be employed as elicitors [ 323 , 324 , 325 ]. Elicitors trigger the immune response of the plant via numerous mechanisms including accumulation of lignin, antimicrobial enzymes, e.g., chitinases, glucanases, phytoalexins, and proteins related to the response to the presence of pathogens, guaiacol, and ribonuclease [ 326 ]. One of the efficient elicitors is chitin and its deacetylated derivative chitosan (N-acetylglucosamine subunits are linked by (1 → 4) -β bonds). For example, chitosan led to an increase in the systemic resistance in tomatoes and an increase in the plant resistance towards Alternaria solani and Xanthomonas vesicatoria [ 327 ]. Treatment of Psammosilene tunicoides with chitosan led to an increased expression of genes encoding antioxidant enzymes and transcription factors controlling stress-response genes. Moreover, the content of secondary metabolites terpenoid saponins increased [ 328 ]. The cost-effective and efficient source of elicitors are fungi belonging both to Ascomycota and Basidiomycota. Research by Nowak et al. [ 326 ] showed that (1 → 3) -α-D-glucooligosaccharides (GOS) obtained by hydrolysis of (1→3)- α- D -glucan from Laetiporus sulphureus induced the growth of wheat seedlings. Moreover, GOS caused the increase in the activity of CAT and APX, in the activity of chitinase, and higher activity of enzymes activating phenylpropanoid-producing pathways. Laminarin, a polysaccharide, consists of β-(1-3)-glucan with β-(1-6)-linkages of 20–25 units isolated from brown algae, which is an example of elicitor belonging to β-glucans. Treatment of grapevine-cultured cells with laminarin led to calcium influx, an oxidative burst, and the induction of pathogen-related genes. Laminarin by the induction of plant resistance indirectly contributes to the reduction of the growth of B. cinerea and Plasmopara viticola on grapevine plants [ 329 ].

6. The Stringent Response in Plant–Microorganism Interactions

Among several plant mechanisms regulating growth, development, and the response to environmental factors, the stringent response is of particular interest. The stringent response was first discovered in Escherichia coli in response to amino acid starvation [ 330 ]. The hallmark of the stringent response is the accumulation of atypical regulatory nucleotides guanosine tetra- (ppGpp) and pentaphosphates (pppGpp) called alarmones that are responsible for pleiotropic adaptation to nutrient deficiency and stress factors [ 331 , 332 ]. Moreover, the bacterial stringent response through regulation of quorum sensing indirectly affects the formation of microcolonies and the development and functioning of biofilm [ 333 ]. Alarmones are synthesized from ATP/GTP or GDP by enzymes possessing active synthetase domain (SYNTH) and are hydrolyzed to GTP/GDP and pyrophosphate by enzymes containing active hydrolytic domain (HD). Gram-negative bacteria usually possess two separate enzymes, i.e., alarmones synthetase RelA and alarmones hydrolase SpoT. Gram-positive bacteria usually possess one bifunctional Rel protein [ 334 , 335 ]. RelA and SpoT belong to the long RSH (RelA/SpoT homologue), i.e., enzymes possessing HD and SYNTH domains. In bacteria, there are also short RSH, i.e., enzymes containing either SYNTH domain, small alarmone synthases (SAS) or HD domain, or small alarmone hydrolases (SAH), whereas in animals, to date only small alarmone hydrolases were identified (Mesh1—metazoan SpoT homologue) [ 336 ]. Alarmones regulate transcription, translation, and DNA replication, and trigger metabolical and physiological changes in response to unfavorable environmental conditions. Upon accumulation of alarmones, bacteria change their lifestyle from growth and proliferation to survival mode [ 335 ]. Sanchez-Vazquez et al. [ 337 ] demonstrated that in E. coli, the elevated (p)ppGpp level affected the expression of 757 genes five minutes after the induction of the stringent response and after another five minutes the expression of 1 224 genes was affected. Activation of the stringent response can be triggered by a deficiency of amino acids [ 330 ], fatty acids [ 338 , 339 ], iron [ 340 ], carbon [ 341 ], nitrogen [ 342 ], phosphorus [ 343 ], and by other types of stress, e.g., increased temperature [ 344 , 345 ], cell wall antibiotics, ethanol and acid treatments, superoxide stress [ 346 ], and alkaline shock [ 347 ].

The presence of (p)ppGpp in photosynthetic Eucaryota was confirmed in the algae Chlamydomonas reinharditi [ 348 ]. In higher plants, RSH genes were identified for the first time in A. thaliana [ 349 ] and subsequently in other plant species, e.g., Nicotiana tabacum L. [ 350 ], rice [ 351 ], Ipomoea nil L. Roth [ 352 ], Sueda japonica Forssk. ex J.F. Gmel. [ 353 ], pepper [ 354 ], and non-vascular plants, e.g., Physcomitrella patens (Hedw.) Bruch and Schimp [ 355 ]. Plant RSH proteins are divided into three groups, i.e., RSH1, RSH2/3, and CRSH. All identified plant RSH proteins belong to the long RSH, i.e., possess both HD and SYNTH domains. In model plants, the A. thaliana SYNTH domain of RSH1 (AtRSH1) is Inactive due to the substitution of conserved glycine residue required for its activity. AtCRSH does not possess a functional hydrolase domain and in AtRSH2/3, both SYNTH and HD domains are active [ 356 ]. In addition to HD and SYNTH domains, RSH possess chloroplast transit peptide [ 357 ], TGS (RSH1, RSH2/3), and ACT domains (RSH1) which were proposed to act as regulatory- or ligand-binding domains [ 358 ]. CRSH are the only proteins involved in alarmones metabolism that possess two EF hand motifs and are activated by Ca 2+ ions [ 359 ]. The domain structure of RSH proteins is highly conserved across plant species. It is now widely accepted that in plants, the place of alarmones action are chloroplasts [ 360 , 361 , 362 , 363 ]. Alarmones act as regulators of plant development and growth, i.e., (p)ppGpp coordinate micro- and macro-elements redistribution during senescent [ 364 ]. They modulate the level of phytohormones [ 365 ], lipids [ 366 , 367 ], and secondary metabolites [ 368 ] in chloroplasts. Moreover, alarmones promote the replication of plastidial DNA [ 364 ]. Plant RSH genes are differently expressed in presence of biotic and abiotic stress factors, which suggest that alarmones contribute to plant response in a number of stress factors, i.e., oxidative stress [ 369 ], nitrogen starvation [ 369 , 370 ], wounding, salination, drought, UV radiation, heat shock, heavy metals, and abrupt change from light to darkness [ 371 ]. Masuda et al. [ 372 ] showed that RSH probably play a role in plant reproduction, as the AtCRSH knockdown mutant produced smaller siliques and a lower number of seeds. An interesting observation was made by Ono et al. [ 373 ], who demonstrated an increased (p)ppGpp concentration in chloroplast upon a light-to-dark transition. The alarmones accumulation was due to higher activity of CRSH caused by elevated levels of Ca 2+ in chloroplasts. As a consequence, the expression of plastidial genes is adapted to darkness. Interestingly, it was demonstrated that the accumulation of alarmones in plants leads to a decreased expression of genes involved in the defense system, which can lead to higher susceptibility to infections [ 365 ].

Plants are probably able to manipulate the level of alarmones synthesis in members of their own microbiome but also in pathogenic bacteria. Through modulation of (p)ppGpp production in bacteria, plants may be able to decrease virulence and inhibit the growth of pathogens. Nowicki et al. [ 374 ] demonstrated the activation of stringent response in E. coli cells by plant secondary metabolites isothiocyanates (ITC). ITC-induced stringent response in E. coli led to growth inhibition, disturbed transcription, and DNA replication. The induction of the E. coli stringent response may be the result of a direct interaction of ITC with cellular proteins. That idea is plausible since sulforaphane (one of the ITCs) inhibits the growth of numerous bacteria and recently potential target proteins of ITC were identified [ 375 ]. Mwita et al. [ 376 ] showed that the expression of SasA (short alarmone synthase) of PGPB Bacillus atrophaeus UCMB-5137 is considerably upregulated by maize root exudates. Further implications of observation on these bacteria metabolisms need, however, further evaluation. On the other hand, inoculation of plants with PGPB can affect plant RSH gene expression; however, the data are scarce. Dąbrowska et al. [ 377 ] demonstrated that B. napus inoculated with S. plymuthica and Serratia liquefaciens exhibited elevated mRNA levels of BnRSH1 in cotyledons and roots, whereas inoculation with Massilia timonae increased BnRSH1 expression only in roots. Moreover, S. plymuthica seemed to affect also the expression of BnRSH2 and BnRSH3 in cotyledons and roots. The relative transcript level of BnCRSH was elevated in cotyledons in presence of S. plymuthica and S. liquefaciens . Inoculation of canola grown in salt-stress conditions with endophytic Pseudomonas stutzeri ISE12 significantly increased mRNA levels of BnRSH1 and BnRSH3 in roots in comparison to non-inoculated plants grown in salt stress [ 34 ]. Moreover, Givens et al. [ 350 ] observed a 10-fold increase in RSH2 protein level in N. tabacum after infecting the plant with the bacterial pathogen Erwinia carotovora .

Microbes might directly and/or indirectly activate the stringent response in other microorganisms. A study on the effect of the pathogenic fungus Rhizoctonia solani on the rhizosphere microbiome of sugar beet ( Beta vulgaris L.) showed that in several rhizobacteria, the expression of genes involved in (p)ppGpp metabolism is upregulated. It is not clear whether the activation of the stringent response in bacteria present in the rhizosphere is triggered directly by oxalic and phenylacetic acids secreted by R. solani or indirectly by signaling molecules in root exudates [ 378 ]. Interestingly, the relA and relA / spoT mutants of Pseudomonas sp. DF41 and Pseudomonas chlororaphis PA23, showed increased antifungal activity against Sclerotinia sclerotiorum . All mutants produced an increased level of antifungal antibiotic pyrrolnitrin, lipase, and protease in comparison to wild-type bacteria. The lack of (p)ppGpp led also to reduced transcription of rpoS [ 379 , 380 ]. Selin et al. [ 381 ] showed that expression of rsmZ , rsmE, and rsmA, i.e., elements involved in the regulation of several processes such as virulence, motility, and biocontrol abilities, was regulated via the stringent response in P. fluorescens , a PGPB inhibiting the growth of a number of pathogenic fungi including S. sclerotiorum . Takeuchi et al. [ 382 ] reported that a mutant of P. fluorescens CHA0 lacking the ability to synthesize alarmones, produced significantly fewer antibiotics and had lower biocontrol activity against P. ultimum . Moreover, the ability of the tested mutant to colonize cucumber roots, both in the presence and absence of P. ultimum , was reduced possibly due to impaired motility. The stringent response was found to strongly influence the production of antibiotics also in Streptomyces which are common members of the plant microbiome. Ochi [ 383 ] reported that rel mutant of Streptomyces antibioticus showed induction of phenoxazinone synthase, an enzyme involved in the production of actinomycin. Interestingly, this mutation did not affect the activity of another enzyme participating in the biosynthesis of actinomycin, i.e., kynurenine formamidase. Moreover, RSH genes regulated the morphological and physiological differentiation of Streptomyces clavuligerus ; the lack of (p)ppGpp affected spore formation [ 384 ].

Recent studies showed that the stringent response may play a crucial role in the interaction between legumes and rhizobia. At the beginning of the interaction, legumes produce antimicrobial compounds that lead to nutritional, osmotic, and oxidative stress in rhizobia [ 385 , 386 , 387 ]. Based on the literature, it might be hypothesized that in order to survive these unfavorable conditions, rhizobia activates the stringent response. Soybean inoculated with the rsh knockout Bradyrhizobium diazoefficiens formed smaller nodules than those present in plants inoculated with wild-type B. diazoefficiens . Moreover, the biomass of plants inoculated with mutant bacteria was smaller in comparison to wild-type bacteria, but still higher than the biomass of non-inoculated plants. Those results suggest that the lack of alarmone signaling altered nodulation and, as a consequence, decreased N 2 fixation. Interestingly, in plants co-inoculated with wild-type bacteria and the rsh mutant in equal proportion, only 26% of nodules were infected by mutant bacteria. This observation strongly suggests that the stringent response is crucial to win the competition for a niche with other rhizobia [ 388 ]. In the early phase of nodulation, establishing a symbiotic relationship between rhizobia and legumes requires plant-bacteria signaling that allows the recognition of bacteria by the host. It was shown that relA mutant of Sinorhizobium meliloti failed to form nodules on M. sativa due to disturbed stringent response, but remarkably the nodulation of Medicago truncatula Gaertn. was successful. The N 2 fixation capacity of mutant bacteria was reduced in comparison to the wild type. It is not clear why there is a difference in nodulation between those two Medicago species; however, it might be hypothesized that different plants influenced bacterial stringent response at different stages of invasion [ 389 ]. Another study also found that S. meliloti mutant unable to synthesize (p)ppGpp did not establish a symbiotic relationship with M. sativa . The relA mutant of S. meliloti produced more succinoglycan, an exopolysaccharide needed for colonization of the host, than the wild-type bacteria [ 390 ]. The inactivation of relA in Rhizobium etli caused nodules on P. vulgaris form, but the level of nitrogen fixation was significantly reduced. Mutants showed significantly lower expression of raiI and cinI genes which encode regulators of quorum sensing in rhizobia [ 391 ]. Calderón-Flores et al. [ 392 ] reported that in P. vulgaris inoculated with R. etli, the rsh mutant nodulation and nitrogen fixation were disturbed. Qiu et al. [ 393 ] demonstrated that the addition of water-soluble humic materials into inoculum containing Sinorhizobium fredii significantly downregulated RSH expression, increased survivability of bacteria in soil, and promoted rhizoplane colonization of Glycine max (L.) Merr.

The stringent response is also a significant mechanism contributing to the virulence of various plant pathogens. A study on E. amylovora showed that cells of relA and relA / spoT mutants were significantly longer both in nutrient-rich and nutrient-limited conditions in comparison to the wild type. Moreover, it was demonstrated that the proliferation rate of relA / spoT mutant in pear fruits was 1000 times slower than the proliferation rate of the wild type. In minimal medium double, the relA / spoT mutant was unable to grow. Small-sized cells are more resistant to stress, and bigger relA / spoT knockouts are unable to survive on plant surfaces. It seems that (p)ppGpp are important regulators of cell growth in E. amylovora during plant infection [ 394 ]. A similar observation was made for P. syringae , one of the most common plant pathogens. P. syringae single ( relA ) and double ( relA / spoT ) knockout mutants grown on nutrient-rich medium were slightly bigger in comparison to the wild-type bacteria. An in vivo study demonstrated that relA / spoT mutants, even though they had bigger cells, were unable to survive on the surface of a tomato leaf. These findings suggest that the stringent response is a crucial element of plant surface colonization [ 395 , 396 ]. A great induction of relA and spoT genes in gram-negative bacterium Pectobacterium atrosepticum , able to degrade plant cell walls, was observed when bacteria were grown in high-density culture in carbon-deficient media [ 397 , 398 ]. Zhang et al. [ 399 ] reported that the Xanthomonas citri double knockout spoT / relA mutants showed a significant decrease in pathogenicity and inhibited growth in planta. Interestingly, the deletion of only the main alarmones synthase in the X. citri relA did not affect the virulence of the bacterium.

Several lines of evidence showed that the stringent response plays a crucial role in the adaptation of bacterial growth and metabolism to nutrient-limited conditions. The mentioned studies above show the importance of the stringent response for the establishment of plant–PGPM interactions and proper functioning of the plant microbiome. We hypothesize that the stringent response probably allows members of the microbiome to survive in unfavorable conditions during the first stages of interaction establishment. The data about the possible role of alarmones in an intricate network of interactions between plants and microorganisms, among members of microbiomes, and between PGPM and plant pathogens are rather limited. The possible crucial role of the plant and the microbial stringent response in the functioning of microbiomes is an exciting but rather overlooked research area that needs further experiments.

7. Trichoderma –Plant Interaction—A Case Study

Among several other microbes belonging to the PGPM group, fungi from the genus Trichoderma are of great interest. Adaptability to unfavorable environmental conditions and the ability to utilize many different substrates as nutrients determine the ubiquitous occurrence of fungi belonging to Trichoderma in soils. It is estimated that one gram of soil contains 10–10 3 CFU (colony-forming unit) of fungi belonging to Trichoderma [ 400 , 401 ]. It was estimated that there are around 438 species in the genus Trichoderma , grouped into 10 phylogenetic lineages: Brevicompactum, Deliquescens, Harzianum, Hypocreanum, Longibrachiatum, Polysporum, Psychrophilum, Semiorbis, Stromaticum, and Viride [ 402 ].

Through interaction with plant fungi belonging to Trichoderma gains, a convenient niche for growth and development since root exudates are a rich source of carbon and other nutrients. The presence of fungi belonging to Trichoderma enhances growth and increases yield [ 403 , 404 ], improves uptake of nutrients by plants [ 405 , 406 ], and leads to a higher vigor and germination ratio of seeds [ 407 , 408 ]. In addition, fungi belonging to Trichoderma increase the level of photosynthesis [ 409 ], the level of amino acid synthesis [ 410 ], the level of transpiration [ 411 ], and the water content in tissues in drought conditions [ 412 ]. Fungi from the genus Trichoderma can colonize the roots of mono- [ 56 , 57 , 413 ] and di-cots [ 58 , 131 , 132 ] and when plants are grown in acidic soils [ 414 ], alkaline soils [ 415 , 416 ], and soils contaminated with heavy metals [ 417 , 418 ]. Trichoderma are potential symbionts of non-mycorrhizal plants belonging to Brassicaceae [ 59 ], Chenopodiaceae [ 302 ], Caryophyllaceae [ 419 ], Polygonaceae [ 420 ], and others. Recently, marine isolates of Trichoderma have been identified [ 421 , 422 , 423 , 424 , 425 ], which have the potential to serve as plant growth-promoting fungi for plants grown in saline soils [ 426 ]. Several mechanisms have been shown to contribute to the promotion of plant growth and development by fungi belonging to Trichoderma . Colonization of plants by Trichoderma changes host proteome [ 413 ] and secretome [ 427 ], affecting the level of synthesis of phytohormones [ 428 ] in soluble sugars [ 409 ] and phenolic compounds [ 173 , 429 ]. The inoculation of A. thaliana seedlings with Trichoderma virens and Trichoderma atroviride increased biomass production and promoted lateral root growth. Mutations in plant genes involved in auxin transport and signaling, i.e., AUX1, BIG, EIR1 , and AXR1 caused reduced stimulation of root growth and development by tested Trichoderma isolates [ 92 ]. Fungi belonging to Trichoderma compete with pathogens for ecological niches and nutrients, which efficiently limits the growth of pathogens. Secreting antibiotics, siderophores, a range of volatile and non-volatile metabolites (n-alkanes, cyclohexane, cyclopentane, esters, alcohols, sulfur-containing compounds, pyrane, and benzene derivatives), and through mycoparasitism fungi belonging to Trichoderma, protect plants against various pathogens, such as R. solani [ 430 , 431 , 432 ], Rhizopus oryzae [ 433 ], Fusarium spp. [ 434 , 435 ], Alternaria alternate [ 436 ], S. sclerotiorum [ 432 , 437 ], Botrytis cinerea [ 438 , 439 ], Pythium spp. [ 433 ], and Ustilago maydis [ 440 ]. Several secondary metabolites produced by fungi belonging to Trichoderma peptaibols seem to be of great importance for Trichoderma biocontrol activity. Peptaibols are amphipathic polypeptides composed of 5–10 amino acids with molecular masses between 500 and 2200 Da. These non-ribosomally synthesized polypeptides contain not only typical amino acids but also non-proteinogenic amino acids and α-aminoisobutyric acid. Peptaibols are synthesized not only by fungi belonging to Trichoderma but also by other soil-born fungi as well as by plant-pathogen fungi [ 441 , 442 ]. Several lines of evidence have confirmed that peptaibols exhibit antibacterial and antifungal properties. Trichoderma pseudokoningii produces trichokonin VI that induces apoptotic cell death in F. oxysporum [ 443 ]. Trichokonins A produced by Trichoderma longibrachiatum damages the cell membrane of Gram-negative pathogenic bacteria Xanthomonas oryzae pv. Oryzae , leading to a significant reduction of the pathogenicity of these bacteria [ 444 ]. The same inhibitory effect was observed for several other peptaibols produced by various Trichoderma species against a range of plant pathogens, e.g., B. cinerea [ 445 ], Septoria tritici [ 446 ], A. solani , and R. solani [ 447 ]. Moreover, it was also demonstrated that peptaibols can act against viruses. Luo et al. [ 448 ] showed that trichokonins isolated from T. pseudokoningii induces resistance of tobacco against the tobacco mosaic virus probably via induction of reactive oxygen species and phenolic compound production. Peptaibols isolated from T. virens might act as elicitors and induce a defense response in cucumber against pathogenic bacteria Pseudomonas syringae pv. lachrymans via up-regulation of hydroxyperoxide lyase, phenylalanine ammonia lyase, and peroxidase gene expression. In addition, T. virens mutant tex1 lacking one of the non-ribosomal peptide synthetases was less effective in the inhibition of P. syringae pv. lachrymans growth [ 247 ]. It should be pointed out that high concentrations of peptaibols might have a negative impact on the growth of plants, as shown for peptaibols produces by Trichoderma reesei and their negative effect on A. thaliana . However, peptaibols at lower concentrations are still sufficient to inhibit the growth of plant pathogens with no adverse effect on plant growth [ 449 ].

Moreover, some strains of Trichoderma can induce ISR (induced systemic resistance) and/or SAR (systemic acquired resistance) in the host plant through the secretion of fungal elicitors. Shoresh et al. [ 450 ] demonstrated that the treatment of cucumber with T. asperellum T203 activated ISR via the JA/ethylene signaling pathway. Inoculated plants were more resistant to P. syringae than non-inoculated control plants. Another study showed that soil inoculation with T. harzianum enhanced tomato defense against root-knot nematode ( Meloidogyne incognita ) by SAR activation and increased ethylene synthesis [ 132 ]. Inoculation of canola with T. harzianum TH12 triggered SAR and ISR defense mechanisms and decreased the severity of disease symptoms caused by S. sclerotiorum [ 132 ]. Changes in host cells caused by inoculation with Trichoderma are also visible in tissues distant from the penetration site. Yedidia et al. [ 451 ] demonstrated that the cell walls of cucumber root epidermis and cortical cells after T. harzianum inoculation were strengthened also beyond the penetration site. The activity of plant peroxidases and chitinases was upregulated by the presence of a fungus both in roots and leaves. These findings are in agreement with the fact that microbial invasion of host plant cells induces systemic resistance mechanisms. Huang et al. [ 452 ] reported that inoculation of cucumber with T. harzianum SQR-T37 significantly promoted growth as well as suppressed the damping off disease caused by R. solani . It was shown that the main mechanism of biocontrol was mycoparasitism. Between the pathogen and T. harzianum SQR-T37, a direct interaction was observed. The hyphae of T. harzianum were densely coiled, and hooks and appressorium-like bodies were formed. As a consequence, the cell walls of R. solani were broken and leakage of cytoplasm was noted.

Fungi belonging to Trichoderma are able to colonize plants due to the mechanisms allowing the recognition and the adhesion to the surface of the root ( Figure 2 ). Moreover, these fungi are able to penetrate the root tissues and suppress the plant’s immune system in order to avoid strong responses from the host, as reviewed in [ 453 , 454 ]. The plant’s immune system recognizes Trichoderma MAMPs, including swolenin [ 250 ], alamethicin [ 455 ], xylanase [ 456 ], cellulases [ 457 ], and polygalacturonase [ 458 ]. Plant responses to MAMPs are quick and transitional in the early stages, they involve ion level fluctuation, overproduction of ROS, nitric oxide, and ethylene [ 459 ]. Later stages involve the production of callus wall and antifungal compounds and, as a consequence, further penetration of the plant by hyphae is stopped [ 429 , 460 ]. It was demonstrated that salicylic acid has a particular role in callus synthesis during the colonization of plants by fungi. In a A. thaliana sid2 (salicylic acid induction-deficient2) mutant with a disturbed SA signalization, T. harzianum penetrated root vascular tissues whereas in wild-type plants, penetration of plants by fungi were restricted to outer root layers [ 460 ]. Inoculation of Z. mays with T. virens caused the reduction of plant secretome by 36%, which deprives plants of essential signaling molecules and proteins crucial for proper plant growth and development. At the same time, a fungus secretes similar compounds which do not activate the plant’s immune system [ 427 ]. The ability to colonize plant tissues by Trichoderma is tightly linked with the fungal capacity to tolerate secreted plants’ antimicrobial compounds [ 459 ]. An ABC transporter system is crucial for the resistance of Trichoderma to antifungal compounds secreted by plant pathogens. Deletion in the Taabc2 gene in T. atrioviride caused the loss of the ability of the fungus to protect the tomato against P. ultimum and R. solani attacks [ 461 ]. Another mechanism exploited by fungi belonging to Trichoderma is directly decreasing the synthesis of the antifungal compound. For example, Masunaka et al. [ 462 ] reported that inoculation of Lotus japonicus L. with Trichoderma koningi down-regulated the production of isoflavonoid vesitol, i.e., the main phytoalexin produced by lotus species. Fungi belonging to Trichoderma were found proficient in the degradation of allelochemicals secreted by plants which exhibit fungitoxicity to a number of fungi [ 173 ].

Colonization of root by a fungus belonging to Trichoderma . Adhesion and protection of hyphae are mediated by the layer of hydrophobins, whereas lytic enzymes enable penetration of the epidermis. Swollenins facilitate penetration of apoplast through an expansion-like effect on plant cell walls. Recognition of Trichoderma -derived MAMP molecules (swollenins, hydrophobins, cellulolytic enzymes, and chitin) triggers plant responses to infection, i.e., synthesis of antimicrobial compounds (defensins and phytoanticipins), synthesis of the callose wall in order to physically inhibit further penetration, and overproduction of ROS and possibly also alarmones. See text for more details.

Adhesion of fungi belonging to Trichoderma to the surface of plants is mediated by hydrophobins, i.e., small, cysteine-rich hydrophobic proteins ( Figure 2 ). Hydrophobins are synthesized by filamentous fungi. The amino acid sequence of hydrophobins is highly evolutionarily conserved. Hydrophobins are classified into two classes based on the arrangement of cysteine residues, differences in solubility, and physical properties. Hydrophobins form amphipathic monolayers at hydrophobic-hydrophilic interfaces. Those proteins are involved in the formation of aerial hyphae, fruiting bodies, and spores as reviewed in [ 463 , 464 ]. It was shown that class I hydrophobins produced by T. asperellum enabled adhesion to cucumber roots. The authors hypothesized that hydrophobins protect hyphae against antimicrobial compounds were secreted by the host during colonization [ 244 ]. Inoculation of tomato and cucumber with a T. harzianum mutant with a deletion in the gene encoding hydrophobin showed that the mutant fungi were able to colonize the roots of both plants; however, the lateral roots were significantly shorter than those present in plants inoculated with the wild-type fungus [ 245 ]. Further penetration of roots by hyphae is possible due to fungal proteolytic enzymes, e.g., aspartyl protease (PapA) [ 465 ], and cellulolytic enzymes, e.g., endopolygalacturonase (ThPG1) [ 458 ], and arabinofuranosidases (Abf1, Abf2) [ 465 ] that allow for degradation of the plant cell wall. Another important element allowing Trichoderma for tissue penetration are swolenins ( Figure 2 ), i.e., proteins possessing a cellulose-binding domain (CBD), similar to plant proteins—expansins. Swollenins disrupt the structure of the cellulose which results in changes to the plant cell wall architecture and the expansion of intercellular space [ 466 ]. Swollenins facilitate penetration of apoplast by the hyphae and give fungi an advantage during the competition for the niche with other microbes. Brotman et al. [ 250 ] reported that T. asperellum overexpressing swollenin showed a significantly improved ability to colonize cucumber roots, whereas swolenin knockout mutants showed a reduced ability to colonize roots. Moreover, it was found that the CBD domain acts as the MAMP, and can induce plant defense against B. cinerae and P. syringae . Similarly, T. atroviride overexpressing the swolenin-coding gene Taswo1 improved the colonization rate and enhanced the growth of tomatoes and peppers. Moreover, the induction of the plant immune system was stronger by mutants overexpressing swollenins than by knockouts and wild-type fungi [ 467 ].

Sucrose plays important role in plant colonization by Trichoderma . As demonstrated by Macías-Rodríguez et al. [ 468 ], the concentration of carbohydrates, mainly arabinose, xylose, myo-inositol, fructose, and glucose in root exudates of L. esculentum is higher before colonization by T. atrioviride . Colonization of the root by T. atrioviride changed the exudation pattern and sucrose became a major component of exudates. Root-derived sucrose specifically enables better growth of fungi belonging to Trichoderma, since AMF fungi prefer glucose and fructose as a source of carbon. Analysis of the proteome of maize inoculated with T. harzianum T22 showed that 40 proteins involved in carbohydrate/starch metabolism were upregulated and 13 proteins were downregulated, which suggests that T. harzianum is able to modulate carbohydrate metabolism in colonized roots [ 413 ]. T. virens was shown to produce invertase that hydrolyses plant-derived sucrose. The sucrolytic activity of fungal cells is crucial for root colonization but also to increase the photosynthetic rate in maize leaves [ 409 ].

Funding Statement

This research received no external funding.

Author Contributions

Conceptualization, G.B.D.; investigation, M.A. and A.M.-A.; data curation, M.A.; writing—original draft preparation, M.A. and G.B.D.; writing—review and editing, G.B.D. and A.M.-A.; supervision, G.B.D. and A.M.-A.; funding acquisition G.B.D. and A.M.-A. All authors have read and agreed to the published version of the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Economic Importance of Bacteria

Class 9 - concise biology selina, progress check 1.

Name the four common shapes of bacteria.

• Cocci (spherical bacteria)
• Bacilli (rod-shaped bacteria)
• Spirilla (twisted or spiral bacteria)
• Vibrio (comma-shaped)

Give the technical terms for the following patterns of occurrence of bacteria

• In pairs ...............
• In long chains ...............
• In clusters ...............
• Streptococci
• Staphylococci

List the kinds of nutrition in bacteria.

Bacteria mostly shows saprotrophic and parasitic nutrition.

What is the common method of reproduction in bacteria?

The common method of reproduction in bacteria is fission or cell division.

Why do bacteria produce spores ?

Bacteria produce spores to overcome unfavourable conditions.

Multiple Choice Type

Bacteria are no more classified as plants primarily because:

• These are unicellular and prokaryotic
• These are motile
• Many of them are parasitic
• They have no chlorophyll

These are unicellular and prokaryotic.

Reason — Bacteria are single-celled organisms that lack a nucleus and membrane-bound organelles. Unlike plants, which are multicellular and have eukaryotic cells, bacteria are classified as prokaryotes. This fundamental difference in cellular structure and organization led to their separation from the plant kingdom.

A particular species of which one of the following, is the source bacterium of the antibiotic, discovered next to penicillin, for the treatment of tuberculosis?

• Escherichia

Streptomyces

• Nitrobacter

Reason — Streptomycin was discovered next to penicillin by Selman Waksman. It was derived from Streptomyces griseus .

Which bacteria is rod shaped?

Reason — Rod-shaped bacteria are called bacillus.

Which bacteria fixes nitrogen in the soil?

• Nitrosomonas
• Clostridium

Reason — Rhizobium is the nitrogen fixing bacteria present in root nodules of legumes.

Cell wall of bacteria is composed of:

Peptidoglycan

• Lipoproteins

Reason — The bacterial cell wall is made up of Peptidoglycan and not cellulose as in plants.

Which of the following structures is suspended in the cytoplasm of a bacterial cell ?

Reason — Plasmid is a small circular DNA suspended in the Cytoplasm.

Bacteria mainly reproduces by means of :

• Multiple fission

Binary fission

• Regeneration

Reason — Bacteria divides into two by simple cell division. This is known as binary fission.

Bacteria are referred to as prokaryotes because:

• They are unicellular
• They are free living-

They do not have a well defined nucleus enclosed in a nuclear membrane.

Reason — The cells in which the nuclear membrane is absent is called prokaryotes.

Which of the following diseases can be prevented by TAB?

• Tuberculosis

Reason — TAB is the vaccine of Typhoid. It contains killed typhoid bacteria.

Question 10

A preparation consisting of weakened or dead germ substances is:

Reason — Vaccine consists of weakened or dead germ substances. Administration of vaccine results in resistance in body against the particular disease.

Very Short Answer Type

Name the following:

(a) The locomotory structure of a bacterium that enables it to swim.

(b) The process of flavouring tea by certain bacteria.

(c) The process of making leather from the animals skin.

(d) Bacterial disease of mustard.

(e) The scientist who discovered the antibiotic streptomycin.

(a) Flagella

(c) Leather tanning

(d) Black rot of mustard

(e) Selman Waksman

Match the items in Column A with those in Column B

Fill in the blanks:

(a) The first antibiotic penicillin was discovered by ............... .

(b) ............... bacteria is found living in the nodules on the roots of leguminous plants.

(c) The hormone ............... was the first substance produced by Escherichia coli .

(d) ............... is an example of denitrifying bacteria.

(e) ............... and ............... are the two heterotrophic modes of nutrition in bacteria.

(a) The first antibiotic penicillin was discovered by Alexander Fleming .

(b) Rhizobium bacteria is found living in the nodules on the roots of leguminous plants.

(c) The hormone insulin was the first substance produced by Escherichia coli .

(d) Pseudomonas is an example of denitrifying bacteria.

(e) Saprotrophic and parasitic are the two heterotrophic modes of nutrition in bacteria.

Name the bacteria that converts

(a) ammonium compounds to nitrites

(b) nitrites to nitrates

(a) Nitrosomonas

(b) Nitrobacter

Short Answer Type

In what form bacteria may be present in the air?

In air, bacteria can be present in the form of spores.

Why is spore formation in bacteria not considered a form of reproduction?

Spore formation in bacteria cannot be considered as a form of reproduction as they can reproduce through asexual means only such as cell division or fission. The formation of spores in bacteria is only an escape tactic from unfavorable condition that is exhibited by them.

In what respect do you consider bacteria as simple organisms?

Bacteria are unicellular organisms that lack membrane bound cell organelles like chloroplast, mitochondria, etc. and even a well-defined nucleus is absent which states that they have a simpler cellular organization.

Define the terms :

(a) Antibiotics

(b) Antitoxins

(d) Botulism

(e) Pasteurization

(a) Antibiotics — An antibiotic is a chemical substance produced by a living microorganism which can stop the growth of or kill some disease-producing bacteria and fungi.

(b) Antitoxins — Antitoxin is a substance produced in animal bodies which reacts with the poison (toxin) produced by the invading germs.

(c) Serum — Serum actually means blood plasma from which fibrinogen has been removed. It may contain numerous chemical substances including anti-bodies and antitoxins.

(d) Botulism — Botulism is a very serious food poisoning due to a special bacterium sometimes found in tinned or sealed foods.

(e) Pasteurization — Pasteurization is the process of food preservation, applied usually to milk. In this process, the milk is heated at 60°C for 30 minutes and then chilled quickly. It kills majority of bacteria.

Give two examples of each :

(a) Bacterial diseases of cattle

(b) Bacterial diseases in plants

(c) Bacterial diseases in humans

(d) Nitrifying bacteria

(e) Free living nitrogen-fixing bacteria found in soil

(a) Anthrax and Bovine tuberculosis

(b) Bacterial blight of cowpea and Black rot of mustard

(c) Cholera and Tuberculosis

(d) Nitrosomonas and Nitrobacter

(e) Azotobacter and Clostridium

Write the full forms of the following abbreviations:

(a) TAB — Typhoid-paratyphoid A and B

(b) BCG — Bacille Calmette-Guerin

(c) DNA — Deoxyribonucleic Acid

(d) GMO — Genetically Modified Organism

Give reasons :

(a) Every room in the house should get direct sunlight at least for a short time.

(b) Tinned and sealed food is not always safe to eat.

(a) Direct sunlight contains ultraviolet radiations of the Sun, which help in killing of mould spores present in air. Hence, it is advised that every living room in the house should get direct sunlight at least for a short time.

(b) No, tinned and sealed food are not always safe to eat as it may contain harmful bacteria like Clostridium botulinum that causes food poisoning. Clostridium botulinum releases toxins under low-oxygen conditions. These toxins are very lethal and can block nerve functions leading to muscular and respiratory paralysis. Moreover, the chemicals used in the inner coating of the container can be harmful for humans.

State the differences between:

(a) Decay and putrefaction.

(b) Pasteurization and sterilization of food/objects/equipments.

(a) Difference between Decay and Putrefaction:

(b) Difference between Pasteurization and Sterilization:

Would there be any bacteria in an aquarium?

Yes, bacteria can exist in aquarium. Bacteria can exist practically everywhere, as they can withstand any climatic condition.

Long Answer Type

How do bacteria obtain their nourishment?

Most bacteria are heterotrophic i.e. they depend on ready-made food from different sources. In this category, the bacteria maybe:

• Saprophytic — Such bacteria draw nourishment from decaying dead organisms.
• Parasitic — Such bacteria draw nourishment from the body of their living hosts.

The bacteria secrete powerful enzymes from their cells into the surrounding food containing material. The enzymes make the food material soluble which is then absorbed as a solution into the bacterial cell.

Describe any two uses of bacteria in industry.

Uses of bacteria in industry:

• Tanning of leather — It is brought about by sunlight with the involvement of a few bacteria which breakdown the soft perishable parts of the skin.
• Tea curing — Different flavours of tea are produced by certain bacteria.

What are antibiotics? Name any two examples.

Antibiotics are chemical substances produced by a living organism which inhibits or kills the growth of micro-organisms that cause the diseases such as fungi and bacteria. Examples of antibiotics are:

• Streptomycin

Briefly describe how nitrogen of the atmosphere is converted to nitrates by leguminous plants.

A special category of soil bacteria (Rhizobium) is found living in small nodules on the roots of leguminous plants. These bacteria pick up free nitrogen from the soil and atmosphere and convert it into soluble nitrates. These nitrates are used by the host plant and also by other plants sown later in the same soil.

State how the nitrates in the soil get converted to nitrogen of the atmosphere.

Denitrifying bacteria in the soil break down nitrates present in the soil to release nitrogen gas which enters the atmosphere. Pseudomonas is an example of denitrifying bacteria.

Structured / Application / Skill Type

Draw a diagram showing the Nitrogen cycle and answer the following questions.

(a) Define the terms:

• Nitrification
• Denitrification

(b) Distinguish between biological nitrogen fixation and industrial nitrogen fixation.

(c) Name the kind of relationship that exists between Rhizobium and leguminous plants.

(a) Below diagram shows the Nitrogen cycle:

• Nitrification — The conversion of atmospheric nitrogen to nitrates is called nitrification.
• Denitrification — The conversion of nitrates into atmospheric nitrogen is called Denitrification.

(b) Difference between biological nitrogen fixation and industrial nitrogen fixation are:

(c) Symbiotic relationship.

Would there be any bacteria in an aquarium ?

(a) A balanced aquarium contains certain animals as well as some plants. How many kinds of animals can you make out in the aquarium shown here. Name any two such animals.

(b) Do you think there would be some bacteria in it? If so in which part of the aquarium would they be occurring in abundance and what for?

(a) Fishes and snails are present in the aquarium shown here.

(b) Yes, aquariums contain bacteria. A balanced aquarium contains some nitrifying bacteria like Nitrosomonas and Nitrobacter which converts the ammoniacal waste released by fish to nitrates. The filter media and various solid surfaces in the aquarium, such as gravel, rocks, plants, and decorations, harbor these bacteria in abundance.

Write an essay on the economic importance of bacteria

Bacteria are unicellular and ultra-microscopic organisms, yet they play an important role in nature. They are of tremendous importance to man. They play an important role in agriculture and medicine and are the basis of many industries. Some are beneficial to man directly or indirectly, others are very harmful as they cause various plant and animal diseases. Bacteria are considered as our friends and foes due to their beneficial and harmful activities. Their economic importance can be studied under two aspects:

(A) Beneficial aspects.

(B) Harmful aspects.

(A) Beneficial Aspects:

The beneficial activities of the bacteria can be classified as follows:

ADVERTISEMENTS:

(1) Role in agriculture.

(2) Role in industry and medicine.

(1) Role in Agriculture:

The activities of bacteria are very important in agriculture in the following aspects:

(a) Decaying of organic substance:

Most of the bacteria are very useful in bringing about decomposition of dead organic matter of plants and animals by the secretion of enzymes. The enzymes convert the fats, carbohydrates and nitrogenous compounds into simpler forms, such as, CO 2 water, ammonia, hydrogen sulphide, phosphates, nitrates etc that are used as raw material by the green plants. Thus, these bacteria not only decompose the organic compounds but also remove the harmful waste from the earth and thus function as nature’s scavengers.

{b) Fertility of the soil:

Some bacteria maintain and others increase the fertility of the soil. They bring about physical and chemical changes in the soil by converting insoluble materials into soluble ones. These bacteria are the ammonifying, nitrifying and the nitrogen fixing Bacteria.

(i) Ammonifying Bacteria:

The decay bacteria decompose the proieinous compounds into amino acids, which are reduced to ammonia by ammonifying bacteria. The free ammonia combines in the soil to form ammonium salts. This conversion is known as ammonification. Examples are Bacillus ramosus, B. vulgaris etc.

(ii) Nitrifying Bacteria:

These bacteria convert ammonium salts into nitrates, which are absorbed by the plants. The nitrifying bacteria are the Nitrobacter and Nitrosomonas. The Nitrosomonas oxidize the ammonium salts into nitrous acid, which forms nitrites in the soil. The Nitrobacter then converts the nitrites into nitrates. This conversion of ammonium salts into available nitrates is called nitrification.

(iii) Nitrogen Fixing Bacteria:

These bacteria take up nitrogen from the atmosphere and convert it into organic nitrogen compounds. It is known as nitrogen fixation. The nitrogen-fixing bacteria are of two types. One type includes Azotobacter and Clostridium, which live freely in the soil and fix nitrogen of the air in their bodies in the form of nitrogenous organic compounds. The other types of bacteria are the nodule bacteria, the Bacillus radicicola. Rhizobium lives as symbiont in the roots of leguminous plants and forms nodules. These bacteria absorb free nitrogen from the bacterial cell. The leguminous plants thus enrich the fertility of the soil. They are grown for green manuring and rotation of crops.

(2) Role in Industry and Medicine:

Bacteria play a very important role in various industries. The products obtained as a result of bacterial activities cannot be chemically prepared. Their activities are involved in the following industries:

(a) Preparation of Alcohols:

Ethyl alcohol and butyl alcohol are manufactured by the bacterial acivities in the sugar solution, e.g., Clostridium acetobutylicum.

(b) Preparation of Vinegar:

Vinegar is prepared by the activities of Acetobacter aceti in the sugarcane juice.

(c) Preparation of Butter, Cheese etc.:

The preparation of butter, cheese etc. is done by bacteria. The Lactobacillus lactis is responsible for souring of milk resulting in curd (dahi) preparation. Bacterial activities also impart the typical flavours.

(d) Preparation of Tea, Coffee etc.:

Bacteria are very useful in preparation and flavouring of tea, coffee, cocoa etc. e.g., Micrococcus.

(e) Preparation of Tobacco:

Tobacco leaves are cured and flavoured by the bacteria. Typical types of bacteria are cultured for this purpose, e.g., Micrococcus.

(f) Preparation of Hemp fibres:

Fibres from the hemp are isolated after rotting the stems by activity of bacteria (e.g., Clostridium butyricum). The bacteria eat up the protoplasmic tissues but leave the sclerenchyma fibres.

(g) Preparation of Leather and Tanning:

The hairs and fats are removed from the skin by the action of bacteria in the leather industry.

(h) Preparation of Antibiotics:

The bacteria are also used in the preparation of antibiotics. According to Sir Alexander Fleming, the growth of harmful Staphylococcits is checked by Penicillium natatum. With this discovery, large number of antibiotics has been prepared which are of great importance in the medical world. Tyrothricin, Subtillin, Polyximin-B, Bacitracin, Streptomycin, Aureomycin, Terramycin are some well-known antibiotics.

(B) Harmful Aspects:

Bacteria are also harmful to man directly or indirectly. They cause various diseases in plants, human beings or domestic animals. The harmful bacteria are of the following types ;

(i) Animal pathogenic Bacteria.

(ii) Plant pathogenic Bacteria.

(iii) Food destroying Bacteria.

(iv) Soil fertility destroying Bacteria.

(i) Animal Pathogenic Bacteria:

There are a large number of parasitic bacteria, which cause various serious diseases in man and domestic animals, sometimes in epidemic form. They arc invisible enemies. Some of the common human diseases producing bacteria are Mycobacterium tuberculosis causing tuberculosis, Eberthela typhosa causing typhoid, Clostridium tetani causing tetanus, Shigella dysenteriae causing dysentery, Hemophilous influenzea causing influenza, Corynebacteriaum diphtlteriea causing diphtheria, Diplococats pneumonias causing pneumonia, Vibrio cholerae causing cholera, Streptococcus causing blood poisoning, Treponema pallidium causing syphilis, Gonococcus causing gonorrhoea, Bacillus pestis causing plague etc. In domestic animals various diseases are caused by bacteria, e.g., Anthrax, Pneumonia, Tuberculosis, Cholera, Glanders etc.

(ii) Plant Pathogenic Bacteria:

Many parasitic bacteria cause serious diseases in cultivated plants, which cause great harm to the crops. Important diseases are Citrus canker, fire blight of pear, cotton root rot, walnut blight, potato rot, pineapple rot etc. The Canker of Citrus (orange and lemon) is caused by Xanthonionas citri. The rot diseases cause black spots on potato, tomato, cabbage, carrot etc.

(iii) Food destroying Bacteria:

Some saprophytic bacteria are responsible for the decay of human foodstuffs including meat, milk, vegetables, fruits etc. These bacteria spoil foodstufs and make them unpalatable and poisonous, e.g., souring of milk, rotting of meat, vegetables, fruits etc. Staphylococcus and Clostridium botulinum cause food poisoning when rotten food is eaten,

(iv) Soil Fertility destroying Bacteria:

These are denitrifying bacteria in the soil, which reduce the nitrates, and the ammonium salts to free nitrogen, which escapes into the atmosphere. This process is known as denitrification, which decreases the fertility of the soil, e.g., Bacillus denitrificans.

These bacteria are often abunbant in the poorly drained and heavily manured soil. So the denitrifying bacteria are the natural enemies of the farmers.

Thus with the study of economic importance of bacteria we conclude that bacteria are our friends due to their beneficial aspects and enemies due to their harmful aspects. But in the bacteria beneficial aspects overweigh their harmful aspects. We can control the harmful activities but their beneficial activities cannot be replaced by artificial processes. So the bacteria are our friends more and enemies less.

Related Articles:

• Write a short note on the beneficial effects of bacteria
• What are the Harmful Effects to Bacteria?
• Structure, mode of nutrition of bacteria and briefly describes their economic importance
• How to classify bacteria on the basis of modes of nutrition?

Write an essay on the economic importance of bacteria

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