Soil microbiology
Encyclopedia
Soil microbiology is the study of organisms in soil, their functions, and how they affect soil properties. It is believed that between two to four billion years ago, the first ancient bacteria
and microorganisms came about in Earth's primitive seas. These bacteria could fix nitrogen, in time multiplied and as a result released oxygen into the atmosphere. This release of oxygen led to more advanced microorganisms. Microorganisms in soil are important because they affect the structure and fertility of different soils. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae, and protozoa. Each of these groups has different characteristics that define the organisms and different functions in the soil it lives in.
. All of the other microorganisms are eukaryotic
, which means they have a more advanced cell structure with internal organelles and the advanced ability to reproduce sexually. A prokaryote has a very simple cell structure with no internal organelles. Bacteria are the most abundant microorganisms in the soil, and serve many important purposes, one of those being nitrogen fixation among other biochemical processes.
can metabolize a wide range of chemicals and fertilizers. In contrast, another species known as Nitrobacters can only derive its energy by turning nitrite into nitrate, which results in a gain of oxygen and is known also as oxidation. Furthermore, the species Clostridium
is also an example of bacteria’s versatility because it, unlike most species, can actually grow in the absence of oxygen.
, which is the conversion of atmospheric nitrogen into nitrogen which can be used by plants to uptake. Autotrophic bacteria, or bacteria that derives its energy making its own food by oxidation, like the Nitrobacters species, rather than feeding on plants or other organisms. The bacteria that are autotrophic are responsible for nitrogen fixation, and the amount of autotrophic bacteria is small compared to heterotrophic bacteria (the opposite of autotrophic bacteria, heterotrophic bacteria acquires energy by consuming plants or other microorganisms), but are very important because almost every plant and organism require nitrogen in some way, and would have no way of obtaining it if not for nitrogen-fixing bacteria.
are soil microorganisms that are very similar to both bacteria and fungi, and have characteristics linking them to both groups. Actinomycetes are often believed to be the missing evolutionary link between bacteria and fungi, but they have many more characteristics in common with bacteria than they do fungi.
is a common technique used to classify organisms into two main groups: Gram-positive and Gram-negative, by staining organisms to distinguish its cell wall properties. Gram-positive means that the cell has a thin, penetrable cell wall and gram-negative means the opposite, that the cell wall is thick and difficult to penetrate. Cell wall properties can help distinguish different types of microorganisms from each other.
, neomycin
, erythromycin
and tetracycline are only a few examples of the antibiotics derived from actinomycetes. Streptomycin is used to treat tuberculosis
and infections caused by certain bacteria and neomycin is used to reduce the risk of bacterial infection during surgery. Erythromycin is a very important antibiotic that is used to treat certain infections caused by bacteria, such as bronchitis
; pertussis
(whooping cough); pneumonia
; and ear, intestine, lung, urinary tract, and skin infections. This ability to produce these useful antibiotics is the basis of our entire pharmaceutical industry and has saved human lives.
can make its own nutrients through a process known as photosynthesis
. Photosynthesis is when light energy is converted to chemical energy that can be stored as nutrients. For algae to grow, it must be exposed to areas of light because photosynthesis requires light, so algae is typically distributed evenly wherever sunlight and moderate moisture is available. Algae, however, do not have to be on the soil surface or directly exposed to sun rays, but it can live below the soil surface as long as the algae has uniform temperature and moisture conditions. Bacteria are not the only organism that can fix nitrogen, because algae are capable of performing nitrogen fixation as well.
, which is the molecule that absorbs sunlight and uses that energy to make carbohydrates from carbon dioxide and water, and also pigments that make it blue-green to violet in color. The Chlorophycease usually only has chlorophyll in it which makes it green, and the Bacillariacease contains chlorophyll as well as pigments that make the algae brown in color.
are eukaryotic organisms which are some of the first microorganisms to develop a means of sexual reproduction, which is a huge evolutionary step from duplication of spores, like many of the other soil microorganisms depend on. Protozoa can be split up into three categories: flagellates, amoebae, and ciliates.
It is important to understand the many different groups and species of microorganisms in different soils because they affect so much of the soil. Microorganisms contribute to nutrient availability in soil, manage soil stability by means of different biochemical processes such as nitrogen fixation, and they contribute to the growth and success of the plants and overall ecosystem of a soil environment.
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and microorganisms came about in Earth's primitive seas. These bacteria could fix nitrogen, in time multiplied and as a result released oxygen into the atmosphere. This release of oxygen led to more advanced microorganisms. Microorganisms in soil are important because they affect the structure and fertility of different soils. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae, and protozoa. Each of these groups has different characteristics that define the organisms and different functions in the soil it lives in.
Bacteria
Bacteria are the smallest organisms in the soil and are the only soil microorganisms that are prokaryoticProkaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...
. All of the other microorganisms are eukaryotic
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
, which means they have a more advanced cell structure with internal organelles and the advanced ability to reproduce sexually. A prokaryote has a very simple cell structure with no internal organelles. Bacteria are the most abundant microorganisms in the soil, and serve many important purposes, one of those being nitrogen fixation among other biochemical processes.
Biochemical processes
One of the most distinguished features of bacteria as a whole is their biochemical versatility. A species called PseudomonasPseudomonas
Pseudomonas is a genus of gammaproteobacteria, belonging to the family Pseudomonadaceae containing 191 validly described species.Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the...
can metabolize a wide range of chemicals and fertilizers. In contrast, another species known as Nitrobacters can only derive its energy by turning nitrite into nitrate, which results in a gain of oxygen and is known also as oxidation. Furthermore, the species Clostridium
Clostridium
Clostridium is a genus of Gram-positive bacteria, belonging to the Firmicutes. They are obligate anaerobes capable of producing endospores. Individual cells are rod-shaped, which gives them their name, from the Greek kloster or spindle...
is also an example of bacteria’s versatility because it, unlike most species, can actually grow in the absence of oxygen.
Nitrogen fixation
Bacteria are responsible for the process of nitrogen fixationNitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
, which is the conversion of atmospheric nitrogen into nitrogen which can be used by plants to uptake. Autotrophic bacteria, or bacteria that derives its energy making its own food by oxidation, like the Nitrobacters species, rather than feeding on plants or other organisms. The bacteria that are autotrophic are responsible for nitrogen fixation, and the amount of autotrophic bacteria is small compared to heterotrophic bacteria (the opposite of autotrophic bacteria, heterotrophic bacteria acquires energy by consuming plants or other microorganisms), but are very important because almost every plant and organism require nitrogen in some way, and would have no way of obtaining it if not for nitrogen-fixing bacteria.
Actinomycetes
ActinomycetesActinobacteria
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
are soil microorganisms that are very similar to both bacteria and fungi, and have characteristics linking them to both groups. Actinomycetes are often believed to be the missing evolutionary link between bacteria and fungi, but they have many more characteristics in common with bacteria than they do fungi.
Similar to bacteria
Actinomycetes are similar to bacteria because they, like bacteria, are prokaryotic, are sensitive to antibacterial and affected in the same way that bacteria is by them. Actinomycetes can hardly be distinguished from bacteria at its early stages because of how much they resemble bacteria in size, shape and gram-staining properties. Gram stainingGram staining
Gram staining is a method of differentiating bacterial species into two large groups ....
is a common technique used to classify organisms into two main groups: Gram-positive and Gram-negative, by staining organisms to distinguish its cell wall properties. Gram-positive means that the cell has a thin, penetrable cell wall and gram-negative means the opposite, that the cell wall is thick and difficult to penetrate. Cell wall properties can help distinguish different types of microorganisms from each other.
Similar to fungi
Actinomycetes are most commonly linked to fungi, but they do share some characteristics with fungi. Actinomycetes are similar to fungi by their shape and branching properties, spore formation, which related to how fungi and actinomycetes reproduce by forming spores and duplicating.Ability to produce antibiotics
One of the most notable characteristics of the actinomycetes is their ability to produce antibiotics. StreptomycinStreptomycin
Streptomycin is an antibiotic drug, the first of a class of drugs called aminoglycosides to be discovered, and was the first antibiotic remedy for tuberculosis. It is derived from the actinobacterium Streptomyces griseus. Streptomycin is a bactericidal antibiotic. Streptomycin cannot be given...
, neomycin
Neomycin
Neomycin is an aminoglycoside antibiotic that is found in many topical medications such as creams, ointments, and eyedrops. The discovery of Neomycin dates back to 1949. It was discovered in the lab of Selman Waksman, who was later awarded the Nobel Prize in Physiology and medicine in 1951...
, erythromycin
Erythromycin
Erythromycin is a macrolide antibiotic that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people who have an allergy to penicillins. For respiratory tract infections, it has better coverage of atypical organisms, including mycoplasma and...
and tetracycline are only a few examples of the antibiotics derived from actinomycetes. Streptomycin is used to treat tuberculosis
Tuberculosis
Tuberculosis, MTB, or TB is a common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis. Tuberculosis usually attacks the lungs but can also affect other parts of the body...
and infections caused by certain bacteria and neomycin is used to reduce the risk of bacterial infection during surgery. Erythromycin is a very important antibiotic that is used to treat certain infections caused by bacteria, such as bronchitis
Bronchitis
Acute bronchitis is an inflammation of the large bronchi in the lungs that is usually caused by viruses or bacteria and may last several days or weeks. Characteristic symptoms include cough, sputum production, and shortness of breath and wheezing related to the obstruction of the inflamed airways...
; pertussis
Pertussis
Pertussis, also known as whooping cough , is a highly contagious bacterial disease caused by Bordetella pertussis. Symptoms are initially mild, and then develop into severe coughing fits, which produce the namesake high-pitched "whoop" sound in infected babies and children when they inhale air...
(whooping cough); pneumonia
Pneumonia
Pneumonia is an inflammatory condition of the lung—especially affecting the microscopic air sacs —associated with fever, chest symptoms, and a lack of air space on a chest X-ray. Pneumonia is typically caused by an infection but there are a number of other causes...
; and ear, intestine, lung, urinary tract, and skin infections. This ability to produce these useful antibiotics is the basis of our entire pharmaceutical industry and has saved human lives.
Fungi
Next to bacteria, fungi are abundant in soil population compared to other microorganisms. Fungi are important in the soil as food sources for other, larger organisms, pathogens, beneficial symbiotic relationships with plants or other organisms and help to reduce crop residues and biochemically process nutrients to improve the soil they inhabit. Fungi can be split into different species based on primarily on the size, shape and color of their spores, which are used to reproduce.Factors that influence fungi growth
Most of the environmental factors that influence the growth and distribution of bacteria and actinomycetes also influence fungi. The quality as well as quantity of organic matter in the soil has a direct correlation to the growth of fungi, because most fungi consume the organic matter for nutrition. Fungi thrive in acidic environments, while bacteria and actinomycetes cannot survive in acid, which results in an abundance of fungi in acidic areas. Fungi also grows well in dry, arid soils because fungi are aerobic, or dependent on oxygen, and the higher the moisture content in the soil, the less oxygen is present for fungi.Algae
AlgaeAlgae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
can make its own nutrients through a process known as photosynthesis
Photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
. Photosynthesis is when light energy is converted to chemical energy that can be stored as nutrients. For algae to grow, it must be exposed to areas of light because photosynthesis requires light, so algae is typically distributed evenly wherever sunlight and moderate moisture is available. Algae, however, do not have to be on the soil surface or directly exposed to sun rays, but it can live below the soil surface as long as the algae has uniform temperature and moisture conditions. Bacteria are not the only organism that can fix nitrogen, because algae are capable of performing nitrogen fixation as well.
Types
Algae can be split up in to three main groups: the Cyanophycease, the Chlorophycease, and the Bacillariacease. The Cyanophycease contain chlorophyllChlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...
, which is the molecule that absorbs sunlight and uses that energy to make carbohydrates from carbon dioxide and water, and also pigments that make it blue-green to violet in color. The Chlorophycease usually only has chlorophyll in it which makes it green, and the Bacillariacease contains chlorophyll as well as pigments that make the algae brown in color.
Blue-green algae and nitrogen fixation
Blue-green algae, or Cyanophycease, are the algae that are responsible for nitrogen fixation. The amount of nitrogen fixed by these algae depends more on physiological and environmental factors rather than the organism’s abilities. Some of these factors include intensity of sunlight, concentration of inorganic and organic nitrogen sources, and temperature and stability of the environment.Protozoa
ProtozoaProtozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...
are eukaryotic organisms which are some of the first microorganisms to develop a means of sexual reproduction, which is a huge evolutionary step from duplication of spores, like many of the other soil microorganisms depend on. Protozoa can be split up into three categories: flagellates, amoebae, and ciliates.
Flagellates
Flagellates are the smallest members of the protozoa group, and can be divided further based on whether they can participate in photosynthesis. Nonchlorophyll-containing flagellates are not capable of photosynthesis because chlorophyll is the green pigment that absorbs sunlight in the process. These flagellates are found mostly in soil and flagellates that contain chlorophyll typically occur in aquatic conditions. Flagellates can be distinguished by their flagella, which is their means of movement. Some have several flagella, and other species only have one, but it resembles a long branch or appendage that helps the flagella move.Amoebae
Amoebae are larger than flagellates and move in a different way. Amoebae can be distinguished from other protozoa by their slug-like properties and pseudopodia. A pseudopodia or “false foot” is a temporary obtrusion from the body of the Amoebae that helps pull it along surfaces for movement or helps to pull in food. The amoebae does not have permanent appendages and the pseudopodia is more of a slime-like consistency than a flagella.Ciliates
Ciliates are the largest of the protozoa group, and move by means of short, numerous cilia that produce beating movements. Cilia resembles small, short hairs, and they can move in different directions to propel the organism in different direction, giving it more mobility than flagellates or amoebae are capable of.It is important to understand the many different groups and species of microorganisms in different soils because they affect so much of the soil. Microorganisms contribute to nutrient availability in soil, manage soil stability by means of different biochemical processes such as nitrogen fixation, and they contribute to the growth and success of the plants and overall ecosystem of a soil environment.