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1ESC 590

Intro, Microbial Growth & Metabolism

Reading Assignment Soil Microbiology: An exploratory Approach Chapters 1 and 2

1. Soil Microbiology

Soil microbiology is the study of organisms that live in the soil. The main trust of study is on their metabolic and their roles in energy flow and cycling of nutrients associated with primary productivity the energy flow and activities. The discipline is also concerned with the environmental impacts, both favorable and unfavorable, of soil microorganisms and the processes the mediate.

1. Soil Microbiology
Soil microbiology is concerned with microbial communities in soil and what they do. It uses a synecology approach process oriented Autoecology approach - uses more of an individual approach.

2. Soil Biochemistry
Traditionally biochemistry has been defined as the chemistry that deals with life processes of plants and animals. The scientific discipline of soil biochemistry follows this tradition. Many of the reactions the soil biochemist investigates result from the activities of living tissues, e.g. microorganisms and plants.

2. Soil Biochemistry

In addition, the study of soil organic matter its origin and biochemical reactivities, are also included in the domain of soil biochemistry even though these may no longer be in association with any living system.

2. Soil Biochemistry

In 1946 J.H. Quastel proposed that the soil as a whole can be considered an organ comparable in some respect to a liver or a gland to which may be added various nutrients, pure or complex degraded plant materials, rain, air and in which enzymatic reactions occur.

2. Soil Biochemistry

The products of these reactions are important steps in elemental cycles, in the percolation of iron and aluminum humates, in the formation of soil crumb structure, and in other processes.

2. Soil Biochemistry

The notion here is that the soil biochemist is concerned more with what the microbes are doing in the soil than with precisely what the microbes are with respect to size and shape or the ingredients of taxonomic schemes.

2. Soil Biochemistry

In this course we will study soil biochemistry using this concept which views the soil as a tissue, containing many kinds of compounds, to which biochemical principles can be applied. Soil Cell Membrane

3. Overview of Metabolism
Metabolism refers to all the chemical processes that take place within a cell. It is composed of two basic reactions:

- A. - B.

Anabolism Catabolism

Anabolic reactions require energy to synthesize complex molecules from simpler ones.

3. Overview of Metabolism
Catabolic reactions release energy by braking complex molecules. All catabolic reactions involve electron transfer, which allows energy to be captured in high energy bonds

4. Microbial Nutrition

Nutrients
- Chemical tools needed to make monomers.

Essential Nutrients
- C H,O, P,K,N, S, Ca, Fe, Mg,

Macronutrients
- Needed in large amounts - Include C, H, O, P, S, K, Mg, Na, Ca, Fe

4. Microbial Nutrition

Micronutrients (Trace Elements)


- Required in small amounts - Mainly metals and play role in enzymes - Include Cr, Co, Mn, Mo, Ni, Se, W, V, Zn, Fe

Growth Factors
- Organic compounds required in very small amounts and only by some cells. - Include vitamins, amino acids, and nucleotides .

Culture Media
Culture media are nutrients solutions used to grow microorganisms. Two broad classes

- A. Chemically defined-prepared by adding precise amounts of highly purified inorganic or organic chemicals and distilled water. - B. Undefined (complex)-These are made up of digest of casein, beef, soybean, yeast cells other highly nutritious substances.

5. Energy Classes of Microorganisms

One of the fundamental properties of living organisms is their requirement of energy. Phototrophs, meet their energy requirements by absorption of a quanta of solar radiation.

Chemotrophs obtain energy needs by oxidation of preformed organic molecules.

Characterization of Metabolic Reactions Based on Electron Donors/Acceptors


Class Photoautotrophic (Photolithotroph) H O, H S, H R 2 2 2 Respiration (organothrops) CO 2 Electron Donor Electron Acceptor

Organic Compounds

Biological Oxidations
Biological oxidations reactions are frequently dehydrogenation reactions. Biological oxidation reactions almost always involve two electron transfers. In chemotrophic energy metabolism the ultimate energy acceptor of electrons is frequently oxygen.

Biological Oxidations
The electrons are generally passed to the final electron acceptor through intermediate electrons acceptors In most biological oxidations, the immediate electron acceptor is one of several coenzymes-specialized molecules that function specifically as carriers of electrons.

Biological Oxidations
The most common coenzymes are NAD+, NADP+ and FAD Aerobic energy metabolism involves stepwise process collectively called respiration. Under anaerobic conditions, oxygen is not available as electron acceptor, and the electrons are passed instead to some organic or inorganic molecule .

Biological Oxidations

All anaerobic processes are called fermentations and they are usually further identified in terms of the principal end product i.e. the reduced form of the organic or inorganic electron acceptor.

6. Oxygen Requirements

Organisms with an absolute requirement for oxygen are strict or obligate aerobes.
- Most higher animals are in this category.

Strict or Obligate anaerobes cannot tolerate the presence of oxygen.


- Some bacteria , including soil Clostridia and those responsible for denitrification are found in this category

6. Oxygen Requirements

Facultative organisms are those which can exist anaerobically, extracting energy from glucose (or other organic substrates) by fermentative processes, but which can also function in the presence of oxygen, in which case they carry out the full respiratory sequence.

7. Methods of Metabolism
All classes of energy yielding reactions can be classed under four main groups: 1. Respiration 2. Fermentative reactions 3. Chemoautotrophic reactions. 4. Photosynthetic

7.1a Aerobic Respiration


Aerobic Respiration is properly defined as the oxidation of organic molecules with molecular oxygen serving as the ultimate electron acceptor. The result of aerobic respiration is the complete degradation of organic molecules to the products, CO2 and H2O.

7.1b Anaerobic Respiration


Anaerobic Respiration is a variation of respiration in which electron acceptors other than oxygen are used. Electron acceptors used include NO3-, Fe3+ , SO4-, CO3 Under anaerobic respiration, less energy is released compared to aerobic respiration.

7.1 Aerobic vs. Anaerobic Respiration


Class Electron Donor Electron Acceptor

Aerobic Respiration

Organic Compounds

O2

Anaerobic Respiration

Organic Compounds

Inorganic compound

7.2 Fermentation Reactions


In fermentation reactions, organic molecules are oxidized with the electrons being given to electron acceptors other than O2. One common fact concerning each of the classes of fermentation is that the source of electrons involved is organic compounds.

Comparision of Fermentation, Aerobic Respiration, and Anaerobic Respiration.


Energy-Producing Process Fermentation Aerobic respiration Growth Conditions

Aerobic or anaerobic Aerobic

Anaerobic respiration

Anaerobic

7.2 Fermentation Reactions


The distinguishing feature of the fermentative reactions, however is the nature of the electron acceptors and the products formed. The yield of energy obtained from a fermentative reaction is much less compared to that of respiration contained in a given substance.

7.2. Fermentation Reactions


Class Electron Donor Electron Acceptor

Heterofermentative

Organic Compounds

Same molecule or fragment of it. Different organic compound or CO

Multifermentative

Organic Compounds

Isofermentative

Organic Compounds

Another molecule of substrate

Comparison of Fermentation, Aerobic and Anaerobic Respiration.


EnergyProducing Process Growth Conditions Final Electron Acceptor Type of Phosphorylation used to build ATP Molecules of ATP Produced

Fermentation

Aerobic or anaerobic

An organic molecule

Substrate-level

Aerobic respiration

Aerobic

Free oxygen (O2)

Substrate-level and oxidative

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Anaerobic respiration

Anaerobic

Usually an inorganic substance (such as NO3-, SO42-, CO32- ), but not free oxygen (O2).

Oxidative

Variable

7.3. Chemolithotrophic Metabolism


In this mode of energy generation, organisms use inorganic chemicals as electron donors. It usually involves aerobic respiratory processes but uses an inorganic energy source rather than an organic one. Examples inorganic electron donors include H2S, H2, Fe2+ and NH3.

Class

Electron Donor

Electron Acceptor

Products

Photoautotrophic (Photolitotroph) Respiration (Heterotrophs) Homofermentative

H2O, H2S, H2R

CO2

(HCHO)x and other reduced compounds CO2 + H2O

Organic Compounds

O2

Organic Compounds

Same molecule or fragment of it Same molecule or fragment of it. Different organic compound or CO2

Single organic species + CO2 in some cases Mixture of organic compounds

Heterofermentative

Organic Compounds

Multifermentative

Organic Compounds

Organic compounds

Isofermentative

Organic Compounds

Another molecule of substrate

Reduced organic compound and Oxidized organic compound

Anerobic Respiration

Organic Compounds

Inorganic compound

Organic Compound or CO2 + H2O: more reduced inorganic compound

Chemoautotrophic (Chemolitotroph)

Inorganic Compounds

O2 or another inorganic compound

Oxidized inorganic compound

7.4 Photosynthetic Reactions


Photosynthesis may be defined as a series of reactions which utilize solar energy to convert CO2 into cellular components. It is important both to the carbon and oxygen cycle. It is also the chemical source of oxygen which is absolutely required by aerobic organisms.

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