What is microbial physiology?

Microbial physiology is the branch of microbiology that is associated with studying the physiology of fungi, bacteria, and viruses. It is an important field of science concerning functional genomics and metabolic engineering.

What is the focus of microbial physiology?

In microbiology, Escherichia coli is a microscopic organism that is considered a paradigm because certain E. coli strains are harmless, having been proven to be beneficial for humans. On the contrary, certain other strains are harmful, resulting in food poisoning in humans. The fundamental biology of microbes and their interactions with other organisms, and the environment form the prime focus of microbial physiology. Microbes are organisms that are not visible to the naked eye. They are cosmopolitan and are even found in extreme environments. They can be found in extremely acidic or alkaline environments, in scorching environments such as hydrothermal vents of deep-sea and hot springs, in freezing environments such as Antarctic ice, and extremely salty environments.

Microbial cell structure

Bacteria are classified into three basic models: spiral, rod, and spherical. Since these bacteria and other related organisms do not have a membrane-bound nucleus like eukaryotes, they are prokaryotic. Thus, bacteria do not possess cell organelles (apart from ribosomes).

Cell surface

The cell wall acts as the cell surface by surrounding the bacterial cell and separating it from the external environment. It guards the cell's interior against external damage and regulates the cell integrity as a separate entity. It also functions to import and export various ions and molecules of different sizes from the cell. These molecules comprise amino acids, nucleotides, vitamins, and carbohydrates. The composition and structure of different cell surfaces can vary on a considerable level depending on the organism.

Microbial growth

Growth is one of the characteristic features of living organisms. It is a phenomenon that involves an increase in both size and mass of cells during the developmental phase of living organisms. Nutritional factors and physical factors play a vital role in the growth of organisms.

Bacteria are unicellular organisms. When bacteria grow up to a particular size, these cells divide through binary fission, where one cell splits into two, two into four, and so on.

Bacterial growth can be studied by culturing (growing) “viable” bacteria in a sterile nutrient medium under optimized conditions, such as temperature and pH. The growth of bacteria is determined by measuring the absorbance or optical density of the bacterial culture and plotting it against time.

Lag phase

Initially, during the lag phase, bacteria have to adapt to their new surroundings. These organisms remain metabolically active due to which they exhibit an increase in cell size only. During the lag phase, bacteria synthesize substances necessary to facilitate growth under the new environmental conditions.

Logarhithmic or exponential phase

During the log or exponential phase, bacterial populations exhibit an increase in the number of cells in a logarithmic manner. The bacterial population doubles after every generation time; for example, 20 minutes for E. coli. Bacteria in this phase are fast-dividing and continue this logarithmic division until the available nutrients are depleted and toxic by-products are accumulated in the growth medium. Bacteria reproduce through binary fission at a constant rate during this stage, and a balanced increase in the constituents, such as proteins, carbohydrates, and other biomolecules was observed that are important for the growth and development of the cells.

Stationary phase

Microbes utilize all nutrients present in the growth medium to multiply during the growth of the bacterial population. It results in the deposition of waste matter, toxins, and inhibitory compounds in the media. It affects the media conditions, such as temperature and pH, which creates an unfavorable environment for bacterial growth. The number of bacteria cell deaths gradually equals the number of viable or actively dividing cells due to decreased reproduction rate. Here, the growth rate becomes stabilized.

Death or decline phase

The stationary phase is followed by the decline phase, which is characterized by the death of bacterial cells; either due to gradual and constant depletion of nutrients or the deposition of metabolic wastes in the nutrient medium. During this phase, bacteria do not reproduce. Individual bacterium starts to die because of unfavorable conditions. Thus, during the death phase of microbial growth, the number of living cells is less than dead bacterial cells.

Most resistant and least resistant microorganisms

The property of resistance in microorganisms can be defined as the ability to repel or tolerate unfavorable abiotic conditions and biotic agents. The microorganisms can become resistant by developing new properties or by undergoing mutations. Antibiotic resistance by microorganisms is one of the examples in which the microorganism's growth cannot be inhibited as they are not affected by antibiotics.

The most resistant microorganisms are as follow:

• Prions: Prions are a type of infectious protein extraordinarily resistant to chemicals and heat. Instruments contaminated by prions are usually discarded.
• Bacterial endospores: Earlier bacterial endospores have been considered the most resistant microbial entities. This is because they are 18 times harder to destroy than their vegetative cells.

The least resistant microorganisms are as follow:

• Viruses: Enveloped and naked viruses are small infectious entities known to infect all forms of life. They are the least resistant to control measures.
• Gram-positive bacteria: Due to the presence of a thick peptidoglycan layer, most of the gram-positive bacteria are the least resistant to control measures.

Respiration in bacteria

Cellular respiration is the series of biochemical reactions involving the conversion of stored energy in the metabolites into the molecules of adenosine triphosphate (ATP). There are three phases of cellular respiration: “glycolysis,” “Krebs cycle,” and “electron transport chain.” There are two types of reactions in glycolysis: “energy investment reactions” and “energy harvest reactions.”  Also, the net gained molecules of ATP in “glycolysis” are two.

The conversion of sugar molecules into metabolites in anaerobic conditions is called fermentation. The products of the fermentation process include gases, such as carbon dioxide, organic acids, and alcohol.

The pyruvate undergoes the preparatory reaction and converts into Acetyl CoA (acetyl coenzyme A) before entering the Krebs cycle. Two molecules of carbon dioxide are released along with Acetyl CoA. The Krebs cycle takes place in organisms undergoing aerobic respiration after glycolysis. In this cycle, the stored energy is released from the oxidation of Acetyl CoA (Acetyl-coenzyme A) derived from fat, proteins, and carbohydrates. NADH (Nicotinamide adenine dinucleotide hydrogen) and FADH₂ (Flavin adenine dinucleotide hydrogen) are released from the Krebs cycle. The Krebs cycle also facilitates the release of four molecules of carbon dioxide. The net gain of ATP molecules in the “citric acid cycle” is two. The series of complex reactions involving the transfer of electrons across the membrane is called the electron transport chain (ETC). This process occurs in the presence of oxygen. 32 or 34 ATP molecules are produced in the ETC.

Molecular processes in bacteria

Molecular processes in bacteria comprise replication, transcription, and translation.

DNA replication in bacteria

Bacterial deoxyribonucleic acid (DNA) is double-stranded and circular. A replication fork is formed when the helicase enzyme separates the DNA strands at the origin of replication. The DNA molecules become highly coiled ahead of the replication fork. The sugar-phosphate backbone is broken by topoisomerase and is reformed before the replication fork. This results in reducing the pressure formed by supercoiling.

Single-stranded binding proteins attach to the separated DNA strands and help to keep the strands separated. Primase enzyme is used to synthesize ribonucleic acid (RNA) primer as the enzyme DNA polymerase III requires a free 3'-OH end of the primer to initiate elongation. DNA is formed continuously on the leading strand, whereas on the lagging strand, DNA is formed in short fragments named Okazaki fragments. DNA polymerase I replaces the RNA primer with a DNA molecule. The gaps between the Okazaki fragments are sealed by the DNA ligase, which joins the segments into a single molecule of DNA.

Transcription in bacteria

The process of transcription is initiated by RNA polymerase holoenzyme from a particular point termed the promoter sequence. The major enzyme used in transcription is bacteria RNA polymerase. The core polymerase is the single RNA polymerase present in bacteria and is composed of alpha, beta, dash beta, and omega sub-units. It attaches to the particular sequence on the template DNA strand, known as the promoter. The attachment of core polymerase to the promoter is promoted and specified by the sigma factor.

The core polymerase and the sigma factor are collectively known as the holoenzyme. In the case of E. coli, the promoter comprises two conserved sequences of 5'- TATAAT'-3 at -ten element and 5'-TTGACA-3' at -35 element. These sequences are located upstream in the region of initiation of transcription. The holoenzyme is attached to two conserved sequences of a promoter from the close complex.

After the synthesis of RNA, which is longer than ten base pairs, the sigma factor detaches and the enzyme moves along the 5'-3' direction continuously while synthesizing the RNA. As the formed RNA leaves the RNA exit channel, it is proofread by hydrolytic editing. This method tracks one or more nucleotides and cleaves the RNA while removing the error. Besides, there is a pyro-phosphorolytic editing mechanism that removes the altered nucleotide.

There are two mechanisms of transcription in prokaryotes. The first is the Rho-independent mechanism, where the transcription is terminated because of a specific sequence in the terminator DNA. The second mechanism of termination is the Rho-dependent mechanism, where the termination process is brought to an end by the rho-protein.

Translation in bacteria

Translation is the mechanism by which the triplet base sequence of the transcribed mRNA guides the linking of a specific sequence of amino acids to form a polypeptide on the ribosome. In bacteria, transcription and translation occur simultaneously as these processes take place in the cytoplasm.

The initiation stage brings together an mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of the ribosomes. The union of all these components forms the translation initiation complex.

In the elongation stage of translation, the amino acid is added to the first amino acid one by one. Each addition requires the help of certain proteins called elongation factors in prokaryotes. The elongation factors in prokaryotes are termed EF -TUs, EF-G, and EF-T. There is a more complex set of elongation factors in the eukaryotes.

A stop or terminator codon, connected to the “A-site,” is present at the end of the mRNA chain. This codon is not read and gets attached to the transfer RNA-amino acid complex. The stop codon inhibits translation by preventing further attachment of amino acids to the corresponding polypeptide chain.

A water molecule gets incorporated into the newly synthesized polypeptide chain and cleaves or hydrolyses the entire polypeptide, detaching it from the transfer RNA at the “P-site.” The ribosome is then separated from the mRNA chain at the stop codon, and it splits into its two subparts. The detached transfer RNAs and ribosomes can now start a new cycle of polypeptide synthesis.

Virus

Viruses are acellular entities that are considered small infectious agents. They infect all life forms present on earth; from microbes to plants and animals. The viruses that infect bacteria are called bacteriophages. An example of a human-infecting virus is the Covid-19 (coronavirus disease) causative pathogen.

Filtration studies reveal that virions or virus particles range from the smallest unicellular size (300 nanometers) to the largest protein molecules (20 nanometers). The generalized complete virus particle or virion comprises a single nucleic acid molecule enclosed by a protein coat known as a capsid. Nucleocapsid is the term used for the complete composition of the nucleic acid and the capsid. In some viral species, a lipid membrane called an envelope is also present surrounding the capsid coat.

Viral physiology involves processes and activities that usually occur in the infected host cell and result in the replication of viral particles. Viruses can only exist with the help of living host cells. The reproduction and growth processes of viruses do not involve cell division. A virus attached to the surface of a susceptible host cell or a cell of a host organism either releases its genetic material inside the cell or itself enters the cell. The virus manipulates and uses the molecular machinery of the host cell to produce new viral particles. Further, these invade other host cells and allow this multiplication to continue. Virus-infected host cells may either be completely destroyed or left unharmed.

Common Mistakes

Students can evaluate the least resistant and the most resistant microbes based on their control measures. Endospores have their walls developed so that these cannot be broken easily in unfavorable conditions.

Context and Applications

This topic is significant in the professional exams for undergraduate, graduate, and postgraduate courses, especially for the following:

• Bachelor of Science in Microbiology
• Master of Science in Microbiology
• Doctor of Philosophy in Microbiology
• Master of Philosophy in Microbiology

Related Concepts

• Microbiology
• Genetics
• Biochemistry
• Molecular Basis of Inheritance

Practice Problems

Q1: What branch of science deals with the structure-function relationships in microbes, particularly their response to the environment?

(a) Evolution

(b) Immunology

(c) Microbiology

(d) Physiology

Correct Choice: (c)

Explanation: The branch of science that deals with the study of microbes, their structure-function relationships, particularly by associating their response with the environment, is microbiology. It helps us to understand the world of microbes, their usage, and their harms.

Q2: Which of the following is not a phase of microbial cell growth?

(a) Infinity phase

(b) Lag phase

(c) Exponential phase

(d) Death phase

Correct Choice: (a)

Explanation: The microbial cell growth comprises the lag phase (slow phase of growth), exponential (fast phase of growth) phase, and death phase. There is no such phase called the infinity phase in microbial cell growth.

Q3: What are the most resistant microbes?

(a) Bacterial endospores

(b) Gram-positive bacteria

(c) Adenovirus

(d) Rhinovirus

Correct Choice: (a)

Explanation:-Bacterial endospores are tough, hard, non-reproductive, and dormant structures. These structures are formed when conditions are not favorable for the bacteria. They are known for their resistance in the microbe world.

Q4: Which of the following is not a phase of cellular respiration?

(a) Electron transport chain

(b) Krebs cycle

(c) Glycolysis

(d) Fermentation

Correct Choice: (d)

Explanation: Fermentation is not a phase of cellular respiration; it is a metabolic process that causes changes in the organic substance like starch and converts it into acid or alcohol. The process occurs with the help of enzymes produced by microbes like yeast.

Q5: Which enzyme separates the DNA strands at the origin of replication?

(a) Helicase

(b) Ligase

(c) Single-stranded proteins

(d) Polymerase

Correct Choice: (a)

Explanation: Helicases are necessary enzymes encountered in the replication process, where they separate the double stranded DNA. The separation of double-stranded DNA allows the single strands to be copied, which is essential for replication.