Nucleolus

Nucleolus (plural nucleoli) is the largest and most noticeable structure within the nucleus of a eukaryotic cell. They are composed up of DNA, RNA and proteins. They vary in number from one to many nucleoli in the nucleus. They are complex, not membrane enclosed organelle of a eukaryotic cell that separates granular and fibrillar regions.  They are present in nondividing cells but generally disappears during the beginning of mitosis and then begins to reassemble in telophase around nucleolar organizer.

They are the site of ribosome biogenesis and forms rRNA (ribosomal RNA). The rRNA combines with ribosomal proteins and forms ribosomal subunits. These ribosomal subunits are immature and they leave the nucleus through nuclear envelope pores. Then, they matures in the cytoplasm. Nucleoli also help in the assembly of signal recognition particles, modification of tRNA (transfer RNA) and also play a major role in cell’s response to stress. 

Mitochondria

Mitochondria, also known as the powerhouse of cell, is a double membrane bound organelle present in all eukaryotic cells. The word is derived from the Greek word, ‘mitos’ means thread and ‘chondrion’ means granule or grain like. Generation of ATP (adenosine triphosphate) by electron transport and oxidative phosphorylation and the activity of tricarboxylic acid (TCA) cycle takes place here. Major ATP requirement of a cell is fulfilled by mitochondria and hence it is known as powerhouse of cell. Mitochondria also play a central role in calcium signaling and apoptosis i.e. programmed cell death.

Structurally, mitochondria is cylindrical in shape and about 0.75 to 3.0 μm in diameter. They vary considerably in number; a cell contain as many as 1000 mitochondria or a single mitochondria (in some yeasts, trypanosome protozoa etc.). The ribosome of mitochondria is smaller in size than that of cytoplasmic ribosomes. The mitochondrial ribosomes resembles that of bacterial one in size and composition. Also, mitochondrial DNA is like that of bacterial DNA i.e. closed circle and they reproduce by binary fission. They synthesize their own proteins with the help of their DNA and ribosome. Since mitochondria has its own independent genome and as it resembles the bacterial genome to some extent, it is generally believed that they arose from symbiotic associations between bacteria and larger cells. 

The two membranes of mitochondria are outer mitochondrial membrane and inner mitochondrial membrane. The two membranes are mainly composed of phospholipid bilayer and proteins. The space between these two membrane is known as intermembrane space and the space within the inner membrane is called the matrix, containing mainly ribosomes, DNA and calcium phosphate granules. The special infoldings of the inner membrane which increases its surface area is known as cristae (singular crista). Cristae varies in shape from species to species. For instance: in fungi, they are plate like, amoebae possesses vesicles shaped cristae, tubular shaped cristae are found in many eukaryotes and so on. Mitochondria that has stripped of its outer membrane is known as mitoplasts. Mitoplasts have intact inner membrane.

Although mitochondria is the site for Krebs cycle, electron transport and oxidative phosphorylation, they occurs in the different mitochondrial compartments. Electron transport and oxidative phosphorylation takes place in inner membrane as the enzymes and electron carriers involved in these processes are present in the inner membrane. TCA cycle and oxidation pathway for fatty acids takes place in matrix as it contains their associated enzymes. F₁ particles are attached as small spheres on the inner surface of inner membrane and synthesizes ATP during cellular respiration.

Halophiles

Halophiles or halophilic extremophiles are the organisms that live in extremely salty environments i.e. they requires high level of sodium chloride to grow. The name comes from the Greek word meaning “salt-loving". Halobacterium (a genus of archaea), bacterium Salinibacter ruber etc. are halophiles. Halophiles can be aerobic or anaerobic. They modifies the structure of their proteins and membranes. Their internal potassium concentration is very high around 4 to 7 M; this helps them to  remain hypertonic to their environment and also their intracellular machinery (ribosomes, enzymes and proteins) require high level of potassium in order to be stable and active. On the contrary, their plasma membrane and cell wall are stabilized by high concentration of sodium ions which will otherwise disintegrate.

Influence of pressure on microbial growth

Pressure is generally defined as the force acting per unit area. It  is one of the major physical factor that affects the growth of microorganisms. Microorganisms that grow on the land or on the surface of water are generally exposed to the pressure of 1 atmosphere. On the basis of pressure, microorganisms are classified into two types:

Barotolerant: They are not affected by increase in pressure. They require standard atmospheric pressure for their growth but they can also grow at high pressure.

Barophilic: They are also called piezophile, which means pressure-lover. They grow best at high pressure like deep-sea bacteria and archaea. Example includes Halomonas salaria, Photobacterium profundum, Methanococcus jannaschii, Shewanella benthica etc. They play an important role in nutrient recycling in the deep sea.

Eukaryotic Organelles Or Structures : Definition & Function

The following cell structures or organelles are found in a typical eukaryotic cell:

Eukaryotic Organelles or Structures	Definition and Function
Plasma membrane	boundary between cell and environment; regulate what enters and exits the cell, acts as selectively permeable barrier, mediates cell-cell interaction and adhesion to surfaces
Ribosome	consists of RNA and proteins; site of protein synthesis
Golgi complex	composed of groupings of flattened sacs known as cisternae; process, packages and exports protein molecules; lysosome formation
Cytoplasmic matrix	liquid inside the cell; site of many metabolic process, helps in transport of metabolites
Endoplasmic reticulum	contains interconnected network of flattened sac like structure called cisternae; synthesis and transport of proteins, lipids and steroid hormone; detoxification
Lysosome	spherical vesicles containing hydrolytic enzymes; major role in protein destruction
Mitochondria	power house of cell; produces ATP through tricarboxylic acid cycle, electron transport, oxidative phosphorylation and other pathways
Cilia and flagella	protrusions from a cell; helps in movement and cellular locomotion; helps cell to adhere to solid surface
Nucleus	membrane enclosed organelle; house of genetic information as DNA; control centre for cell
Vacuole	found in plant and fungal cells; enclosed compartments filled with water containing inorganic and organic molecules; helps in storage, transport, digestion and water balance
Choloroplast	specialized subunit in plant and animal cells;a plastid that contains chlorophyll; site of photosynthesis-traps sunlight and forms carbohydrate from carbon dioxide and water
Cell wall	tough, flexible layer;consist mainly of cellulose; found in plants; provides shape, support and protection to cell
Centrioles	cylindrical groupings of microtubules; found in animal cells but absent in plant cells;  helps to organize spindle fibers during cell division
Cytoskeleton	a network of fibers throughout the cytoplasm, support the cell and aids in organelle movement; consists of microfilaments, intermediate filaments and microtubules
Peroxisomes	tiny structures that detoxify alcohol; use oxygen to break down fats; contains reducing enzymes like catalase and oxidase
Nucleolus	present in nucleus; dense spherical structure; site of ribosome biogenesis
Microtubule	microscopic tubular structure; component of cytoskeleton; maintains structure of cell, helps in intracellular transport and movement of secretory vesicles and organelles

RNA: Ribonucleic acid

ATP: Adenosine triphosphate

DNA: Deoxyribonucleic acid

Batch culture, Continuous culture & Synchronous culture - Definition & Brief Description

Batch culture

It is a technique used to grow microorganism or cells. In this, microorganisms are grown in a closed system where a limited supply of nutrients are provided at the beginning. The temperature, pressure and pH are maintained accordingly. In the beginning, microorganisms will grow utilizing the provided nutrients. Over the time, nutrients become limited and waste products begins to accumulate. Hence, microbes begin to die, following the four stages of microbial growth curve i.e. lag phase, log phase, stationary phase and death phase. The major advantage of this technique is that it runs for a certain period of time and under limited nutrients. This technique is widely used for the purification of antibiotics, pigments etc.

Continuous culture

It is another technique used to grow microorganisms. In this technique, fresh nutrients are supplied and waste products are removed continuously at the same rate and other conditions like temperature, pressure and pH are kept optimum. This technique maintains the continuously growing microbial culture at exponential phase of growth curve. The chamber used to grow organisms is known as chemostat in which sterile medium is added from one end and medium containing microorganism is removed from the other end thereby keeping the volume of culture at constant level. This technique is useful in extracting primary metabolites like amino acids, organic acids etc.

Synchronous culture

Synchronous culture is a microbiological culture that contains population of the cells that are in the same growth stage. The entire population of culture is kept constant with respect to growth and division. This technique is used to study cell cycle, growth and effect of various factors on microbial cell cycle and growth. Synchronous culture can be obtained by various ways. By the use of certain chemical growth inhibitor like nocodazole, cell growth can be arrested. Once the growth has been completely stopped, inhibitor is removed and cells will begin to grow synchronously. In other method, instead of growth inhibitor, external conditions are changed which will arrest the cell growth. Then the external condition is changed again to resume the growth and all the cells will grow synchronously.

Classification of microorganisms on the basis of oxygen requirement and tolerance

Two most common terms related to oxygen (O₂) are aerobe and anaerobe. Aerobes are those organisms which grows in the presence of O₂ i.e. they grow in an oxygenated environment. Anaerobes are those organisms that grow in the absence of O₂. Mainly most of the organisms require O₂ for their growth and depending upon their O₂ requirement and tolerance, they are classified into five different classes:

Obligate aerobe

Obligate aerobes are those organisms that require O₂ for their growth; they are completely dependent on O₂. For instance, Mycobacterium tuberculosis, Nocardia asteroids etc. Most of the fungi and algae also belongs to this class. In aerobic respiration, O₂  serves as the terminal electron acceptor in electron transport chain. Also, O₂ is utilized for the synthesis of unsaturated fatty acids and sterols.

Obligate anaerobe

Obligate anaerobes dies in the presence of O_2. For instance bacterial genera like Clostridium, Fusobacterium, Prevotella, Actinomyces etc. Aerobic respiration does not take place in these organisms and they are dependent on fermentation and anaerobic respiration for energy generation. However, fermentation and anaerobic respiration pathway yields less energy as compare to aerobic respiration.

Facultative anaerobes

They do not require O₂ for their growth but they can grow in its presence also. When O₂ is present, they make ATP (Adenosine triphosphate) by aerobic respiration and when O₂ is absent, they switch to fermentation or anaerobic respiration pathway. Examples include Staphylococcus, Escherichia coli, Streptococcus, Shewanella oneidensis etc.

Aerotolerant anaerobes

This group of microorganisms ignore O₂ and they grow equally well in its presence and also in its absence. They does not use O₂  for their growth but they can tolerate the presence of O₂ unlike obligate anaerobe. They use fermentation or anaerobic respiration pathway to produce ATP. They include Clostridium, Actinomyces, Streptococcus etc.

Microaerophiles

Microaerophiles are those organisms that require O₂ for their growth but they are damaged by the normal atmospheric level of O₂ (20%). They require O₂ level below the range of 2 to 10% for their growth.  For example, Campylobacter sp, Helicobacter pylori etc. are microaerophilic.

Effect of pH on microbial growth

pH is defined as the negative logarithm of the hydrogen ion concentration and it is the measurement of the hydrogen ion activity of a solution. A solution whose pH is less than 7 is acidic and the solution whose pH is more than 7 is basic; whereas pure water is neither acidic nor basic having pH 7. It is measured by pH scale which range from pH 0 to pH 14 where each pH unit represents a tenfold change in hydrogen ion concentration.

Majority of the microorganisms grow at the neutral pH value of 6.5 to 7.0, they are known as neutrophiles.  However, some can grow at acidic pH, between pH 0 to 5.5 and are called acidophiles. They includes Helicobacter pylori, Acetobacter aceti, Thiobacillus acidophilus etc. Alkalophiles also occurs that can grow at alkaline pH range of 8.5 to 11; for instance Natronomonas pharaonis, Thiohalospira alkaliphila etc. Fungi generally prefers acidic pH of 4 to 6 similar to algae.

Though microorganisms can grow over a wide range of pH value, there is a limit to their tolerance. Significant change in the pH value from optimum harms microorganisms by inhibiting enzyme activity and membrane transport proteins. It also disrupts the plasma membrane of cell. Ionization of the nutrient molecules gets altered due to the change in the external pH and this makes nutrient unavailable to cells.

Extreme alkalophiles like  Bacillus alcalophilus maintains their neutral cytoplasmic pH by exchanging internal sodium ions for external protons.  Other methods are also their for the maintenance of internal pH like neutrophiles uses antiport transport system for the exchange of  potassium for protons.

But with this antiport system, small variations in pH get corrected. Other mechanisms are there to correct drastic environmental pH changes. When pH becomes too acidic, some microorganisms begins to synthesize new proteins due to the activation of acidic tolerance response. Also, chaperones and heat shock proteins are also synthesized. This prevents the denaturation of the proteins and helps in the refolding of denatured proteins.

Some microorganism also has the ability to change the pH of their habitat by synthesizing basic or acidic metabolic waste products. They can make their environment alkaline by producing ammonia through amino acid degradation. Also, they can make their surrounding acidic by fermenting carbohydrates to form organic acids or by oxidizing reduced sulfur components to sulfuric acid as seen in Thiobacillus.

In laboratories, when media are prepared for the growth and study of microorganism, buffers are added to it. Buffer resists the change in pH by the addition of acidic or basic components. For example: phosphate buffer etc.

Types of microorganisms on the basis of their nutrition source

Carbon, hydrogen, oxygen, energy and electrons- all are required for the growth of microorganisms. On the basis of the source from which microorganism fulfills their requirement, they are classified into different classes.

On the basis of carbon source:

Autotrophs: They obtain carbon from inorganic sources like carbon dioxide (CO₂).

Heterotroph: They uses organic compound as a carbon source.

On the basis of energy source:

Phototrophs: They uses energy from sunlight.

Chemotrophs: They obtain energy from the oxidation of either organic (chemoorganotrophs) or inorganic (chemolithotrophs) chemical compounds by a process called chemosynthesis.

On the basis of electron source:

Lithotrophs: The word 'lithos' means rock and 'troph' means consumer; lithotrophs means “eaters of rock”. They uses inorganic substances to obtain electrons.

Organotrophs: They obtain electrons from organic substances.

Now, on the basis of the primary source of carbon, electron and energy; microorganisms are classified into four nutritional classes. They are mentioned below:

Photoautotrophs: They are also called as photolithotrophic autotroph or photolithoautotroph. As the name implies, their source of energy is light, carbon source is CO₂ and they uses inorganic substances as a source of electron. For instance, Purple and green sulfur bacteria extracts electron from inorganic donors like hydrogen, elemental sulfur and hydrogen sulfide. Algae and cyanobacteria also belongs to this class.

Photoorganotrophs: They are also known as photoorganotrophic heterotrophs or photoorganoheterotrophs. They are generally found in polluted lakes and streams. They use energy from sunlight, electron from organic substances and carbon from organic source. Purple nonsulfur bacteria and green nonsulfur bacteria are the examples of photoorganotrophs.

Chemolithotrophs: They are also known as chemolithotrophic autotrophs or chemolithoautotrophs. They basically oxidize reduced inorganic compounds like iron, nitrogen or sulfur to get energy and electron. As they are autotrophs, they use CO₂ as carbon source. They are involved in the chemical transformation of elements like conversion of ammonia to nitrate or sulfur to sulfate etc. Few examples of this includes sulfur-oxidizing bacteria, iron-oxidizing bacteria like Acidithiobacillus ferrooxidans, nitrifying bacteria like Nitrobacter etc.

Chemoorganotrophs: They are also known as chemo- heterotrophs or chemoorganoheterotrophs. As the name implies, they uses organic matter as electron and carbon source. Energy is obtained from either organic or inorganic compound. For this group of microorganism, a same organic source can satisfy all the requirements. Protozoa, fungi and non-photosynthetic bacteria belongs to this class.

Note: Some microbial species are present in nature that has metabolic flexibility i.e. they can change their metabolic patterns in response to environmental changes. Such microbes are known as mixotrophic. In other words, they can mix different source of carbon and energy depending upon the environmental condition. For instance, purple nonsulfur bacteria are photoorganoheterotrophs in the absence of oxygen but at normal oxygen level, they become chemotrophs and oxidize organic molecules to meet their energy requirement.