BIO 320/ Diploma ScienceIntroduction to Biological Diversity CHAPTER 3 : MONERA BACTERIA Introduction. Initially, organisms are divided into Eukaryote and Prokaryote. In the five-kingdom system, organisms are further divided into five kingdoms: Monera, Protista, Plantae, Fungi and Animalia. The taxonomic Kingdom Monera consists of the bacteria. Bacteria are prokaryotes, and their cell structure is basically different from the cells of other living organisms. The other four kingdom in five kingdom system are consists of eukaryotic organisms. In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea because of the major differences in the structure and genetics between the two groups of organisms. This arrangement of Eukaryota (also called "Eukarya"), Bacteria, and Archaea is called the threedomain system. Bacteria consist of kingdom Eubacteria, Archaea consists of kingdom Archaeabacteria and Eukarya consists of kingdom Protista, Fungi, Plantae and Animalia. Figure 3.1 Classification of living things Metabolic diversity Metabolic diversity of bacteria can be divided into heterotrophic and autotrophic. Autotrophic bacteria can be divided into photoautotrophic and chemoautrophic. Like plants, photoautotrophic bacteria synthesize organic compound by photosynthesis and they are “selffeeders”. Chemoautotrophs bacteria are also self feeders. Carbon dioxide is the normal carbon source. Some species strip organic compounds for electron and hydrogens. Others use inorganic substances, such as gaseous hydrogen, sulfur, nitrogen compounds, and a form of iron. Heterotrophic bacteria can be divided into photoheterotrophic and chemoheterotrophic. Photoheterotrophic bacteria are not self-feeders. They use energy from the sun for 1 Ainun Jariah Manaf/UiTM Pahang . complex carbohydrates and other compounds that other various organisms produce. Cells may be grouped in two (diplococci). Bacteria with rigid shape of long helix are known as spirillum (pl. Bacteria typically have one of three shapes: rodsshaped.. spherical or spiral. coccus). but their carbon sources are fatty acid. 3. occur singly or in groups..BIO 320/ Diploma Science Introduction to Biological Diversity photosynthesis. 2. Chemoheterotrophic bacteria are parasites or free-living saprobes and they are not self-feeder. spirilla) while with flexible long helical shape is known as spirochete. Rod-shaped bacteria. 2 Ainun Jariah Manaf/UiTM Pahang . known as bacilli (sing. referred to as cocci (sing. in long chains (streptococci) or in cluster that looks like bunches of grapes (staphylococci). Shape of bacteria Bacteria come in many shapes and sizes. Bacteria that have a shape of short helix is known as vibrio. Spherical bacteria. bacillus) can occur as single rods or as long chain of rods. 1. The following are the important structures that make up the bacteria. but the most important are to keep the bacterium from drying out and to protect it from phagocytosis (engulfing) by larger microorganisms.Some species of bacteria have a third protective covering. such as Escherichia coli and Streptococcus pneumoniae.BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. The capsule is a major virulence factor in the major disease-causing bacteria. where they donot cause disease. 1. Biochemical processes that normally occur in a chloroplast or mitochondrion of eukaryotes will take place in the cytoplasm of prokaryotes. Nonencapsulated mutants of these organisms are avirulent. 3 Ainun Jariah Manaf/UiTM Pahang . Capsules play a number of roles. a capsule made up of polysaccharides (complex carbohydrates). Bacterial Structure Bacteria lack a nuclear membrane and membrane-bound organelles. Capsule .2 Shapes and grouping forms of various bacteria. 3 Diagram of bacteria cell 2. 4 Ainun Jariah Manaf/UiTM Pahang . Cell Wall . a complex polymer consists of two unusual type of sugar (long polysaccharides) linked with short polypeptides to form a single macromolecules that surrounds the entire plasma membrane. In gram-negative bacteria. The wall provides rigid framework in order to maintain its shape. gram-positive bacteria retain the purple color of the stain because the structure of their cell walls traps the dye. When exposed to a gram stain. The wall surrounds the cytoplasmic membrane. It also helps to anchor appendages like the pili and flagella. uses a staining and washing technique to differentiate between the two forms of bacteria. gram-positive and gram-negative bacteria.The strength of the wall is responsible for keeping the cell from bursting under hypotonic condition or under stress. protecting it from the environment.BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. which originate in the cytoplasm membrane and protrude through the wall to the outside. Cell wall composition varies widely amongst bacteria and is one of the most important factors in bacterial species analysis and differentiation.Each bacterium is enclosed by a rigid cell wall composed of peptidoglycan. A technique devised by Danish physician Hans Christian Gram in 1884. enzymes. in the case of the photosynthetic cyanobacteria. Figure 3. Flagella . continuous strand of DNA.BIO 320/ Diploma Science Introduction to Biological Diversity the cell wall is thin and releases the dye readily when washed with an alcohol or acetone solution.Flagella (singular. 5 Ainun Jariah Manaf/UiTM Pahang . They can be found at either or both ends of a bacterium or all over its surface. The flagella beat in a propeller-like motion to help the bacterium move toward nutrients. flagellum) are hair like structures that provide a means of locomotion for those bacteria that have them. nutrients.3(a) Gram staining 3. a chromosome. in a region of the cell called the nucleoid. toward the light. Cytoplasmic Membrane – Consists of a layer of phospholipids and proteins. of bacterial cells is where the functions for cell growth. or protoplasm. wastes. Membranes are also dynamic. away from toxic chemicals. regulating the flow of materials in and out of the cell. The cell wall of gram negative bacteria consists of two layers. and gases and contains cell structures such as ribosomes. 5. metabolism. The chromosome. It encloses the interior of the bacterium. The cell envelope encases the cytoplasm and all its components. Unlike the eukaryotic (true) cells. The cell wall of gram positive bacteria is very thick and consists mainly of peptidoglycans which held together by amino acids. a single. bacteria do not have a membrane enclosed nucleus. Membranes are highly organized and asymmetric. and replication are carried out. or. 4. having two sides. It is a gel-like matrix composed of water. but not contained. is localized. Cytoplasm . where each side with a different surface and different functions. constantly adapting to different conditions. a layer of peptidoglycans and another layer of thick outer membranes. The outer membrane resembles plasma membrane but contains polysaccharide linked to lipids. and plasmids.The cytoplasm. All the other cellular components are scattered throughout the cytoplasm. 7. DNA is found attached to the cell wall as a single circular thread. Figure 3. copies in the cytoplasm are passed on to daughter cells during binary fission. In addition to DNA . Only the chromosome has the genetic instructions for initiating and carrying out cell division.4 Structure of a bacterium highlighting the bacterial plasmid 6 Ainun Jariah Manaf/UiTM Pahang . most bacteria have small amount of genetic information in the form of smaller circular fragments of DNA strands. or binary fission. but simply an area of the cytoplasm where the strands of DNA are found. Most bacteria have a single. plasmids are made of a circular piece of DNA. however. resistance to heavy metals. Introduction to Biological Diversity Nucleoid .BIO 320/ Diploma Science 6. Unlike the chromosome. Like the chromosome. extrachromosomal genetic structures carried by many strains of bacteria. circular chromosome that is responsible for replication. and virulence factors necessary for infection of animal or plant hosts. a process by which bacteria exchange genetic information. Plasmids are passed on to other bacteria through two means. specifically in the area of genetic engineering. Plasmids replicate independently of the chromosome or become integrated into it. form a tubelike structure at the surface called a pilus that passes copies of the plasmid to other bacteria during conjugation.Plasmids are small. although a few species do have two or more. The ability to insert specific genes into plasmids have made them extremely useful tools in the fields of molecular biology and genetics.The nucleoid is a region of cytoplasm where the chromosomal DNA is located. Plasmids often have gene that codes for catabolic enzymes. Plasmids . For most plasmid types. the primary means of reproduction in bacteria. for genetic exchange or for resistance to antibiotic drug. called plasmids. they are not involved in reproduction. are also found in the cytoplasm. It is not a membrane bound nucleus. Other types of plasmids. but are free-standing structures distributed throughout the cytoplasm. pilus). there are then two cells of identical genetic composition. dividing by binary fission. that become bigger. Figure 3. They translate the genetic code from the molecular language of nucleic acid to that of amino acids—the building blocks of proteins. Following cell splitting (cytokinesis). then attaches each copy to a different part of the cell membrane. 9. Ribosome .BIO 320/ Diploma Science 8. many disease-causing bacteria lose their ability to infect because they're unable to attach to host tissue. Specialized pili are used for conjugation. Bacterial ribosome’s are similar to those of eukaryotes. A less common form of asexual reproduction among bacteria is budding. E.Ribosome are microscopic "factories" found in all cells.5 Rod-Shaped Bacterium. but are smaller and have a slightly different composition and molecular structure. Bacterial ribosome’s are never bound to other organelles as they sometimes are (bound to the endoplasmic reticulum) in eukaryotes. matures. and finally separates from the mother 7 Ainun Jariah Manaf/UiTM Pahang . Bacterial Reproduction The usual method of asexual reproduction of bacteria is through cell division known as binary fission. small hair like projections emerging from the outside cell surface.Many species of bacteria have pili (singular. Without pili. In budding a cell develops a swell. The bacterial chromosome is a single DNA molecule that first replicates. Introduction to Biological Diversity Pili . When the cell begins to pull apart. and rocks. or bud. These outgrowths assist the bacteria in attaching to other cells and surfaces. Proteins are the molecules that perform all the functions of cells and living organisms. coli. intestines. the replicate and original chromosomes are separated. such as teeth. including bacteria. during which two bacteria exchange fragments of plasmid DNA. 5 Donation of DNA. random pieces of host chromosome are package within a phage capsid. In transformation. In the DNA-transfer process known as transduction. This later on causes an alteration of the bacterial cell’s genotype by taking up of foreign DNA.coli. no phages genes. The phages carry only bacterial genes. divide by fragmentation. Genetic material exchanged also occurs in bacteria. which separates into several new cells. This process takes place by three different mechanisms: transduction. Transduction can be divided into generalized transduction and specialized transduction. The recombination is the bacterial equivalent of sexual reproduction in eukaryotes. the transferred DNA may recombine with the genome of the new host cell. fragments of DNA released by dead bacteia or secreted by live bacteria cell are taken in by another bacterial cell. 1. In both type of transduction. transformation. A few species of bacteria such as actinomycetes. In generalized transduction. only a small piece. it involves the transfer of only a few specific genes from ane bacterial cell to another by means of a phage. Note that the entire DNA is not usually transferred. 2.BIO 320/ Diploma Science Introduction to Biological Diversity cell. and conjugation. Figure 3. bacteriophages or virus that infect bacteria carry portion of bacterial DNA or genes from one bacterial host to another as a result of abnormality in the phage reproductive cycle. Walls form within the cell. In specialized transduction. which infects E. the lambda phage. 8 Ainun Jariah Manaf/UiTM Pahang . 5 Generalized transduction. it may also transfer part of the chromosome.BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. 3. The DNA transfer is one way. F factor may exist as a plasmid or become integrated into the chromosome. a bacterial cell with DNA called F (fertility) factor is able to replicate and transfer a copy of it's DNA to another cell without F factor through a tube called a sex pilus. which can also be referred to as ‘male’ and the recipient. and the other receives the DNA. where one cell donates DNA. If it is integrated into the chromosome. The donor. sometimes called the ‘female’. 9 Ainun Jariah Manaf/UiTM Pahang . The DNA that is transferred is used to replace similar genes in the recipient cell. Enzymes destroy the replaced genes. In conjugation. The sex pilus usually breaks before the entire DNA from the donor cell is transferred. 6 Diagram of bacterial conjugation. 10 Ainun Jariah Manaf/UiTM Pahang .BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. 7 Conjugation and recombination in E. Certain disease causing bacteria. extremely durable cells. the cell wall of the original cell lyses. such as the one that causes the disease Anthrax can be virulent or capable of causing an infection 1300 years after forming their endospore! 11 Ainun Jariah Manaf/UiTM Pahang . coli Some bacteria form a spore within their cell membrane and this is known as endospores. forming an active. Endospores can survive in very dry. When the condition becomes favorable. This endospore will germinates. Endospores are a method of survival. growing bacterial cell. hot or frozen environment.BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. Endospore allows bacteria to wait for favorable environmental conditions. not one of reproduction. Endospores are dormant. releasing the endospore. or when food is insufficient. Grouping of Bacteria There are two different ways of grouping bacteria. pickles. get their energy by oxidizing inorganic chemicals. the sequence illustrated above goes from left to right. 1. They can be divided into three types based on their response to gaseous oxygen. Bacteria that able to manufacture their own organic molecules from simple raw materials are known as autotroph. Many bacteria have symbiotic relationship with other organism and some are important pathogens of plants and animals. Facultative anaerobes prefer oxygen. and cheeses. 12 Ainun Jariah Manaf/UiTM Pahang . most bacteria cells are aerobic. olives. but can live without it. obtain their energy from light. 2. 2. Bacteria also involve in the production of antibiotics. yogurt. Obligate anerobic bacteria cannot tolerate gaseous oxygen at all and die when exposed to it. Note.8 Electron micrographs illustrating formation of an endospore. The can be grouped by how they obtain their energy. Whether they are heterotroph or autotroph. or photoautotroph.BIO 320/ Diploma Science Introduction to Biological Diversity Figure 3. Importance of Bacteria Bacteria play important ecological function as decomposers and are important in recycling nutrients. Aerobic bacteria require oxygen for their health and existence and will die without it. Photosynthetic autotroph. Bacteria also involve in fermentation of many food and beverages. 1. Chemosynthetic autotroph or chemoautroph. They are also used in the production of industrial compounds such as acetone. This includes species that are found in decaying material as well as those that utilize fermentation or respiration. 3. Bacteria that have to consume and break down complex organic compounds are heterotrophs. Lactic acid bacteria are used in the production of acidophilus milk. and found that there were two distinctly different groups. strong poisons that either is secreted from the cell or leak out when the bacterium is damaged. Woese proposed that life be divided into three domains as in the fundamental three-domain system of classification: Eukarya. However. and all known living things except the Archaea. Archaea are. and Archaebacteria or Archaea. Endotoxins can cause systemic symptoms such as fever and they are destroyed by heating. Eubacteria or Bacteria. in Archaea there is no peptidoglycan in their cell wall. the Archaea. There are even features of archaeal tRNA that are more like eukaryotic than bacteria. Those "bacteria" that lived at high temperatures or produced methane clustered together as a group different from the usual bacteria and the eukaryotes. Dr. animals. Characteristics of Archaea Like bacteria.BIO 320/ Diploma Science Introduction to Biological Diversity Some pathogenic bacteria produce exotoxins. similarly to bacteria. Unlike most bacteria. their tRNAs have a number of features that differ from all other living things. These substances affect the host only when they are released from dead bacteria. Endotoxins are not secreted by the pathogenic bacteria but are components of the cell walls of most gram-negative bacteria. fungi. Carl Woese and his colleagues at the University of Illinois were studying relationships among the prokaryotes using DNA sequences. meaning that Archaea share certain features in common with eukaryotic and not with bacteria. known as Monera in the five kingdom taxonomy. The tRNA or transfer RNA molecules are important in decoding the message of DNA and in building proteins. This may suggest a close relationship between Archaea and eukaryotes. plants. archaeans have no internal membranes and their DNA exists as a single loop called a plasmid. ARCHAEA Introduction The scientific community was understandably shocked in the late 1970s by the discovery of an entirely new group of organisms. The same is true of their ribosomes. 13 Ainun Jariah Manaf/UiTM Pahang . Because of this huge difference in genetic makeup. Several other characteristics also distinguish Archaea from Bacteria. Exotoxin can cause specific symptoms Other pathogenic bacteria produce endotoxins. whereas archaea have membranes composed of glycerol-ether lipids. the giant processing molecules that assemble proteins for the cell. single-celled organisms lacking nuclei and are therefore classified as prokaryotes. archaeal and eukaryotic ribosomes are not sensitive to those agents. both bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids. Certain features of tRNA structure are the same in bacteria. While bacterial ribosomes are sensitive to certain chemical inhibiting agents. Further. BIO 320/ Diploma Science Introduction to Biological Diversity These differences may be an adaptation on the part of Archaea to be hyperthermophe. Table 1: A Comparison of the Three Domains of Life 14 Ainun Jariah Manaf/UiTM Pahang . Archaeans also have flagella that are particularly different in composition and development from the superficially similar flagella of bacteria. or cyanobacteria. These prokaryotes require salt for growth and will not grow at low salt concentrations. Methanogens have an incredible type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth. and enzymes are stabilized by Na+. Methanogens are normal inhabitants of the rumen of cows and other ruminant animals. This is the only example in nature of non photosynthetic photophosphorylation. and sewage treatment facilities. The pigment is a type of rhodopsin called bacteriorhodopsin. They also exhibit a variety of different types of metabolism. Extreme halophiles live in natural environments such as the Dead Sea. spiral. They occur in various shapes. but the gas is usually wasted rather than trapped for recycling. Anaerobic environments are plentiful. algae. which is as high as 5 molar or 25 percent NaCl. the Great Salt Lake. and extreme (hyper) thermophiles (archaea that live at very high temperatures). Their cell walls. the methanogens produce methane (CH4) in a unique energygenerating process. Bacteriorhodopsin captures and reacts with light in a way that forms a proton gradient on the membrane allowing the synthesis of ATP. The process is different from photosynthesis carried out by plants. found in the vertebrate retina. or evaporating ponds of seawater where the salt concentration is very high. or rectangular. such as spherical. 2. Habitats Based on their physiology. In the process of making cell material from H2 and CO2. ribosomes. This bacteriorhodopsin protein is chemically very similar to the light-detecting pigment rhodopsin. adapts to the high-salt environment by the development of "purple membrane". rod-shaped. extreme halophiles (archaea that live at very high concentrations of salt (NaCl).BIO 320/ Diploma Science Introduction to Biological Diversity Form Individual archaeans range from 0. Methanogens represent a microbial system that can be exploited to produce energy from waste materials. the Archaea can be divided into three types: methanogens (archaea that produce methane). 1. Methanogens are obligate anaerobes that will not tolerate even brief exposure to oxygen. the prevalent species in the Great Salt Lake. actually patches of light-harvesting pigment in the plasma membrane. bogs (swamps) and deep soils. Halobacterium halobium. Large amounts of methane are produced during industrial sewage treatment processes. and some form aggregates or filaments up to 200 μm in length. lobed. 15 Ainun Jariah Manaf/UiTM Pahang . The end product (methane gas) accumulates in their environment. intestinal tracts of animals. and these include marine and fresh-water sediments.1 to over 15 μm in diameter. Methanogen metabolism produced most the natural gas (fossil fuel) reserves that are tapped as energy sources for domestic or industrial use. Their membranes and enzymes are unusually stable at high temperatures. archaeans are not restricted to extreme environments. These hyperthermophiles are inhabitants of hot.BIO 320/ Diploma Science 3. Some are lithotrophs that oxidize sulfur as an energy source. sulfur-rich environments usually associated with volcanism. One species. 16 Ainun Jariah Manaf/UiTM Pahang . Introduction to Biological Diversity The extreme thermophiles or hyperthermophiles require a very high temperature (45o – 110o C) and sometimes acidic environment for growth. found in and thermal deep-sea vents ("smokers") and cracks in the ocean floor able to live at temperature from 80o to 110o C Archaeans may be the only organisms that can live in extreme habitats such as thermal vents or hypersaline water. new research is showing that archaeans are also quite abundant in the plankton of the open sea. They may be extremely abundant in environments that are hostile to all other life forms. Others live in volcanic areas under the sea. such as hot springs and geysers in Yellowstone National Park at pH values 1 to 2 and at temperature near 60o C. Sulfur-oxidizers grow at low pH that is less than pH 2 because they acidify their own environment by oxidizing S (sulfur) to SO4 (sulfuric acid). Nevertheless. Lithotroph is an organism that depends on inorganic compounds as electron donors for energy production. Most of these Archaea require element sulfur for growth. Some are anaerobes that use sulfur as electron acceptors for respiration in place of oxygen. transduction. Compare between binary fission. Archaea can be divided into three types: methanogens. Explain the metabolic diversity of bacteria of each of the group below a. c. transformation and conjugation 5. What are the differences between the archaebacteria and the eubacteria.BIO 320/ Diploma Science Introduction to Biological Diversity QUESTIONS 1. Make sketches of the three basic shapes of bacterial cells 2. extreme halophiles and extreme thermophiles. Obligate anaerobes Facultaive anaerobes Aerobes Autotrophic bacteria Heterotrophic bacteria (10 marks) Illustrate a prokaryote. e.? 3. 6. Briefly describe each of the types of archaea. 7. b. 4. By using labeled diagrams. Describe the important metabolic and structural features of bacteria. 8. d. Label the diagram accordingly Compare between extreme halophiles and extreme thermophiles 17 (6 marks) (4 marks) Ainun Jariah Manaf/UiTM Pahang . Contrast the cell wall of a gram-positive bacterium with that of a gram-negative bacterium. describe conjugation processes of bacteria.