Lecture 5: Prokaryotes - Biodiversity of Bacteria & Archaea

Lecture 5: Prokaryotes - Monera - Biodiversity of Bacteria & Archaea with ecosystems and adaptations Topic’s / Unit’s Learning Outcome: At the end of the unit/topic, students will be able to: Define and distinguish between the two lineages of prokaryotes (bacteria and archaea) Describe the fe...

Lecture 5: Prokaryotes - Monera - Biodiversity of Bacteria & Archaea with ecosystems and adaptations Topic’s / Unit’s Learning Outcome: At the end of the unit/topic, students will be able to: Define and distinguish between the two lineages of prokaryotes (bacteria and archaea) Describe the features (structure and function) of prokaryotes Explain the factors that promote genetic diversity in prokaryotes Describe the overview of prokaryotic diversity  1. Introduction: Prokaryotes Earth’s first organisms were likely prokaryotes Prokaryotes do not have nucleus and most of them are T. unicellular namibiensis Most prokaryotic cells have diameters of 0.5 – 5 µm, much smaller than the 10–100 µm of many eukaryotic cells. Exception: e.g. Thiomargarita namibiensis (750 μm) Most prokaryotes are smaller & structurally simpler than eukaryotes, but what they lack in size they make up for in numbers Prokaryotes - thrive almost everywhere, including places too acidic, salty, cold, or hot for most other organisms Prokaryotes are divided into two lineages – Bacteria and Archaea Bacteria and Archaea are both prokaryotes (nucleoid) belong to Kingdom Monera  2. Features of prokaryotes Shape Cell-surface structure Motility Internal organisation and DNA Reproduction Mode of nutrition  2.1 Shape Three common forms for bacteria and archaea: 1. Spherical (cocci; singular coccus) can occur singly, in pairs (diplococci), in chains Spheric (streptococci) and in clusters (staphylococci) al 2. Rod-shaped (bacilli; singular bacillus) usually occur in solitary, sometimes the rods are arranged chain-like (streptobacilli) 3. Spiral Rod- shaped Include spirilla (ranging from comma-like shapes to loose coils) and spirochetes (corkscrew-shaped) Example of exceptions: Flat and square-shaped Haloquadratum walsbyi Spir al 2.2 Cell Surface Structure Important feature of nearly all prokaryotic: cell wall, which maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment Eukaryote cell walls are usually made of cellulose or chitin Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides Archaeal cell walls contain a variety of polysaccharides and proteins but lack of peptidoglycan  2.2 Cell Surface Structure The amount of peptidoglycancan differ among bacteria GRAM GRAM NEGATIVE POSITIVE A method called Gram-staining can be used to differentiate bacteria according to their cell wall composition Based on this method, there are two types of bacteria: gram-positive and gram negative Gram-negative bacteria have an outer membrane that contains  2.2 Cell Surface Structure Concept behind Gram-staining (named as the physician Hans Christian Gram) - Stains peptidoglycan Procedure: Bacterial samples are stained with crystal violet dye and iodine, then rinsed with alcohol and finally stained with a red dye (e.g. safranin). Gram-negative bacteria have a Gram-positive bacteria thin layer of peptidoglycan and have a thicker stain red. peptidoglycan layer and stain purple.  2.2 Cell Surface Structure Adaptation of gram negative bacteria based on their cell wall composition Lipopolysaccharides = toxic (can cause fever or shock) Outer membrane protects it from the human body’s defence Outer membrane impedes the entry of drugs Therefore, gram-negative bacteria are generally more virulent compared to gram-positive bacteria For example, many antibiotics (e.g. penicillin) target peptidoglycan and damage bacterial cell walls. Gram-negative bacteria are more likely to be antibiotic resistant. 2.2 Cell Surface Structure Adaptation of many prokaryotes 1. Cell wall surrounded by sticky layer of polysaccharide or protein. This layer is known as capsule if it is dense and well define and slime layer if it is not as well organised. Allow prokaryotes to adhere to their substrate/individuals in a colony  Protect against dehydration Some can shield pathogenic prokaryotes from attacks by host’s immune system 2. Develop tough multi-layered resistant cells (endospores) when they lack essential nutrient.  2.2 Cell Surface Structure 3. Some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae (singular, fimbria).  Fimbrae are usually shorter and more numerous than pili (singular, pilus), appendages that pull two cells together prior to DNA transfer from one cell to the other. 2.2 Cell Surface Structure  2.3 Motility 50% of prokaryotes are capable of taxis (a directed movement towards or away from a stimulus). Towards: positive taxis, away: negative taxis. Most motile bacteria propel themselves by flagella (singular, flagellum) scattered about the surface or concentrated at one or both ends. The flagellum has three main parts: motor, hook and filament. Flagella of three domains perform similar functions but are not related by common descent. 2.4 Internal Organisation & DNA Cells of prokaryotes are simpler than those of eukaryotes in both internal structure and physical arrangement of their DNA. Prokaryotes Eukaryotes Complex No, but somehave Yes compartmentalis specialised membranes ation via that perform metabolic enclosed functions organelles Amount of DNA Less More Chromosome Circular with fewer proteins Linear Nucleus No. Chromosome is located Yes in nucleoid. Some have smaller rings of independently replicating 2.4 Internal Organisation & DNA Specialised membranes that perform metabolic functions These are usually infoldings of the plasma membrane 0.2 m 1 m Respiratory membrane Thylakoid membranes (a) Aerobic prokaryote (b) Photosynthetic prokaryote 2.5 Reproduction Many prokaryotes can reproduce quickly in favourable environments Via binary fission, where a single cell divides into 2 cells, which then divide into 4, 8, 16 and so on… Many can divide every 1-3 hours while some can produce an entire new generation in only 20 minutes! 2.5 Reproduction Key features of prokaryotic reproduction: – They are small – They reproduce by binary fission – They have short generation times – Evolve rapidly 2.6 Mode of nutrition  3. Factors influencing genetic diversity in prokaryotes Prokaryotes have considerable genetic variation. There are 3 main factors that give rise to high levels of genetic diversity in prokaryotes: A. Rapid reproduction B. Mutation C. Genetic Recombination 3.1 Rapid Reproduction and Mutation Prokaryotes reproduce by binary fission, and offspring cells are generally identical Mutation rates during binary fission are low, but because of rapid reproduction, mutations can accumulate rapidly in a population High diversity from mutations allows for rapid evolution 3.2 Genetic Recombination Genetic recombination, the DNA from two combining of contributes sources, to diversity Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation Movement of genes among individuals from different species is called horizontal gene transfer What is vertical gene transfer?  3.2.1. Transformation & Transduction A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria) 3.2.2. Conjugation Conjugation is the process where genetic material is transferred between prokaryotic cells that are temporarily joined In bacteria, the DNA transfer is one way A donor cell attaches to a recipient by a pilus, pulls it closer, and transfers DNA Sex pilus  4. The role of oxygen in metabolism Prokaryotic metabolism varies with respect to O2 – Obligate aerobes require O2 for cellular respiration – Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration – Facultative anaerobes can survive with or without O2 5. Prokaryotic Diversity Until the late 20th century, systematists based prokaryotic taxonomy on phenotypic criteria Applying molecular systematics to the investigation of prokaryotic phylogeny has produced dramatic results Molecular systematics led to the splitting of prokaryotes into bacteria and archaea Molecular systematists continue to work on the phylogeny of prokaryotes  Eukarya Domain Phylogeny & Eukaryotes Systematics Korarchaeotes Archaea Domain Euryarchaeotes UNIVERSAL Crenarchaeotes Nanoarchaeotes ANCESTOR Proteobacteria Domain Bacteria Chlamydias Spirochetes Previously – Bergey’s Gram-positive Cyanobacte bacteria ria Classification of Bacteria Comparison of the 3 Domains of life 5.1 Archaea Some live in environmen Archaea extreme and extremophiles ts are Extreme calledlive in highly halophiles saline environments Extreme thermophiles thrivein very hot environments Methanogens live in swamps and marshes and produce methane as a waste product Methanogens are strict anaerobes and are poisoned by O2 Lake Retba, Senegal 5.2 Bacteria  Group Description Chlamydias Parasites that survive only within animal cells Depend on their hosts for resources (including ATP) Unusual gram-negative wall (lack of peptidoglycan) E.g. Chlamydia trachomatis, common cause of blindness and STD Spirochetes Gram-negative heterotrophs Many are free-living Others are notorious pathogenic parasites (e.g. Treponema pallidum, syphilis; Borrelia burgdorferi, Lyme disease) Cyanobacteria Gram-negative photoautotrophs Possess plantlike oxygen-generating photosynthesis Can be solitary or filamentous Some filaments have cells specialized for N2 fixation Gram-positive Most actinomycetes are free-living, help to decompose organic matter bacteria in soil Streptomyces –cultured as source of many antibiotics, including streptomycin Include other species like Clostridium botulinum, Bacillus anthracis, Proteobacteria Large and diverse clade of gram- bacteri (include negative photoautotrophs, chemoautotrophs a s and heterotrophs. Some are aerobic, some are anaerobic. According to molecular systematics, there are currently 5 subgroups. 6.0 Roles of prokaryotes in the biosphere CHEMICAL RECYCLING Prokaryotes play a major role in the recyclingof chemical elements between the living and nonliving components of ecosystems Chemoheterotrophic prokaryotesfunction as decomposers, breaking down dead organisms and waste products Prokaryotes can sometimes increase the availability of nitrogen, phosphorus, and potassium for plant growth  6.0 Roles of prokaryotes in the biosphere ECOLOGICAL INTERACTIONS Symbiosis is an ecological relationship in which two species live in close contact: a larger host and smaller symbiont In mutualism, both symbiotic organisms benefit In commensalism, one organism benefits while neither harming nor helping the other in any significant way In parasitism, an organism called a parasite harms but does not kill its host Parasites that cause disease are called pathogens 7.0 Impact of prokaryotes on humans MUTUALISTIC BACTERIA Mutualistic bacteria in human guts. Our intestines = home to an estimated 500 – 1,000 species of bacteria Many of these species are mutualists, digesting food that our own intestines cannot brak down. 7.0 Impact of prokaryotes on humans PATHOGENIC BACTERIA Prokaryotes cause about half of all human diseases For example, Lyme disease is caused by a bacterium and carried by ticks  Pathogenic prokaryotes typically cause disease by releasing exotoxins or endotoxins Exotoxins are secreted and cause disease even if the prokaryotes that produce them are not present Endotoxins are released only when bacteria die and their cell walls break down Horizontal gene transfer can spread genes associated with virulence Some pathogenic bacteria are potential weapons of bioterrorism 8.0 Prokaryotes in Research & Technology Experiments using prokaryotes have led to important advances in DNA technology For example, Escherichia coli is used in gene cloning For example, Agrobacterium tumefaciens is used to produce transgenic plants For example, Thermus aquaticus gives us Taq DNA polymerase for our Polymerase Chain Reaction (PCR) Bacteria can now be used to make bio-plastics 8.0 Prokaryotes in Research & Technology Prokaryotes are the principal agents in bioremediation, the use of organisms to remove pollutants from the environment Bacteria can be engineered to produce vitamins, antibiotics, and hormones Bacteria are also being engineeredto produce ethanol from waste biomass  Q&A Thank You