MIKROBIOLOGI LANJUT (MIK500) Penyusun: Dr. Ir. Yulin Lestari dan Tim Departemen Biologi IPB 1

The study of microorganism About cells and how they work (esp. bacteria) Microbial diversity and evolution How different kinds of microorganism arose and why What microorganism do in the world at large (humans, animals, plants) Introduction What is Microbiology all about ??? The science of microbiology is of enormous importance

Pathway of Discovery in Microbiology Introduction

Microorganism as Cells Characteristics of Living System: 1. Metabolism Uptake the nutrient from the environment, their transformation within the cell, and elimination of wastes into the environment. The cell is thus an open system. Cell Structure And Evolutionary History

2. Reproduction (growth) Chemical from the environment are turned into new cells under the direction of preexisting cells. 3. Differentiation Formation of a new cell structure such as spore, usually as part of cellular life cycle. Cell Structure And Evolutionary History

4. Communication Cells communicate or interact primarily by means of chemicals that are released or taken up. 5. Movement Living organism are often capable of self population. Cell Structure And Evolutionary History

6. Evolution Cells contain genes and evolve to display new biological properties. Phylogenetic trees show the evolutionary relationship between cells. Cell Structure And Evolutionary History

Cell Structure Cell Structure And Evolutionary History Prokaryotic Cells Have simple internal structure Lacking membrane-enclosed organelles Consist of The Bacteria and The Archaea

Eukaryotic Cells Generally larger Structurally more complex than prokaryotic Presence of membrane- enclosed structures called organelles (nucleus, mithocondria, chloroplasts ) Algae, Fungi, Protozoa, all multicelullar Plants and Animals Cell Structure And Evolutionary History

Viruses a major class of microorganism but they are not cells. Lack many attributes of cells. Not dynamic open system, taking in nutrient and expelling wastes. Virus particle is a static structure, quite stable and unable to change or replace its parts. Have no metabolic abilities of their own.

Cell Structure And Evolutionary History

Arrangement of DNA in Microbial Cells How genomes are organized in prokaryotic and eukaryotic cells? ProkaryoticEukaryotic DNA Chromosome Present in a large double- stranded molecule (bacterial chromosome). Circular (most) Many prokaryotes contain small amounts of circular extra chromosomal DNA (plasmids) Aggregates to form a visible mass (nucleoid). Single chromosome Haploid Present in linear molecules within the nucleus, package, and organized in chromosome. Chromosome number varies with the organism. Contain more than just DNA, they also include proteins Contain two copies of each gene, diploid. Cell Structure And Evolutionary History

The Tree of Life Evolution is the change in a line of descent over time leading to new species or varieties. The evolutionary relationships between life forms are the subject of the science of phylogeny. Phylogenetic relationship can be deduced by comparing sequences of certain macromolecules. Ribosomal RNAs, are excellent tools for determining evolutionary relationships. The greater the difference in ribosomal RNA gene sequence between two or more organism, the greater their evolutionary distance.

Cell Structure And Evolutionary History (a) Cells are broken open. (b) The gene-encoding rRNA is isolated, and many identical copies are made by technique called the polymerase chain reaction (PCR). (c) The gene is sequenced. (d) The sequences obtained are aligned by computer. An algorithm makes pair wise comparison and generate a tree. (e) That depicts the differences in rRNA sequence between the organism analyzed. Ribosomal RNA (rRNA) gene sequencing and phylogeny

Cell Structure And Evolutionary History The Three Domain of Life

Cell size and Cell Morphology (shape) Metabolic Strategies (physiology) Motility Mechanism of Cell Division Pathogenicity Developmental Biology Adaptation to Environmental Extremes MICROBIAL DIVERSITY Microbial Diversity

Physiological Diversity of Microorganism Chemoorganotrophs Organism that obtain energy from organic compound. Energy is obtained by oxidizing (removing electrons from) the compound and is conserved in the cell as the energy-rich compound, adenosine triphosphate (ATP). Most microorganism that have been cultured are chemoorganotrophs. Chemolithotrophs This organism can tap the energy available in inorganic compounds. This form of energy yielding metabolism is found only in prokaryotes and is widely distributed among Bacteria and Archaea. A particular prokaryote specializes in the use of one or a related group of inorganic compounds. Many of the inorganic compounds oxidized (H 2, H 2 S) are actually the waste product of chemoorganotrphs. Microbial Diversity

Phototrophs Phototrophic microorganism contain pigments that allow them to use light as an energy source, and thus their cells are colored. Phototrophs do not require chemicals as a source of energy; ATP is made from the energy of sunlight. Two major forms: 1. Oxygenic photosynthesis, O 2 is evolved (cyanobacteria and their phylogenetic relatives) 2. Anoxygenic photosynthesis, (purple and green bacteria) The phototrophic purple sulfur bacterium, Chromatium. The large chemolitotrophic sulfur- oxidizing bacterium, Achromatium. Microbial Diversity

Metabolic Option for Obtaining Energy Microbial Diversity

Heterotrophs and Autotrophs All cells require carbon as a major nutrient. Heterotrophs, requiring one or more organic compounds as their carbon source. Autotrophs, use CO 2 as the carbon source. Chemoorganotrophs are also clearly heterotrophs. By contarast, many chemolitotrophs and virtually all phototrophs are autotrophs. Autotrophs are sometimes called primary producers because they synthesize organic matter from CO 2 for both their own benefit and that of chemoorganotrophs. Habitats and Extreme Environment Organism inhabiting extreme environments are called extremophiles, a remarkable group of primarily prokaryotes that, collectively, define the physiochemical limits of life. Extremophilic prokaryotes abound in such harsh environments as boiling hot springs, on or within the ice covering lakes, glaciers, or the polar seas, in extremely salty bodies of water, and in soils and waters having a pH lower than 0 or as high as 12. Microbial Diversity

Interestingly, these prokaryotes are not just tolerant of these extremes, but actually require the environmental extreme in order to grow. This why they are called extremophiles (“phile” means “loving”) Microbial Diversity

Bacteria Microbial Diversity Prokaryotic Diversity

Proteobacteria The largest division of bacteria, Many chemoorganotrophic bacteria, such as Eschericia coli. Several phototropic and chemolitotrophic Several common prokaryotes of soil and water Species that live in or on plants and animals Species of Pseudomonas, many of which can degrade complex and otherwise toxic natural and synthetic organic compound Azotobacter, a nitrogen-fixing bacterium A number of key pathogens, Salmonella, Rickettsia, Neisseria Microbial Diversity

Gram-Positive Bacteria Contains a number of species united by common phylogeny and cell wall structure Endospore-forming Bacillus, Clostridium, and related spore-forming prokaryotes such as the antibiotic- producing Streptomyces The lactic acid bacteria, common inhabitants of decaying plant material and dairy products, Streptococcus, Lactobacillus. Mycoplasma; lack of cell wall, have very small genomes, often pathogenic. Microbial Diversity

Cyanobacteria Phylogenetic relatives of gram-positive bacteria and oxygenic phototrophs. The first oxygenic phototrophs to have evolved on Earth. OscillatoriaSpirulina Microbial Diversity

Spirochetes Helically shaped Cause Syphylis and Lyme disease Spirochaeta zuelzerae Microbial Diversity Planctomyces Characterized by cells with a distinct stalk that allows the organism to attach to a solid substratum. The morphologically unusual stalked bacterium Planctomyces

Microbial Diversity Phototrophic Green Bacteria Green sulfur bacteria and Green nonsulfur bacteria (Chloroflexus group). Contain photosynthetic pigments and can grow as autotrophs. Filamentous prokaryote that inhabits hot spring and shallow marine bays. The dominant organism is stratified microbial mats containing a community of microorganism. It is believe to be an important link in the evolution of photosynthesis.

Microbial Diversity Chlorobium (green sulfur bacteria) Chloroflexus (green nonsulfur bacteria)

Microbial Diversity Chlamydia Most species of which are pathogens, harbors a variety of respiratory and venereal pathogens of human. Chlamydia are obligate intracellular parasites. Deinococcus Contains species with unusual cell walls and an innate resistance to high levels of radiation. Deinococcus radiodurans can withstand radiation levels far above that sufficient to kill human. The highly radiation-resistant bacterium Deinococcus radiodurans

Archaea Microbial Diversity

Euryarchaeota Methanogens Strict anaerobes Energy is obtained by the production of an energy-rich subtance, methane. Methanobacterium Halophiles (salt lovers) Require oxygen Require very large amounts of salt (NaCl) for metabolism and reproduction. Halobacterium Microbial Diversity

Thermoacidophiles Have a cell membrane but lack cell walls. Grow best at moderately high temperature and extremely low pH Thermoplasma, Picrophilus Pyrolobus. A hyperthermophylic archaeon that grows optimally above the boilling point of water Thermoplasma, grow at moderately high temperature and extremely low pH Microbial Diversity

Eukaryotic Microorganism Microbial Diversity

Protista Algae Phototrophic, contain chlorophyll-rich organelles called chloroplasts. Can live in environments containing only a few minerals (K,P,Mg,N,S,H2O,CO2,and light). Inhabit both soil and aquatic habitats. Major primary producers in nature. Microbial Diversity The colonial green alga, volvox.

Fungi Lack photosynthetic pigments Unicellular (yeast) or filamentous (molds). Major agents of biodegradation in nature. Recycle much of the organic matter in soils and other ecosystem. Microbial Diversity Fungi; the spore-bearing structures of a typical mold

Protozoa Do not have cell walls. Most protozoas are motile, and different species are widespread in nature in aquatic habitats and as pathogens of humans and other animals. Protozoa; the cilliated protozoan Paramecium Slime Molds Motile, lack cell walls. During their life cycle, motile cell aggregate to form multicelullar structure called a fruiting body from which spore are produced that yield new motile cells. Microbial Diversity

Lichens Leaf-like structures. Example of microbial mutualism. Consist of fungus, and a phototropic partner, either algae (eukaryote) or cyanobacterium (prokaryote). Te phototropic component is the primary producer while the fungus provides the phototroph with an anchor and protection from the elements. Microbial Diversity An orange-pigmented lichen growing on a rock A yellow-pigmented lichen growing on a dead tree stump

Microbial Diversity THE END