1. What is the unique features of Microorganisms◆
1.1 Small size, Simple structure
Antoni Van Leeuwenhock: The word microorganism is used to describe an organism that is so small that, normally, it can not be seen without use of microscopy.
The living organisms of microscopic size
Most microorganisms are unicellular
Some of them are non---cellular structure
1.2 High diversity
species.Bacteria ( actinomyce, algae, cyanobacteria)
fungi ( yeast, mold )
1.3 Widely distributed in various environment with large numbers
soil. 109 CFU/g
plants, animals, human body
extreme environment, e.g. hot springs
1.4 Fast growing, easy cultivation
generation time, min.- hr.
1.5 Easy mutation
2.The place of microorganisms in the living world
2.1 whittaker’s five kingdom concept (1969)
This classification system was based on nutrition, photosynthesis, absorption and ingestion.
2.2 Woese’s three domains ( kingdoms)
3. The scope of microbiology
Microbiology is the study of living organisms of microscopic size, which include bacteria, fungi, algae, protozoa and viruses. It is concerned with theirmorphology, reproduction, physiology, metabolism, genetics and classification. It includes the study of their distribution and function in nature, their relationship to each other and to other living organisms, their effects on human beings, animals and plants.
4. Why do we study microbiology◆
Microorganisms affect the well-being of people in a great many ways. They occur in large numbers in most natural environments. Some of them are beneficial and others are detrimental.
4.1 The beneficial aspects
◆ In Agriculture
◆ Microbial fertilizer
◆ Biological control
◆ Microbial energy: methane gas for rural consumption
◆ In food production
◆ yogurt, cheese, wine(alcohol fermentation)
◆ food ingredients
◆ In environment protection
◆ treatment of waste materials
◆ to decompose materials: pesticides, herbicides
◆ In Biochemical industry
◆ Amino acides
◆ organic acids
◆ in medicine
◆ Antibiotics penicillin
◆ The potential applied areas of Microbiology
◆ GMO Recombinant DNA technology
◆ Microbial plastics
◆ Microbial pesticides
◆ Microbiosensor M传感器
◆Microbial fuel cells 微生物燃料电池
◆Microbial DNA chip 微生物DNA芯片
◆Exploitation of microorganisms in extreme environments
4.2 The detrimental aspects
◆ Cause diseases: human beings animals Plants
◆ spoil food
◆ deteriorate materials: iron pipes, wood, cloth
Objectives: make full use and exploitation of the beneficial aspects; avoid and control the detrimental aspects
Chapter 1 The Morphology and Fine Structure of Microorganisms
1. Procaryotic Microorganisms
1.1 Features distinquishing procaryotic from Eucaryotic cells
Bacteria ( archaea)
Eucaryotic cells(fungi, protozoa, plant, animal)
Peptidoglycan as component
Generally do not contain sterol; contain part of respiratory and, in some, photosynthetic machinery invagination
Not bounded by nuclear
membrane; one circular
Chromosome does not
Contain histones; no mitotic divirsion
Absente of peptidoglycan
Sterols present; do not carry out respiratory and photosynthesis
Bounded by nuclear membrane;
More than one chromosome
Chromosomes have histones;
Mitotic nuclear division
1.2.1 The size, shape and arrangement of bacterial cell
◆straight rods: widnthxLengthum, bacilli, bacillus, Lactobacillus
◆ helically curved rods:spirilla, spirillum
widthxLengthum (No. of curve)
◆filament: hyphae, hypha → mycelium
diameter of hyphaum
Actinoinyces: streptomyces species
△ some are not constant, but pleomorphic shape
1.2.2 Simple staining technique
The coloration of bacterial cell by applying a single solution of stain to a fixed smear is termed simple staining.
◆ Smear bacterial cells on a slide
◆ dry and fix
◆ The fixed smear is flooded with a dye solution for a specified period of time
◆ Wash off with H2O and dry the clide
◆ exame the size. Shape and arrangement of bacterial cells under microscope
1.2.3 The structures and functions of bacterial cells
188.8.131.52 Structures external to the cell wall
A. Flagella, Flagellum
Bacterial flagella are hairlike, helical appendages that protrude through the cell wall and are responsible for swimming motility.
◆ chemical composition: protein subunits: flagellin
Location: polar: at one or both ends of the bacterium
Lateral: alone the sides of the bacterium
◆ function: swimming motility
◆ gliding motility:
some bacteria are motile when they are in contact with a solid surface. As they glide they exhibit a sinuous, flexing motion. This kind of movement is comparatively slow, only a few um per second.
◆ Bacterial chemotaxis
many, perhaps most, bacteria are capable of directed swimming toward or away from various chemical compounds—a phemomenon called bacterial chemotaxis
◆ Bacterial phototaxis
phototrophic bacteria move towards increasing light intensities.
◆ Pili, pilus( fimbriae)
Pili are nonhelical, filamentous appendages that are thinner, shorter, and more numerous than flagella. The well known is the F pilus ( or sex pilus), it serves as the port of entry of genetic material during bacterial mating.
◆ Some bacterial cells are surrounded by a viscous substance forming a covering layer or envelope around the cell wall. If this layer can be visualized by light microscopy using special staining method, it it termed a capsule. If it is too thin to be seen by light microscopy, it is termed microcapsule. If is soabundant that many cells are embedded in a common matrix, the material is called slime.
◆ The conditions that some bacteria produce capsule
◆ High carbon content in media, low nitrogen
◆ The chemical composition of capsule
◆ The functions of capsule
◆ They may provide protection against temporary drying by binding water molecules
◆ They may block attachment of bacterophages
◆ They may promote attachment of bacteria to surfaces, e.g. Streptococcus mutans, a bacterium associated with producing dental caries, firmly adheres to the smooth surfaces of teeth because of its secretion of a water-insoluble capsular polysaccharide.
C. spore and cyst
◆ defination: under the undesirable growth conditions,e.g. Lack of nutrients, too acid, temperiture is too high,Some species of bacteria produce thick-walled structure which is metabolically dormant and can undergo germination and outgrowth to form a vegetative cell. This special structure is termed spore which is either within the cell (endospore) or external to the cell (exospore).
◆ function: spores are extremely resistant to desiccation, staining, disinfecting chemicals, radiation, and heat. Some of sproes can resist boiling for several hours, most of spores can resist heat treatment at 80℃ for at least 10 minutes. Dormant structure.
◆ Cyst: cyst resembles endospore, especially desiccation-resistant. But it does not resist to heat treatment. Genus Azotobacter cyst
184.108.40.206 The cell wall
◆ defination: A very rigid layer external to the cytoplasmic membrane. The main function is to give shape to the cell and prevent the cell from expanding and eventually bursting because of uptake of water.
◆ peptidoglycan: an insoluble, porous, cross-linked polymer of enormous strength and rigidity.
◆ Differential staining: staining procedures that make visible the differences between bacterial cells or parts of a bacterial cell are termed differential staining technique. The cells may be exposed to more than one dye solution or staining reagent.
◆ Gram staining: one of the most important and widely used differential staining techniques in microbiology is Gram staining. This technique was introduced by Christian Gram in 1884. In this process the fixed bacterial smear is subjected to the following reagents in the order listed: crystal violet, iodine solution, 95% alcohol (decolorizing agent), and safranin or some other suitable counterstain. Bacteria stained by the gram method fall into two groups: Gram positive bacteria (G+), which retain the crystal violet and hence appear deep violet in color; and Gram negativebacteria (G-), which lose the crystal violet, are counterstained by safranin, and hence appear red in color.
◆ Why does this proceduce stain some bacteria purple-violet and others red◆
● The wall of Gram positive bacteria
● the structure and chamical composition
● The wall of Gram negative bacteria
● The structure and chemical composition
220.127.116.11 The cytoplasmic Membrane
Immediately beneath the cell wall is the cytoplasmic membrane. This structure is approximately 7.5nm thick and is composed mainly of phospholipids (20~30%) and proteins (60~70%).
many bacteria, especially G+ bacteria, possess membrane invaginationsin the form of convoluted and vesicals termed mesosome.
●Functions of mesosome: DNA replication
export of exocellular enzyme
● The functions of cytoplasmic membrane
● the CM is a barrier to penetration by most molecules;
● specific proteins in the memtrane allow and facilitate the passage of small molecules (e.g. nutrients, waste products);
● The CM contains various enzymes involved in respiratory metabolism and phtosynthesis.
● CM is the site of ATP generation, synthesis of capsular and cell wall components.
18.104.22.168 The cytoplasm
In the cytoplasmic area, granular in appearance and rich in the macromolecular RNA-protein bodies known as Ribosomes, on which proteins are synthesized. In the prokaryotic cells, the sedimentation coefficient of ribosome is 70S.
● PHB: poly—β—hydroxybutyrate
22.214.171.124 The genetic materials
● The nucleus
● not bounded by nuclear membrane
● one circular chromosome
● chromosome does not contain histones
● nucleolus absent
In addition to the normal DNA chromosome, extrachromosomal genetic elements are offen found in bacteria. These elements are called plasmids, and are capable of autonomous replication in the cytoplasm in the bacterial cell. Plasmids are circular pieces of DNA that are extra genes.
1.2.2 Bacterial Reproduction and colony
● Transverse Binary Fission
The most common mode of bacterial cell division in the usual growth cycle of bacterial populations is transverse binary fission, in which a single cell divides into two cells after developing a transverse septum. Transverse binary fission isan asexual reproductive process.
some bacteria reproduce by budding, a process in which a small protuberance ( bud ) develops at one end of the cell. This enlarges and eventually develops into a new cell which separates from the parent.
Bacteria that produce extensive filaments, such as Nocardia species, reproduce by fragmentation of the filaments into small bacillary or coccoid cells, each of which gives rise to a new cell.
● Formation of conidiospores or sporangiospores
Species of the genes streptomyces and related bacteria produce many spores by developing crosswalls (septation) at the hyphal tips. Each spore gives rise to a new cell.
126.96.36.199 Colony formation
● Colony: visible aggregate of bacterial growth on a solid culture medium. It is a important characteriastics for identifying a certain bacterial species.
● Colony-forming unit: aggregate of cells gives rise to a single colony in the plate—count technique.
188.8.131.52 The characteristics of Actinomyctes
● G+ bacteria
● Formation of spores
● Size small, round shape, tight, dry, diverse color, smell soil.
● nutrient and environmental factors required for growth
● neutral pH
● optimal growth temperature: 23~37℃
● They are distributed mainly in soils. They can grow in soils which have less water content than that needed for most other bacteria, because of their spores that can survive well in dry soil.
Actinomycetes: Gram positive bacteria that are characterized by the formation of branching filaments and spores.
184.108.40.206 The roles of Actinomycetes in nature
● Many actinomycetes, such as, streptomycetes, can degrade polymeric organic substances in soil that are refractory to being decomposed by many other microorganism, e.g., starch, pectin, chitin
●produce antibiotics, antifungal antibiotics
●Fix N2: Frankia, These group of bacteria are highly efficient microaerophilic N2—fixers that occur within the root nodules of plants. Unlike Rhizobium spcies, however, they infect nonleguminous woody plants, such as alders.
● some species are pathogenic to plants and humans.
● prokaryotic oxygenic photolithotrophs containing chlorophyll a and phycobilins
● Algae: phototrophic eukaryotic microorganisms
An evolutionarily distinct domain of prokaryotes consisting of the methanogens, most extreme halophiles and hyperthermorphiles, and Thermoplasma.
2. Eucaryotic Microorganisms
2.1 Features distinguishing Eucaryotic fro prokaryotic cells, see 1.1
2.2 Fungi—Molds and yeasts
2.2.1 Characteristics of fingi
yeast cells are larger than most bacteria. Yeasts vary considerably in size, ranging from 1~5 μm in width and from 5~30μm or more in length. They are commonly egg—shaped, but some are spherical. Each species has a characteristic shape, but even in pure culture there is considerable variation in size and shape of individual cells, depending on age and environment.
The thallus of a mold consists essentially of two parts: the mycelium (mycelia) and the spores ( resistant, dormant cells)
● The mycelium
The mycelium is a complex of several filaments called hyphae (singular, hypha), New hyphae generally arise from a spore germination. Each hypha is about 5~10μm wide. There are three types of hyphae:
220.127.116.11.1 Asexual Reproduction
Fungi reproduce naturally by a varity of means. Asexual reproduction (also called somatic or vegetative reproduction) does not involve the union of nuclei, sex cells, or sex organs.
● Budding of somatic cells or spores
● Fragmentation of the hyphal cells, each fragment becoming a new cell
● Formation of asexual spores.
Asexual spores are produced in large numbers. There are many kinds of asexual spores:
18.104.22.168.2 Sexual reproduction
sexual reproduction is carried out by fusion of the compatible nuclei of two parent cells. The process of sexual reproduction begins with the joining of two cells and fusion of their protoplasts (plasmogamy), thus enabling the two haploid nuclei of two mating types to fuse together (karyogamy) to form a diploid nucleus. This followed by meiosis, which again reduces the number of chromosomes to the haploid number.
Sexual spores are produced by the fusion of two nuclei. There are several types of sexual spores：
22.214.171.124 Classification of Fungi
Ainsworth classification system
126.96.36.199 Physiology and ecology
● Fungi are chemoorganotrophic organisms that have no chlorophyll. They require organic compounds for energe source and nutrition.
● The saprophytes
Some fungi feed on dead organic matter, they are known as saprophytes. Saprophytes decompose complex Plant and animal remains, breaking them down into simpler chemical substances that are returned to the soil, thereby increasing soil fertility. These simpler chemical substances can be used by other organisms to produce useful products. This is very important to reduce organic waste in environment.
● The parasites
Some fungi are living in or on another organism. They are called parasites.Parasites cause diseases in plants, humans and other animals. Although fungal diseases are less commonly encountered than bacterial or virus diseases in humans and other animals, they are of great importance in causing diseases of plants.
● Fungi are better able to withstand extreme environmental conditions than most other microorganisms. For example, yeasts and molds can grow in a substrate or medium containing high concentrations of sugars that inhibit most bacteria; this is why jams may be spoiled by molds but not by bacteria. Yeast and mold generally can tolerate more acidic conditions than other microbes.
● Some yeasts are facultative; that is they can grow under both aerobic and anaerobic conditions. Molds are aerobic microorganisms.
● Fungi grow over a wide range of temperature the optimal growth temperature:
Some fungi can grow at or near 0℃ and thus can cause spoilage of meat and vegetables in cold storage.
● There are many differences between fungi and bacteria. A summary is listed in the following table.
Comparative features of fungi and bacteria
Sugar concentration in media
Cell-wall stralctural components
facultative (some yeasts)
chitin, cellulose, hemicellulose
resistant to penicillins, tetra- cyclines, chloramphenical; sen- sitive to griseofulvin
some photosynthetic bacteria
inorganic or/and organic
resistant to griseofulvin;
sensitive to penicillins, te- tracyclines, chloramphenical
188.8.131.52 Molds and their associations with other organisms
● There are some interesting partnerships in nature involving a mold and some other organism. In some of these associations the partners are dependent on each other and can not survive alone. In others, The individuals can survive independently.
Lichens are composite organisms composed of fungi and algae, each contributing to the benefit of both. The algae synthesize carbohydrates by photosynthesis and obtain other nutrients from the fungi; the fungi depend on the algae for the organic carbon.
Mycorrhiza is a symbiotic association of a fungus with the roots of a higher plants. This association is usually beneficial to the host plant as well as the symbiont, and sometimes the host can not thrive without the benefits derived from the fungus (e.g. orchid). Mycorrhizas enhance mineral absorption by the plants.
2.3.1 The characteristics of algae
Algae are eucaryotic microorganisms and have a wide range of sizes and shapes. Many species occur as single cells (unicellular) that may be spherical or rod-shaped. Others are multicellular. Some motile algae ( swimming algae) have flagella.
184.108.40.206 Algal pigments
There are three kinds of photosynthetic pigments in algae:
Algae may reproduce either asexually or sexually. Some species are limited to one of these processes, but many have complicated life cycles employing both means of propagation.
fusion ( conjugation) of sex cells
2.3.2 The occurrence of Algae
Many thousands of algal species occur in nature. They occur in great abundance in the oceans, salt or freshwater lakes, ponds and streams. Many are found in damp soil, on rocks, stones, and tree bark.
2.3.3 The biological and economic importance of algae
220.127.116.11 Algae as primary producers
Most algae are aquatic microorganisms. Since 70% of the earth’s surface is covered with water, it is probable that as much carbon is fixed through photosynthesis by algae as is fixed by all land flora. Algae are primary producers of organic matter.
18.104.22.168 Commercial products from algae
Many products of economic value are derived from algal cell walls.
Three of these, agar, alginic acid（藻朊酸） and carrageenan（角叉藻聚扩）, are extracted from the walls of algae. All three compounds are used either to make gels or to make solutions viscous.
22.214.171.124 Algae as food
Porphyra（紫菜）is widely used as food in China and japan.
Chlorella（小球藻）: protein 55-62%
2.4.1 The characteristics of protozoa
The protozoan cell is eucaryotic, and consists of cytoplasm and nucleus (macronucleus, micronucleus). Cell wall is not present. The size and shape of these organisms show considerable variation.
Protozoa may move by three types of specialized organelles: Pseudopodia（伪足）, flagella and cilia（纤毛）.
Pseudopodia: a pseudopodium is a projection of part of the cytoplasm of protozoa ( amoeba变形虫). Pseudopodium is also used for capturing food substances.
Cilia: They are fine and short threadlike extensions from the cell. In addition to their locomotor function, cilia also aid in the ingestion of food.
Many protozoa form resistant cysts at certain times of their life cycle. As indicated before, these cysts are able to survive adverse environmental conditions such as desiccation, low nutrient supply.
2.4.2 Occurrence of protozoa
Protozoa are found in all moist habitats. They are common in the sea, in soil, and in fresh water, and in the atmosphere (cyst).
2.4.3 Ecology of protozoa
From the ecological standpoint, protozoa may be divided into free-living forms and those living in or on other organisms. The latter group is referred to as the symbiotic protozoa. Some of the symbiotic ones are parasitic, and may cause disease.
2.4.4 The ecological importance of protozoa
protozoa serve as an important link in the food chain of communities in aquatic environments. For example, in marine waters, zooplankton (animal like organisms) are protozoa that feed on the photosynthytic phytoplankton (plant like organisms). They in turn become food for larger marine organisms. This food chain can be represented as follows:
(Primary producers)(primary consumers) (secondary consumers)
Protozoa (the saprophytic and bacteria—feeding protozoa) are of particular importance in the ecological balance.
3.1 The general characteristics of viruses
● noncellullar structure
Virion: The structurally complete mature and infectious virus is called the virion.
● Small size
Viruses are so small that they can only be seen at magnifications provided by the electron microscope. They are 10~100 times smaller than most bacteria, with an approximate size range of 20~300nm. Thus they pass through the pores of filters which do not permit the passage of most bacteria.
● Obligate intracellular parasites
Viruses are incapable of independent growth in artificial media. They can grow only in animal、plant cells or microorganicms, because viruses lack metabolic. Machinery of their own to generate energy or to synthesize proteins. They depend on the host cells to carry out these vital functions.
Viruses reproduce in the host cells by replication that is a process in which many copies are made of each viral component and are then assembled to produce progeny virus. During reproduction in the host cells viruses may cause diseases.
● Definition of viruses
Viruses are noncellular infectious entities whose genomes are a nucleic acid, either DNA or RNA; which reproduce only in living cells by replication; and which use the host cells biosynthetic machinery to direct the synthesis of specialized particles (Virions), which contain the viral genomes and transfer them efficiently to other cells.
Virus that infects bacteria. Phage, bacterial virus
● The shape of bacteriophage
● Lytic bacteriophage
When lytic phages infect cells, the cells respond by producing large numbers of new viruses. That is, at the end of the incubation period the host cell bursts or lyses, releasing new phages to infect other host cells. This process is called a lytic cycle.
The viral nucleic acid is replicated in the host bacterial cells from one generation to another without any cell lysis. However, temperate phages may spontaneously become virulent at some subsequent generation and lyse the host cells.