Agriculture Lecture 1 PDF

Dept. of Agricultural Microbiology Dr. Shimaa Abdel Raouf Amin Associate professor of Agriculture Microbiology Fac. Of Agri., Ain Shams University  Microbiology is a branch of bi...

Dept. of Agricultural Microbiology Dr. Shimaa Abdel Raouf Amin Associate professor of Agriculture Microbiology Fac. Of Agri., Ain Shams University  Microbiology is a branch of biology which involves the study of microorganisms. Microorganisms can be defined as living organisms which cannot be seen by the unaided eyes, Micro-organisms are living entities of microscopic size. These organisms include bacteria, fungi, algae, protozoa, viruses, etc. Microorganisms have the following properties:- 1) They are generally too small to be seen with the unaided human eye, and some form of microscopy is required for the study of their structure. 2) Cells or other structures are relatively simple and less than those of higher plants and animals. 3) They are cultured in the laboratory in ways that are generally quite similar. Micro-organisms can also be studied from the applied viewpoint:- Medical microbiology: Includes some aspects of pathology (the study of diseases), immunology (how the immune system operates to prevent invasion by micro-organisms) and epidemiology (how diseases are distributed and spread). Agricultural microbiology: The study of micro-organisms for crop/ plant health and related areas. Industrial microbiology / biotechnology: The study of the use of Microorganisms in large scale industrial processes. Food microbiology: The study of the role that micro-organisms play in food spoilage, food production, food preservation and food-borne disease. Cells of Microorganisms : Two fundamental different types of cells exist among microorganisms; they are prokaryotic and eukaryotic. Prokaryotes: these microbial cells lack membrane-bound nucleus and organelles. Prokaryotes are enclosed by a cell wall containing the polymer peptidoglycan and include bacteria. Eukaryotes: possess a membrane-bound nucleus and organelles. Eukaryotes distinct nucleus enclosed by a nuclear membrane and containing their DNA. Their cell walls containing the polymer chitin and include the moulds and yeasts  Bacterial shapes and arrangement  Bacteria exhibit considerable variety in shape, size, and arrangement; bacterial cells size have an average size of about 1 micron (μm) and great deal of variation in microbial size. The smallest bacteria is Mycoplasma cells that generally measure 0.15 to 0.30 μm.  Bacteria come in many different shapes, but the vast majority are one of three general shapes coccus, bacilli and vibrio.  Cocci can be perfect spheres, but they also can exist as oval, bean- shaped. That is cylindrical (longer than wide) is termed a rod, or bacillus (genus named Bacillus)  Bacterial shapes and arrangement Rods are also quite varied in their actual form. Depending on the species, they can be blocky, spindle-shaped, round ended, long and threadlike (filamentous), or even club-shaped or drumstick-shaped.. When a rod is short and plump, it is called a coccobacillus. Bacterial cells is curved. If it is gently curved, it is a vibrio. A bacterium having a slightly curled or spiral-shaped cylinder is called a spirillum.  Bacterial cells can also be categorized according to arrangement, or style of grouping. The main factors influencing the arrangement of a particular cell type are its pattern of division and how the cells remain attached afterward. Single, in pairs (diplococci), in tetrads (groups of four), in irregular clusters (as in staphylococci and micrococci), chains of a few to hundreds of cells (as in streptococci) Bacilli are less varied in arrangement because they divide only in the transverse plane (perpendicular to the axis). They occur either as single cells, as a pair of cells with their ends attached (diplobacilli), or as a chain of several cells. The Structure of a Generalized Bacterial Cell  External Structures 1. Flagella: The primary role of flagella is to confer motility, or self propulsion (the capacity of a cell to swim freely through an aqueous habitat). Flagellum special architecture; the filament, the hook (sheath), and the basal body. Flagella vary both in number and arrangement according to two general patterns: 1. In a polar arrangement, the flagella are attached at one or both ends of the cell.  Three subtypes of this pattern are monotrichous, with a single flagellum; lophotrichous, with small bunches or tufts of flagella emerging from the same site and amphitrichous, with flagella at both poles of the cell. 2. In a peritrichous arrangement, flagella are dispersed randomly over the surface of the cell.  2. Surface Coatings: The S Layer and the Glycocalyx  Some bacteria are covered with a loose shield called a slime layer that evidently protects them from loss of water and nutrients.  A glycocalyx is called a capsule when it is bound more tightly to the cell than a slime layer and it is denser and thicker.  Bacterial cells protect themselves with S layer or a glycocalyx, or both.  S layers are single layers of thousands of copies of a single protein linked together like tiny chain mail.  Bacteria only produce this layers in a hostile environment.  The glycocalyx develops as a coating of repeating polysaccharide units that may or may not include protein.  Glycocalyces differ among bacteria in thickness, organization, and chemical composition.  Cell envelope 1. Cell wall  The cell wall accounts for a number of important bacterial properties:- 1. It helps determine the shape of a bacterium. 2. Provides the kind of strong structural support necessary to keep a bacterium from changes in osmotic pressure. 3. The cell walls of most bacteria gain their relatively rigid quality from an unique macromolecule called peptidoglycan (PG). 2. Cytoplasmic Membrane Structure Appearing just below the cell wall is the cell membrane, which is often called the cytoplasmic membrane. And referring to the membrane closest to the cytoplasm. It is a very thin (5–10 nm), flexible sheet molded completely around the cytoplasm. Bacterial cell membranes have this typical structure, containing foremost phospholipids (making up about 30%–40% of the membrane mass) and proteins (60%–70%). Importance of the Cytoplasmic Membrane Because bacteria have none of the eukaryotic organelles the cytoplasmic membrane provides a site for roles such as:- Energy reactions (respiration and ATP synthesis).  Nutrient processing.  Biosynthesis. A major action of the cytoplasmic membrane is to regulate transport (the passage of nutrients into the cell and the discharge of wastes). The membrane is a selectively permeable structure with special carrier mechanisms for passage of most molecules.  Bacterial Internal Structure 1. Cytoplasm Cytoplasm is a gelatinous solution encased by the cytoplasmic membrane. It is another important site for many of the cell’s biochemical and synthetic activities. Its major component is water (70%–80%), which serves as a solvent for the cell pool, a complex mixture of nutrients including sugars, amino acids, and salts. The cytoplasm also contains larger, discrete cell masses such as the chromatin body, ribosomes, granules, and spores. The genetic material of most bacteria exists in the form of a single circular strand of DNA designated as the bacterial chromosome. Some bacteria have multiple chromosomes. Many bacteria contain other nonessential pieces of DNA called plasmids, Plasmids exist as separate double-stranded circles of DNA. They are not essential to bacterial growth and metabolism, but they often confer protective traits such as the ability to resist drugs and to produce toxins and enzymes. 2. Ribosomes: Sites of Protein Synthesis Ribosomes, which are made of RNA (called ribosomal RNA, or rRNA about 60%) and protein (40%). Ribosomes show up as fine, spherical specks dispersed throughout the cytoplasm and often occur in chains called polysomes, many are also attached to the cytoplasmic membrane.  The Fungi The Kingdom Fungi is large and filled with forms of great variety and complex. 1. Eukaryotic, non- vascular organisms. 2. Typically not motile, although a few have a motile phase. 3. Vegetative body may be unicellular (yeasts) or multicellular molds 4. Composed of microscopic threads called hyphae. 5. Cell walls composed of mostly of chitin and glucan. 6. Fungi are heterotrophic ( “other feeding,” must feed on preformed organic material), not autotrophic ( “self feeding,” make their own food by photosynthesis). 7. Fungi produce exoenzymes like Amylase. 8. Most fungi store their food as glycogen (like animals). Plants store food as starch. 9. Fungal cell membranes have a unique sterol, ergosterol, which replaces cholesterol. 10. Most fungi have very small nuclei, with little repetitive DNA. 1. The Structure of a Generalized Fungal Cell  The Structure of a Generalized Fungal Cell The cells of eukaryotic organisms are so varied that no one member can serve as a complete example. The flowchart shows the organization of a eukaryotic cell and compares it to the organization for bacterial cells. In general, eukaryotic microbial cells have a cytoplasmic membrane, nucleus, mitochondria, endoplasmic reticulum, golgi apparatus, vacuoles, cytoskeleton, glycocalyx, cell wall, locomotor appendages, and chloroplasts (are found only in some groups). We cover the microscopic structure of the eukaryotic cell as with the bacteria, we begin on the outside and proceed and inward through the cell.  External Structures 1. Flagella: Eukaryotic flagella are much different from those of bacteria. The eukaryotic flagellum is thicker, structurally more complex, and covered by an extension of the cell membrane. 2. The Glycocalyx: Most eukaryotic cells have a glycocalyx, an outermost boundary that comes into direct contact with the environment. This structure is usually composed of polysaccharides and appears as a network of fibers, a slime layer, or a capsule much like the glycocalyx of bacteria. The glycocalyx provides protection.  Boundary Structures Cell wall: Fungi have cell walls. They are rigid and provide structural support and shape, but they are different in chemical composition from bacterial cell walls. Fungal cell walls have a thick, inner layer of polysaccharide fibers composed of chitin or cellulose and a thin, outer layer of mixed glycans.  Internal Structures 1. Nucleus: The nucleus is a compact sphere that is the most prominent organelle of eukaryotic cells. It is separated from the cell cytoplasm by an external boundary called a nuclear envelope. The nucleolus is the site for ribosomal RNA synthesis and a collection area for ribosomal subunits. 2. Endoplasmic Reticulum: A passageway in the Cell The endoplasmic reticulum (ER) is a microscopic series of tunnels used in transport and storage. Two kinds of endoplasmic reticulum are the rough endoplasmic reticulum (RER) and the smooth endoplasmic reticulum (SER). 3. Golgi Apparatus: A packaging machine The Golgi apparatus, also called the Golgi complex or Golgi body, is the site in the cell in which proteins are modified and then sent to their final destinations. 4. Mitochondria: Energy Generators of the cell Although the nucleus is the cell’s control center, none of the cellular activities it commands could proceed without a constant supply of energy, the bulk of which is generated in most eukaryotes by mitochondria. When viewed with light microscopy, mitochondria appear as round or elongated particles scattered throughout the cytoplasm.  5. Chloroplasts: Photosynthesis Machines Chloroplasts are remarkable organelles found in algae and plant cells that are capable of converting the energy of sunlight into chemical energy through photosynthesis. The photosynthetic role of chloroplasts makes them the primary producers of organic nutrients upon which all other organisms (except certain bacteria) ultimately depend. Another important photosynthetic product of chloroplasts is oxygen gas. Although chloroplasts resemble mitochondria, chloroplasts are larger, contain special pigments, and are much more varied in shape. The chloroplast containing the green pigment called chlorophyll. The role of the photosynthetic pigments is to absorb and transform solar energy into chemical energy, which is then used during reactions to synthesize carbohydrates. 6. Ribosomes: Protein Synthesizers  In an electron micrograph of an eukaryotic cell, ribosomes are numerous, tiny particles that give a dotted appearance to the cytoplasm.  Ribosomes are distributed throughout the cell: Some are scattered freely in the cytoplasm and cytoskeleton; others are attached to the rough endoplasmic reticulum. Still others appear inside the mitochondria and in chloroplasts. Multiple ribosomes are often found arranged in short chains called polyribosomes (polysomes).  The basic structure of eukaryotic ribosomes is similar to that of bacterial ribosomes. Both are composed of large and small subunits of ribonucleoprotein.  As in the bacteria, eukaryotic ribosomes are the staging areas for protein synthesis 7. Cytoskeleton: A Support Network The cytoplasm of an eukaryotic cell is crisscrossed by a flexible framework of molecules called the cytoskeleton. This framework appears to have several functions, such as anchoring organelles, moving RNA and vesicles, and permitting shape changes and movement in some cells. The three main types of cytoskeletal elements are actin filaments, intermediate filaments, and microtubules.  Introduction to Food Microbiology  Microbiology is important to food safety, production, processing, preservation, and storage. Microbes such as yeasts, molds, and bacteria are being used for the production of foods and food ingredients. Beneficial microbes are exploited in the fermentative production, processing, and preservation of many foods and beverages. Spoilage microorganisms cost food producers, processors, and consumers millions of dollars annually in lost products. Lost productivity resulting from illness caused by foodborne microorganisms is an enormous economic burden throughout the world. The study of food microbiology includes understanding not only the factors influencing the growth of microorganisms in food systems but also the means of controlling them.  Microorganisms and Food The foods that we eat are rarely if ever sterile, they carry microbial associations whose composition depends upon which organisms gain access and how they grow, survive and interact in the food over time. The micro-organisms present will originate from the natural micro-flora of the raw material and those organisms introduced in the course of harvesting / slaughter, processing, storage and distribution. The numerical balance between the various types will be determined by the properties of the food, its storage environment properties of the organisms themselves and the effects of processing. In most cases this microflora has no discernible effect and the food is consumed without objection and with no adverse consequences.  Microorganisms and Food In some instances though, micro-organisms manifest their presence in one of several ways: (i) They can cause spoilage. (ii) They can cause foodborne illness. (iii) They can transform a food’s properties in a beneficial way – food fermentation. Sources of food contamination Microbial contamination of food products takes places usually on the way from the field to the processing plant, or during processing, storage, transport and distribution or before consumption. The microorganisms that cause food spoilage and also find the maximum exploitation in production of food and food products are mainly bacteria, molds and yeasts.  Significance of Microorganisms in foods  Microorganisms have been used in the production of foods for thousands of years. They are used for baking, brewing, pickling, and winemaking. Buttermilk is made as the result of a souring of low-fat milk, the unique flavor comes from substances such as diacetyl and acetaldehyde. They are formed by different species of Streptococcus, Leuconostoc, and Lactobacillus as they grow. The food industry uses Lactobacillus and Bifidobacterium for their production techniques.  Molds are multicellular filamentous fungi whose growth on foods is usually readily recognized by their fuzzy or cottony appearance.  They are mainly responsible for food spoilage at room temperature 25- 30oC and low pH, and have minimum moisture requirement.  Significance of Microorganisms in foods  Molds can rapidly grow on grains and corns when these products are stored under moist conditions.  Molds require free oxygen for growth and hence grow on the surface of contaminated food.  Molds also find their use in manufacturing of different foods and food products. They are used in ripening of various types of food products as cheese (e.g. Roquefort, Camembert).  Molds are also grown as feed and food and are employed to produce ingredients such as enzymes like amylase used in making bread or citric acid used in soft drinks. Molds are major in the ripening of many oriental foods.  Significance of Microorganisms in foods  Yeast is also used in the manufacture of beer and alcoholic beverages.  Yeasts have the ability to ferment sugars to ethanol and carbon dioxide and hence they are extensively in food industry. Saccharomyces is most frequently used in the fermentation.  The yeast strains which are significant in production include Brettanomyces, Candida, Saccharomyces.  Common Food borne bacteria Bacteria: Bacteria are the largest group of unicellular microorganisms. The pathogenic or disease causing bacteria are usually gram negative.  Bacteria are the root cause of several food poisoning cases, due to improper food handling. Several bacteria, in minute amounts, are not harmful to most healthy adults since the human body is prepared to fight them off. The problem begins when certain bacteria and other destructive pathogens multiply and spread, which can happen when food is mishandled.  Symptoms of food poisoning differ and extend as fast as 30 minutes to as long as many days after eating foodstuff that's been infected.  Common Food borne bacteria Bacillus: These are Gram-positive spore-forming rods that are aerobes. Most are mesophiles. The genus is comprised of only two pathogens: B. anthracis (cause of anthrax) and B. cereus. Micrococcus: These Gram-positive and catalase-positive, cocci are inhabitants of mammalian skin and can grow in the existence of high levels of NaCl. M. luteus and M. roseus. Pseudomonas: These are distinctive soil and water bacteria and they are extensively spread among fresh foods, particularly in vegetables, meats, poultry, and seafood products. P. fluorescens and P. aeruginosa remain in the original genus. Escherichia coli: Is a large assemblage of bacteria. Even though the major strains of E. coli are nontoxic, a few can make you very sick. One strain, E. coli O157:H7 (STEC) is generally related with food poisoning outbreaks as its effects can be tremendously severe. These include eating raw or drinking unpasteurized beverages. Proper washing of foods and keep of internal temperatures; avoid unpasteurized dairy products, juices. Enterococcus: It has been extended to more than 16 species of Gram-positive ovoid cells that occur singly, in pairs, or in short chains.  Common Food borne fungi Aspergillus: The aspergilli appear yellow to green to black on a bulk number of foods. Several species are the source of spoilage of oils. A. niger synthesises β-galactosidase, glucoamylase, invertase, lipase, and pectinase. Several species produce aflatoxins, and others produce ochratoxin A and sterigmatocystin. Penicillium: They are coloured from blue to blue-green. It forms heat resistant spores. Rots are found in several species of citrus fruits and blue mold rot of apples, pears are also found. One species, P. roqueforti, produces blue cheese. A number of species produce citrinin, ochratoxin A, and other mycotoxins. Alternaria: Members are septate and form dark-colored spores on conidia. They cause rot in tomatoes and rancid flavor in dairy products. Some species or strains produce mycotoxins. Species: Alternaria tenuis. Fusarium: Many types are associated with rot in citrus fruits, potatoes, and grains.They form cottony growth. Species: Fusarium solani.  Common Food borne fungi Mucor: It is widely distributed. Members have nonseptate hyphae and produce sporangiophores. They produce cottony colonies. Some species are used in food fermentation and as a source of enzymes. They cause spoilage of vegetables. Species: Mucor rouxii. Botrytis: Long, slender, and regularly pigmented conidiophores are formed. B. cinerea is the mostly widespread in foods. They are prominent as the cause of gray mold rot of apples, pears, grapes, citrus, and some stone fruits. Geotrichum: These yeast-like fungi are usually white, is the majority of vital species in food products. It is referred to as “dairy mold” as it imparts flavor and fragrance to various kind of cheese. The reason for sour rot of citrus fruits and the putrefaction of dairy cream. It is extensively spread and has been found on meats and many vegetables.  Common Food borne yeasts Saccharomyces: Cells are round, oval, or elongated. It is the most important genus and contains heterogenous groups. Saccharomyces cerevisiae used in baking bread and in alcoholic fermentation. They also cause spoilage of food, producing alcohol and CO2. Pichia : Cells are oval. Some are also used in oriental food fermentation. Species: Pichia membranaefaciens. Rhodotorula: They are pigment-forming yeasts and can cause discoloration of foods such as meat, and fish. Species: Rhodotorula glutinis. Candida: Many species spoil foods with high acid, salt, and sugar. Some can cause rancidity in butter and dairy products (e.g., Candida lipolyticum). Zygosaccharomyces: Cause spoilage of high-acid foods, such as sauces, ketchups, pickles, mustards, mayonnaise, salad dressings, especially those with less acid and less salt and sugar (e.g., Zygosaccharomyces bailii).