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MICROBES OVERVIEW DESCRIBE, REVIEW, DISCUSS, COMPARE and IDENTIFY group of microbes i.e. bacteria, fungi and virus. INTRODUCTION Taxonomy is the science of the classification of organisms, with the goal of showing relationships among organisms. Taxonomy also provides a means of identifying organisms. THE STUDY OF PHYLOGENETIC RELATIONSHIPS 1. Phylogeny is the evolutionary history of a group of organisms. 2. The taxonomic hierarchy shows evolutionary, or phylogenetic, relationships among organisms. 3. Bacteria were separated into the Kingdom Prokaryotae in 1968. 4. Living organisms were divided into five kingdoms in 1969. HOW WOULD YOU CLASSIFY ? Taxanomy is the science of classifying microbes into different groups based on their phenotype or genotype characters. Types of classification: natural (introduced by Carolus Linnaeus reflecting biological nature of an organism); phenetic (based on similarities of biological and morphological characters); phylogenetic (considers differences and similarities of evolutionary processess; genotype (comparision of genetic similarity between organisms using newer molecular techniques.) THE THREE DOMAINS Living organisms are currently classified into three domains. A domain can be divided into kingdoms. In this system, plants, animals, fungi, and protists belong to the Domain Eukarya. Bacteria (with peptidoglycan) form a second domain. Archaea (with unusual cell walls) are placed in the Domain Archaea. A PHYLOGENETIC HIERARCHY Organisms are grouped into taxa according to phylogenetic relationships (from a common ancestor). Some of the information for eukaryotic relationships is obtained from the fossil record. Prokaryotic relationships are determined by rRNA sequencing. CLASSIFICATION OF ORGANISMS SCIENTIFIC NOMENCLATURE According to scientific nomenclature, each organism is assigned two names, or a binomial: a genus and a specific epithet, or species. Rules for the assignment of names to bacteria are established by the International Committee on Systematic Bacteriology. Rules for naming fungi and algae are published in the International Code of Botanical Nomenclature. Rules for naming protozoa are found in the International Code of Zoological Nomenclature. THE TAXONOMIC HIERARCHY A eukaryotic species is a group of organisms that interbreeds with each other but does not breed with individuals of another species. Similar species are grouped into a genus; similar genera are grouped into a family; families, into an order; orders, into a class; classes, into a phylum; phyla, into a kingdom; and kingdoms, into a domain. CLASSIFICATION OF PROKARYOTES Bergey’s Manual of Systematic Bacteriology is the standard reference on bacterial classification. Prokaryotes are divided into two domain: Bacteria and Archaea. The classification is based on similarities in nucleotides sequence. A prokaryotic species is defined simply as a population of cells with similar characteristics A group of bacteria derived from a single cell is called a strain. Closely related strains constitute a bacterial species. CLASSIFICATION OF EUKARYOTES Eukaryotic organisms may be classified into the Kingdom Fungi, Plantae, or Animalia. Protists are mostly unicellular organisms; these organisms are currently being assigned to kingdoms. Fungi are absorptive chemoheterotrophs that develop from spores. Multicellular photoautotrophs are placed in the Kingdom Plantae. Multicellular ingestive heterotrophs are classified as Animalia. CLASSIFICATION OF VIRUSES Viruses are not classified as part of any of three domain. Viruses are not placed in a kingdom. They are not composed of cells and cannot grow without a host cell. A viral species is a population of viruses with similar characteristics that occupies a particular ecological niche. THE PROKARYOTES: DOMAINS BACTERIA AND ARCHAEA INTRODUCTION Bergey’s Manual categorizes bacteria into taxa based on rRNA sequences. Bergey’s Manual lists identifying characteristics such as Gram stain reaction, cellular morphology, oxygen requirements, and nutritional properties. PROKARYOTIC GROUPS Prokaryotic organisms are classified into two domains: Archaea and Bacteria. Both domains consist of prokaryotic cells. DOMAIN BACTERIA Bacteria are essential to life on Earth. We should realize that without bacteria, much of life as we know it would not be possible. In fact, all organisms made up of eukaryotic cells probably evolved from bacterialike organisms, which were some of the earlist forms of life. THE PROTEOBACTERIA Members of the phylum Proteobacteria are gram-negative. Alphaproteobacteria includes nitrogen-fixing bacteria, chemoautotrophs, and chemoheterotrophs. The betaproteobacteria include chemoautotrophs and chemoheterotrophs. Pseudomonadales, Legionellales, Vibrionales, Enterobacteriales, and Pasteurellales are classified as gammaproteobacteria. Purple and green photosynthetic bacteria are photoautotrophs that use light energy and CO2 and do not produce O2. Myxococcus and Bdellovibrio in the deltaproteobacteria prey on other bacteria. Epsilonproteobacteria include Campylobacter and Helicobacter. THE NONPROTEOBACTERIA, GRAM-NEGATIVE BACTERIA Several phyla of gram-negative bacteria are not related phylogenetically to the Proteobacteria. Cyanobacteria are photoautotrophs that use light energy and CO2 and do produce O2. Chemoheterotrophic examples are Chlamydia, spirochetes, Bacteroides, and Fusobacterium. THE GRAM-POSITIVE BACTERIA In Bergey’s Manual, gram-positive bacteria are divided into those that have low G + C ratio and those that have high G + C ratio. Low G + C gram-positive bacteria include common soil bacteria, the lactic acid bacteria, and several human pathogens. High G + C gram-positive bacteria include mycobacteria, corynebacteria, and actinomycetes. DOMAIN ARCHAEA Extreme halophiles, extreme thermophiles, and methanogens are included in the archaea. Their cell walls lacked the peptidoglycan common to most bacteria. Most archaea are conventional morphology, that is, rods, cocci and helixes, but some are of very unusual morphology Some are gram-positive, others gram-negative; some may divide by binary fission, other by fragmentation or budding; a few lack cell walls Organisms in this domain are physiologically diverse as well, ranging from aerobic, to facultative anaerobic, to strictly anaerobic. Nutritionally, they include chemoautotrophs, photoautotrophs, and chemoheterotrophs. MICROBIAL DIVERSITY Few of the total number of different prokaryotes have been isolated and identified. PCR can be used to uncover the presence of bacteria that can’t be cultured in the laboratory. THE EUKARYOTES: FUNGI, ALGAE, PROTOZOA, AND HELMINTHS FUNGI Mycology is the study of fungi. The number of serious fungal infections is increasing. Fungi are aerobic or facultatively anaerobic chemoheterotrophs. Most fungi are decomposers, and a few are parasites of plants and animals. CHARACTERISTICS OF FUNGI A fungal thallus consists of filaments of cells called hyphae; a mass of hyphae is called a mycelium. Yeasts are unicellular fungi. To reproduce, fission yeasts divide symmetrically, whereas budding yeasts divide asymmetrically. Buds that do not separate from the mother cell form pseudohyphae. Pathogenic dimorphic fungi are yeastlike at 37°C and moldlike at 25°C. Fungi are classified according to rRNA. These spores can be produced asexually: sporangiospores and conidia. Sexual spores are usually produced in response to special circumstances, often changes in the environment. Fungi can grow in acidic, low-moisture, aerobic environments. They are able to metabolize complex carbohydrates. MEDICALLY IMPORTANT PHYLA OF FUNGI The Zygomycota have coenocytic hyphae and produce sporangiospores and zygospores. The Ascomycota have septate hyphae and produce ascospores and frequently conidia. Basidiomycota have septate hyphae and produce basidiospores; some produce conidiospores. Teleomorphic fungi produce sexual and asexual spores; anamorphic fungi produce asexual spores only. FUNGAL DISEASES Systemic mycoses are fungal infections deep within the body that affect many tissues and organs. Subcutaneous mycoses are fungal infections beneath the skin. Cutaneous mycoses affect keratin-containing tissues such as hair, nails, and skin. Superficial mycoses are localized on hair shafts and superficial skin cells. Opportunistic mycoses are caused by normal microbiota or fungi that are not usually pathogenic. Opportunistic mycoses include Pneumocystis pneumonia; aspergillosis, caused by Aspergillus; and candidiasis, caused by Candida. Opportunistic mycoses can infect any tissues. However, they are usually systemic. ECONOMIC EFFECTS OF FUNGI Saccharomyces and Trichoderma are used in the production of foods. Fungi are used for the biological control of pests. Mold spoilage of fruits, grains, and vegetables is more common than bacterial spoilage of these products. Many fungi cause diseases in plants. LICHENS A lichen is a mutualistic combination of an alga (or a cyanobacterium) and a fungus. The alga photosynthesizes, providing carbohydrates for the lichen; the fungus provides a holdfast. Lichens colonize habitats that are unsuitable for either the alga or the fungus alone. Lichens may be classified on the basis of morphology as crustose, foliose, or fruticose. Lichens are used for their pigments and as air quality indicators. ALGAE Algae are unicellular, filamentous, or multicellular (thallic). Most algae live in aquatic environments. CHARACTERISTICS OF ALGAE Algae are eukaryotic; most are photoautotrophs. The thallus (body) of multicellular algae usually consists of a stipe, a holdfast, and blades. Algae reproduce asexually by cell division and fragmentation. Many algae reproduce sexually. Photoautotrophic algae produce oxygen. Algae are classified according to their structures and pigments. SELECTED PHYLA OF ALGAE Brown algae (kelp) may be harvested for algin. Red algae grow deeper in the ocean than other algae because their red pigments can absorb the blue light that penetrates to deeper levels. Green algae have cellulose and chlorophyll a and b and store starch. Diatoms are unicellular and have pectin and silica cell walls; some produce a neurotoxin. Dinoflagellates produce neurotoxins that cause paralytic shellfish poisoning and ciguatera. The oomycotes are heterotrophic; they include decomposers and plant parasites. ROLES OF ALGAE IN NATURE Algae are the primary producers in aquatic food chains. Planktonic algae produce most of the molecular oxygen in the Earth’s atmosphere. Petroleum is the fossil remains of planktonic algae. Unicellular algae are symbionts in such animals as Tridacna. PROTOZOA Protozoa are unicellular, eukaryotic chemoheterotrophs. Protozoa are found in soil and water and as normal microbiota in animals. CHARACTERISTICS OF PROTOZOA The vegetative form is called a trophozoite. Asexual reproduction is by fission, budding, or schizogony. Sexual reproduction is by conjugation. During ciliate conjugation, two haploid nuclei fuse to produce a zygote. Some protozoa can produce a cyst that provides protection during adverse environmental conditions. Protozoa have complex cells with a pellicle, a cytostome, and an anal pore. MEDICALLY IMPORTANT PHYLA OF PROTOZOA Archaezoa lack mitochondria and have flagella; they include Trichomonas and Giardia. Microsporidia lack mitochondria and microtubules; microsporans cause diarrhea in AIDS patients. Amoebozoa are amoeba; they include Entamoeba and Acanthamoeba. Apicomplexa have apical organelles for penetrating host tissue; they include Plasmodium and Cryptosporidium. Ciliophora move by means of cilia; Balantidium coli is the human parasitic ciliate. Euglenozoa move by means of flagella and lack sexual reproduction; they include Trypanosoma. SLIME MOLDS Cellular slime molds resemble amoebas and ingest bacteria by phagocytosis. Plasmodial slime molds consist of a multinucleated mass of protoplasm that engulfs organic debris and bacteria as it moves. HELMINTHS Parasitic flatworms belong to the Phylum Platyhelminthes. Parasitic roundworms belong to the Phylum Nematoda. CHARACTERISTICS OF HELMINTHS Helminths are multicellular animals; a few are parasites of humans. The anatomy and life cycle of parasitic helminths are modified for parasitism. The adult stage of a parasitic helminth is found in the definitive host. Each larval stage of a parasitic helminth requires an intermediate host. Helminths can be monoecious or dioecious. PLATYHELMINTHS Flatworms are dorsoventrally flattened animals; parasitic flatworms may lack a digestive system. Adult trematodes, or flukes, have an oral and ventral sucker with which they attach to host tissue. Eggs of trematodes hatch into free-swimming miracidia that enter the first intermediate host; two generations of rediae develop in the first intermediate host; the rediae become cercariae that bore out of the first intermediate host and penetrate the second intermediate host; cercariae encyst as metacercariae in the second intermediate host; after they are ingested by the definitive host, the metacercariae develop into adults. A cestode, or tapeworm, consists of a scolex (head) and proglottids. Humans serve as the definitive host for the beef tapeworm, and cattle are the intermediate host. Humans serve as the definitive host and can be an intermediate host for the pork tapeworm. Humans serve as the intermediate host for Echinococcus granulosus; the definitive hosts are dogs, wolves, and foxes. NEMATODES Roundworms have a complete digestive system. The nematodes that infect humans with their eggs are Enterobius vermicularis (pinworm) and Ascaris lumbricoides. The nematodes that infect humans with their larvae are Necator americanus, Trichinella spiralis, and anisakine worms. VIRUSES, VIROIDS, AND PRIONS GENERAL CHARACTERISTICS OF VIRUSES Depending on one’s viewpoint, viruses may be regarded as exceptionally complex aggregations of nonliving chemicals or as exceptionally simple living microbes. Viruses contain a single type of nucleic acid (DNA or RNA) and a protein coat, sometimes enclosed by an envelope composed of lipids, proteins, and carbohydrates. Viruses are obligatory intracellular parasites. They multiply by using the host cell’s synthesizing machinery to cause the synthesis of specialized elements that can transfer the viral nucleic acid to other cells. HOST RANGE Host range refers to the spectrum of host cells in which a virus can multiply. Most viruses infect only specific types of cells in one host species. Host range is determined by the specific attachment site on the host cell’s surface and the availability of host cellular factors. VIRAL SIZE Viral size is ascertained by electron microscopy. Viruses range from 20 to 1000 nm in length. VIRAL STRUCTURE A virion is a complete, fully developed viral particle composed of nucleic acid surrounded by a coat. NUCLEIC ACID Viruses contain either DNA or RNA, never both, and the nucleic acid may be single- or doublestranded, linear or circular, or divided into several separate molecules. The proportion of nucleic acid in relation to protein in viruses ranges from about 1% to about 50%. CAPSID AND ENVELOPE The protein coat surrounding the nucleic acid of a virus is called the capsid. The capsid is composed of subunits, capsomeres, which can be a single type of protein or several types. The capsid of some viruses is enclosed by an envelope consisting of lipids, proteins, and carbohydrates. Some envelopes are covered with carbohydrate-protein complexes called spikes. GENERAL MORPHOLOGY Helical viruses (for example, Ebola virus) resemble long rods, and their capsids are hollow cylinders surrounding the nucleic acid. Polyhedral viruses (for example, adenovirus) are many-sided. Usually the capsid is an icosahedron. Enveloped viruses are covered by an envelope and are roughly spherical but highly pleomorphic. There are also enveloped helical viruses (for example, influenza virus) and enveloped polyhedral viruses (for example, Simplexvirus). Complex viruses have complex structures. For example, many bacteriophages have a polyhedral capsid with a helical tail attached. TAXONOMY OF VIRUSES Classification of viruses is based on type of nucleic acid, strategy for replication, and morphology. Virus family names end in -viridae; genus names end in -virus. A viral species is a group of viruses sharing the same genetic information and ecological niche. ISOLATION, CULTIVATION, AND IDENTIFICATION OF VIRUSES Viruses must be grown in living cells. The easiest viruses to grow are bacteriophages. GROWING BACTERIOPHAGES IN THE LABORATORY The plaque method mixes bacteriophages with host bacteria and nutrient agar. After several viral multiplication cycles, the bacteria in the area surrounding the original virus are destroyed; the area of lysis is called a plaque. Each plaque originates with a single viral particle; the concentration of viruses is given as plaqueforming units. GROWING ANIMAL VIRUSES IN THE LABORATORY Cultivation of some animal viruses requires whole animals. Simian AIDS and feline AIDS provide models for studying human AIDS. Some animal viruses can be cultivated in embryonated eggs. Cell cultures are cells growing in culture media in the laboratory. Primary cell lines and embryonic diploid cell lines grow for a short time in vitro. Continuous cell lines can be maintained in vitro indefinitely. Viral growth can cause cytopathic effects in the cell culture. VIRAL IDENTIFICATION Serological tests are used most often to identify viruses. Viruses may be identified by RFLPs and PCR. VIRAL MULTIPLICATION Viruses do not contain enzymes for energy production or protein synthesis. For a virus to multiply, it must invade a host cell and direct the host’s metabolic machinery to produce viral enzymes and components. MULTIPLICATION OF BACTERIOPHAGES During the lytic cycle, a phage causes the lysis and death of a host cell. Some viruses can either cause lysis or have their DNA incorporated as a prophage into the DNA of the host cell. The latter situation is called lysogeny. During the attachment phase of the lytic cycle, sites on the phage’s tail fibers attach to complementary receptor sites on the bacterial cell. In penetration, phage lysozyme opens a portion of the bacterial cell wall, the tail sheath contracts to force the tail core through the cell wall, and phage DNA enters the bacterial cell. The capsid remains outside. In biosynthesis, transcription of phage DNA produces mRNA coding for proteins necessary for phage multiplication. Phage DNA is replicated, and capsid proteins are produced. During the eclipse period, separate phage DNA and protein can be found. During maturation, phage DNA and capsids are assembled into complete viruses. During release, phage lysozyme breaks down the bacterial cell wall, and the new phages are released. During the lysogenic cycle, prophage genes are regulated by a repressor coded for by the prophage. The prophage is replicated each time the cell divides. Exposure to certain mutagens can lead to excision of the prophage and initiation of the lytic cycle. Because of lysogeny, lysogenic cells become immune to reinfection with the same phage and may undergo phage conversion. A lysogenic phage can transfer bacterial genes from one cell to another through transduction. Any genes can be transferred in generalized transduction, and specific genes can be transferred in specialized transduction. MULTIPLICATION OF ANIMAL VIRUSES Animal viruses attach to the plasma membrane of the host cell. Entry occurs by endocytosis or fusion. Animal viruses are uncoated by viral or host cell enzymes. The DNA of most DNA viruses is released into the nucleus of the host cell. Transcription of viral DNA and translation produce viral DNA and, later, capsid proteins. Capsid proteins are synthesized in the cytoplasm of the host cell. DNA viruses include members of the families Adenoviridae, Poxviridae, Herpesviridae, Papovaviridae, and Hepadnaviridae. Multiplication of RNA viruses occurs in the cytoplasm of the host cell. RNAdependent RNA polymerase synthesizes a double-stranded RNA. Picornaviridae + strand RNA acts as mRNA and directs the synthesis of RNAdependent RNA polymerase. Togaviridae + strand RNA acts as a template for RNA-dependent RNA polymerase, and mRNA is transcribed from a new – RNA strand. Rhabdoviridae – strand RNA is a template for viral RNA-dependent RNA polymerase, which transcribes mRNA. Reoviridae are digested in host cell cytoplasm to release mRNA for viral biosynthesis. Retroviridae reverse transcriptase (RNA-dependent DNA polymerase) transcribes DNA from RNA. After maturation, viruses are released. One method of release (and envelope formation) is budding. nonenveloped viruses are released through ruptures in the host cell membrane. *Animation: Viral Replication. The Microbiology Place. VIRUSES AND CANCER The earliest relationship between cancer and viruses was demonstrated in the early 1900s, when chicken leukemia and chicken sarcoma were transferred to healthy animals by cell-free filtrates. THE TRANSFORMATION OF NORMAL CELLS INTO TUMOR CELLS When activated, oncogenes transform normal cells into cancerous cells. Viruses capable of producing tumors are called oncogenic viruses. Several DNA viruses and retroviruses are oncogenic. The genetic material of oncogenic viruses becomes integrated into the host cell’s DNA. Transformed cells lose contact inhibition, contain virus-specific antigens (TSTA and T antigen), exhibit chromosome abnormalities, and can produce tumors when injected into susceptible animals. DNA ONCOGENIC VIRUSES Oncogenic viruses are found among the Adenoviridae, Herpesviridae, Poxviridae, and Papovaviridae. The EB virus, a herpesvirus, causes Burkitt’s lymphoma and nasopharyngeal carcinoma. Hepadnavirus causes liver cancer. RNA ONCOGENIC VIRUSES Among the RNA viruses, only retroviruses seem to be oncogenic. HTLV-1 and HTLV-2 have been associated with human leukemia and lymphoma. The virus’s ability to produce tumors is related to the production of reverse transcriptase. The DNA synthesized from the viral RNA becomes incorporated as a provirus into the host cell’s DNA. A provirus can remain latent, can produce viruses, or can transform the host cell. LATENT VIRAL INFECTIONS A latent viral infection is one in which the virus remains in the host cell for long periods without producing an infection. Examples are cold sores and shingles. PERSISTENT VIRAL INFECTIONS Persistent viral infections are disease processes that occur over a long period and are generally fatal. Persistent viral infections are caused by conventional viruses; viruses accumulate over a long period. PRIONS Prions are infectious proteins first discovered in the 1980s. Prion diseases, such as CJD and mad cow disease, all involve the degeneration of brain tissue. Prion diseases are the result of an altered protein; the cause can be a mutation in the normal gene for PrPC or contact with an altered protein (PrPSc). *Animation: Prion Reproduction. The Microbiology Place. PLANT VIRUSES AND VIROIDS Plant viruses must enter plant hosts through wounds or with invasive parasites, such as insects. Some plant viruses also multiply in insect (vector) cells. Viroids are infectious pieces of RNA that cause some plant diseases, such as potato spindle tuber viroid disease.
