Unit 2: Microbial Diversity

I. Orientation — The microbial world and cellular organization

Microbial diversity concerns organisms and infectious agents that differ in cellular organization, nutrition, reproduction, evolutionary history, and relationship with their environments. The central distinction is between prokaryotic cells, which lack a membrane-bound nucleus, and eukaryotic cells, which contain a nucleus and other membrane-bound organelles. Viruses are acellular and therefore fall outside the cellular classification system.

• Cellular principle: All cellular organisms possess a plasma membrane, genetic material, ribosomes, and mechanisms for energy use and reproduction.
• Prokaryotic organization: Bacteria and archaea generally contain circular DNA in a nucleoid, 70S ribosomes, and no membrane-bound nucleus.
• Eukaryotic organization: Algae, fungi, protozoa, plants, and animals contain linear chromosomes inside a nucleus and usually have 80S cytoplasmic ribosomes.
• Microbial size range: Bacteria commonly measure about 0.5–5 μm; many protozoa measure 10–100 μm; viruses commonly measure about 20–300 nm.
• Classification basis: Microorganisms are characterized by cell structure, staining behavior, metabolism, morphology, motility, reproduction, and molecular sequences such as ribosomal RNA genes.
• Ecological distribution: Microbes occur in soil, water, air, food, extreme habitats, and host-associated communities; their distribution reflects temperature, pH, oxygen, salinity, nutrients, and host conditions.

II. Prokaryotic cells — Bacteria and archaea

Prokaryotic cells are small, structurally simple cells that lack a membrane-bound nucleus but possess highly organized membranes, ribosomes, genetic regions, and surface structures. Bacteria are the main prokaryotic group emphasized in medical and general microbiology.

A. Distribution and characterization of prokaryotic and eukaryotic cells

This subsection distinguishes prokaryotes from eukaryotes using structural and functional characteristics.

• Nuclear organization: In bacteria, the chromosome occupies a nucleoid rather than a nucleus; in eukaryotic cells, DNA is enclosed by a double nuclear envelope.
• Genetic material: Most bacteria contain one circular chromosome and may carry plasmids, such as plasmids encoding antibiotic resistance; eukaryotes usually contain multiple linear chromosomes.
• Ribosomes: Bacterial 70S ribosomes consist of 30S and 50S subunits, whereas eukaryotic cytoplasmic ribosomes are 80S, composed of 40S and 60S subunits.
• Cell division: Bacteria commonly reproduce by binary fission, in which DNA replication is followed by septum formation; eukaryotic cells divide by mitosis or meiosis.
• Energy generation: Bacteria carry respiratory enzymes in the plasma membrane because they lack mitochondria; eukaryotes use mitochondria for most aerobic respiration.
• Distribution: Bacteria inhabit soil, freshwater, oceans, animal intestines, skin, and extreme environments; archaea are especially important in hypersaline, acidic, anaerobic, and high-temperature habitats.

B. Morphology and cell structure of major groups of microorganisms, including bacteria, algae, fungi, and protozoa

Prokaryotic morphology is especially useful for identifying bacteria, while cell structures explain their survival, staining, movement, and pathogenic properties.

• Cell shape: Cocci are spherical, bacilli are rod-shaped, vibrios are curved rods, and spirilla or spirochetes are spiral forms; Staphylococcus forms clusters, while Streptococcus forms chains.
• Cell envelope: Gram-positive bacteria possess a thick peptidoglycan wall containing teichoic acids; Gram-negative bacteria have a thin peptidoglycan layer, periplasm, and an outer membrane containing lipopolysaccharide.
• Cytoplasmic membrane: This phospholipid bilayer regulates transport and contains electron-transport chains; bacterial membranes can generate ATP without mitochondria.
• Surface structures: Capsules resist phagocytosis, fimbriae promote attachment, and sex pili allow DNA transfer by conjugation.
• Flagella: Bacterial flagella rotate to produce motility; arrangements include monotrichous, lophotrichous, amphitrichous, and peritrichous patterns.
• Internal structures: The nucleoid contains the chromosome, ribosomes synthesize proteins, and storage inclusions hold materials such as poly-β-hydroxybutyrate or sulfur.
• Endospores: Bacillus and Clostridium produce dormant endospores containing calcium dipicolinate; these resist heat, drying, and chemicals but are not reproductive cells.

C. Significance and limitations

Structural differences provide practical methods for identification but do not alone establish evolutionary relationships.

• Diagnostic value: Gram staining separates bacteria according to envelope structure; cell shape, arrangement, and capsule staining further narrow identification.
• Medical significance: Capsules, endotoxin, pili, and endospores contribute to survival or disease, while peptidoglycan is a target of β-lactam antibiotics.
• Limitation of morphology: Unrelated bacteria may have similar shapes, and environmental conditions can alter size, pigmentation, or arrangement; biochemical and molecular tests are therefore necessary.

III. Eukaryotic microorganisms — Algae, fungi, and protozoa

Eukaryotic microorganisms contain nuclei and membrane-bound organelles and generally have larger, more internally compartmentalized cells than bacteria. The major microbial eukaryotic groups include algae, fungi, and protozoa.

A. Distribution and characterization of prokaryotic and eukaryotic cells

Eukaryotic microbial groups occupy diverse habitats and differ in nutrition, cell walls, motility, and reproduction.

• Algae: Algae occur mainly in freshwater, marine, and moist environments; they are usually photosynthetic and contain chloroplasts with pigments such as chlorophyll a.
• Fungi: Fungi grow in soil, decaying organic matter, food, and host tissues; they are absorptive heterotrophs that secrete enzymes and take up dissolved nutrients.
• Protozoa: Protozoa commonly inhabit freshwater, marine environments, soil, and animal hosts; they are generally unicellular heterotrophs that ingest or absorb nutrients.
• Nuclear structure: Eukaryotic DNA is organized with histone proteins in chromosomes inside a nucleus; nucleoli produce ribosomal components.
• Organelles: Mitochondria generate ATP, endoplasmic reticulum supports protein or lipid processing, and Golgi bodies modify and package cellular products.
• Reproduction: Asexual reproduction may occur by binary fission, budding, fragmentation, or spore formation; sexual reproduction involves fusion of genetic material.

B. Morphology and cell structure of major groups of microorganisms, including bacteria, algae, fungi, and protozoa

The cell structures of algae, fungi, and protozoa reflect their different nutritional and ecological strategies.

• Algal cells: Algae contain chloroplasts and often cellulose-containing cell walls; diatoms possess silica frustules, while dinoflagellates have cellulose plates and two flagella.
• Fungal cells: Fungal walls contain chitin and glucans rather than peptidoglycan; yeasts are usually unicellular and reproduce by budding, whereas molds form multicellular hyphae.
• Hyphae and mycelium: Hyphae may be septate or coenocytic; an interconnected mass of hyphae is a mycelium, as seen in filamentous molds such as Rhizopus.
• Fungal spores: Conidia are asexual spores formed externally, while sporangiospores develop inside a sporangium; spores assist dispersal and reproduction.
• Protozoan forms: Amoebae use temporary pseudopodia, flagellates use one or more flagella, ciliates use numerous cilia, and apicomplexans possess specialized structures for host invasion.
• Protozoan coverings: Some protozoa have flexible pellicles, shells, or tests; Paramecium has a pellicle and cilia, while Amoeba changes shape through cytoplasmic streaming.
• Specialized structures: Contractile vacuoles expel excess water in freshwater protozoa; food vacuoles digest particles, and cysts provide resistance during unfavorable conditions.

C. Significance and limitations

Eukaryotic microbial diversity has ecological, industrial, and medical importance, but classification must account for complex life cycles.

• Ecological roles: Algae contribute oxygen and primary production; fungi decompose cellulose and lignin; protozoa graze on bacteria and recycle nutrients.
• Human uses: Yeast performs alcoholic fermentation, edible algae provide biomass, and fungi produce compounds such as antibiotics and organic acids.
• Disease associations: Fungi can cause candidiasis or dermatophytosis; protozoa cause diseases such as malaria, giardiasis, and amoebic dysentery.
• Identification limitation: A single organism may change between trophozoite, cyst, yeast, or filamentous forms; microscopy should therefore be combined with culture, biochemical, antigen, or molecular methods.

IV. Viruses — Acellular infectious agents

Viruses are acellular genetic entities that replicate only inside suitable host cells. They contain a genome enclosed in a protein capsid, and some possess an additional lipid envelope obtained from a host membrane.

A. Unique features of viruses

Viruses differ fundamentally from cellular microorganisms in structure, metabolism, and reproduction.

• Acellular structure: A virion lacks cytoplasm, ribosomes, mitochondria, and independent metabolic pathways; it cannot synthesize proteins outside a host cell.
• Genome type: Viral genomes may be DNA or RNA, single-stranded or double-stranded, and linear, circular, or segmented; influenza A virus, for example, has a segmented RNA genome.
• Capsid: The capsid is a protein shell built from capsomeres; it protects nucleic acid and helps determine viral symmetry, such as helical, icosahedral, or complex forms.
• Envelope: Enveloped viruses possess a lipid membrane with viral glycoprotein spikes; influenza and HIV are enveloped, whereas adenoviruses are non-enveloped.
• Host specificity: Viral attachment depends on complementary interactions between viral surface proteins and host receptors, such as HIV gp120 binding CD4 and co-receptors.
• Replication strategy: Viral multiplication involves attachment, entry, uncoating, genome replication, protein synthesis, assembly, and release; these stages occur using host-cell machinery.
• Cultivation: Viruses generally cannot grow on ordinary nutrient agar; they require living cells, embryonated eggs, tissue culture, or suitable experimental hosts.
• Evolution: High mutation rates, especially among RNA viruses, reassortment of segmented genomes, and recombination produce antigenic and genetic variation.

B. Morphology and cell structure of major groups of microorganisms, including bacteria, algae, fungi, and protozoa

Viruses do not possess cellular morphology, but their external architecture can be compared with cellular microorganisms.

• Scale: A typical bacterium may be 1 μm wide, whereas a 100-nm virus is about ten times smaller in diameter and requires electron microscopy for direct visualization.
• Symmetry: Icosahedral capsids form geometric shells, helical capsids wind around nucleic acid, and complex viruses combine multiple structural designs.
• Surface projections: Viral spikes mediate attachment and may determine tissue tropism; influenza hemagglutinin binds host-cell sialic acid.
• No organelles: Unlike algae, fungi, and protozoa, viruses contain no nucleus, chloroplast, mitochondrion, cell wall, or cytoplasmic membrane of their own.
• Virion versus infected cell: The extracellular virion is metabolically inactive, while the infected host cell becomes the site of genome replication, viral protein synthesis, and assembly.

C. Significance and limitations

Viruses are important causes of disease and useful biological tools, but their status challenges traditional definitions of life.

• Medical effects: Viral infection may cause cell lysis, persistent infection, transformation, or immune-mediated tissue damage; antibiotics do not treat viral replication.
• Applications: Viral vectors deliver genes, bacteriophages can target bacteria, and attenuated viruses may serve as vaccines.
• Classification limitation: Viruses are classified by genome, replication strategy, capsid, envelope, and host range rather than by cellular taxonomy; they are not placed in the bacterial or eukaryotic domains.