Microbiology Classification, Metabolism & Organism Identification

Worksheet identification clues

Impact = what an organism does. Classification = its general group. Taxonomy or nomenclature = its scientific group or name. Properties = traits that identify it.

Tuberculosis and leprosy — GC classification

High GC. Both diseases are caused by members of Mycobacterium.

Tuberculosis and leprosy — phylum

Actinobacteria in your lecture. Mycobacterium is the genus.

Prokaryotic domains

Bacteria and Archaea lack a membrane-bound nucleus. Eukarya has a membrane-bound nucleus.

Peptidoglycan

Structural material found in most bacterial cell walls. Archaeal walls lack true peptidoglycan.

Eukaryotic cell walls

Fungal walls contain chitin. Plant walls contain cellulose. Animal cells lack cell walls.

Binary fission and budding

Binary fission divides one cell into two. Budding produces a new cell as an outgrowth of the parent.

Thioglycolate oxygen gradient

Oxygen is highest at the top of the tube and lowest at the bottom. The growth pattern reveals oxygen tolerance.

Obligate aerobe

Requires oxygen. Growth appears at the top of a thioglycolate tube.

Obligate anaerobe

Oxygen inhibits growth. Growth appears at the bottom of the tube.

Facultative anaerobe

Grows with or without oxygen. Growth appears throughout the tube and is heaviest at the top.

Aerotolerant anaerobe

Tolerates oxygen while using anaerobic metabolism. Growth is even throughout the tube.

Microaerophile

Requires a low oxygen concentration. Growth forms a narrow band just below the surface.

Trophic classification

Identify the energy source first: light or chemicals. Then identify the carbon source: inorganic carbon or organic compounds.

Photoautotroph

Uses light for energy and inorganic carbon such as CO₂ to build cell material. Cyanobacteria are an example.

Photoheterotroph

Uses light for energy and organic compounds for carbon.

Chemoautotroph

Uses chemical reactions for energy and inorganic carbon such as CO₂ for carbon. Nitrifying bacteria are an example.

Chemoheterotroph

Uses chemical reactions for energy and organic compounds for carbon. Fungi are an example.

GC content

The proportion of DNA bases that are guanine or cytosine. Know high GC and low GC for the exam.

Four archaeal phyla in the lecture

Korarchaeota, Nanoarchaeota, Euryarchaeota, and Crenarchaeota. The worksheet gives the initials K, N, E, C.

Archaea

Prokaryotes with distinctive branched membrane lipids and no true peptidoglycan. The lecture emphasizes environmental roles and the absence of established human pathogens.

Extremophiles

Organisms that thrive under extreme conditions. Thermophiles favor heat, halophiles favor salt, and acidophiles favor acidity.

Methanogens

Archaea that produce methane (CH₄) in anaerobic environments such as sediments and animal guts. Methane is a greenhouse gas and can be collected as fuel.

Deeply branching bacteria

Early-diverging bacterial lineages in the lecture model. Aquifex is a heat-loving example.

Cyanobacteria

Photosynthetic bacteria that helped oxygenate early Earth by releasing oxygen. Some also fix atmospheric nitrogen.

Oxygenic photosynthesis

Light supplies energy, water supplies electrons, and oxygen is released.

Anoxygenic sulfur phototrophs

Green and purple sulfur bacteria use bacteriochlorophyll. They can use hydrogen sulfide as an electron donor and carry out photosynthesis without releasing oxygen.

Sulfur deposits

Green sulfur bacteria deposit sulfur outside their cells. Purple sulfur bacteria store sulfur granules inside their cells in the lecture comparison.

Nonsulfur phototrophs

Chloroflexi include green nonsulfur bacteria. Rhodospirillum is a purple nonsulfur example.

Clostridia

Low-GC Firmicutes that include anaerobic, endospore-forming rods. Disease clues include gas gangrene, tetanus, and botulism.

Mycoplasma

Low-GC bacteria that lack a cell wall. The lecture places them in Tenericutes.

Mycobacterium

High-GC, acid-fast rods with waxy mycolic acids. This genus includes the bacteria that cause tuberculosis and leprosy.

Corynebacterium

High-GC actinobacteria often seen as pleomorphic rods in palisades. C. diphtheriae causes diphtheria.

Chlamydias

Tiny, obligately intracellular bacteria. Exam clues include sexually transmitted infections and neonatal conjunctivitis.

Spirochetes

Flexible, corkscrew-shaped bacteria. Treponema causes syphilis. Borrelia causes Lyme disease.

Bacteroides

Anaerobic Gram-negative rods that help break down complex carbohydrates in the gut.

Rhizobium

Alphaproteobacteria that fix atmospheric nitrogen in legume root nodules, converting N₂ to ammonia.

Bordetella pertussis

Betaproteobacterium that causes pertussis, also called whooping cough.

Cholera and gastric ulcers

Cholera points to Vibrio cholerae in gamma. Gastric ulcers point to Helicobacter pylori in epsilon.

Campylobacter

Epsilonproteobacteria associated with foodborne intestinal disease. Some infections involve the bloodstream. The worksheet uses "food/blood poisoning."

Pseudomonads

Aerobic, flagellated gamma rods that recycle organic matter. The review associates them with food-related GI distress and urinary tract infections.

Bdellovibrio

A delta bacterium in the lecture classification that preys on other Gram-negative bacteria.

Amoeboid phyla

The three phyla grouped as amoeboids in the worksheet are Cercozoa, Radiolaria, and Amoebozoa.

Foraminifera and Radiolaria

Both can have threadlike pseudopodia. Foraminifera commonly have calcium carbonate shells (CaCO₃). Radiolaria have silica skeletons (SiO₂).

Amoebozoa

Amoeboid phylum identified by broad, lobed pseudopodia. The lecture includes slime molds in this group.

Plasmodial and cellular slime molds

A plasmodial slime mold forms one continuous mass with many nuclei. In a cellular slime mold, individual cells gather into a moving slug when food is scarce.

Dinoflagellates

Class Dinoflagellata in phylum Alveolata. Many are plankton with two flagella. Some produce neurotoxins or form red tides.

Fungal classification

Identify the type of spore and the structure that produces or holds it.

Ascospores

Sexual spores produced inside a sac called an ascus. Associated phylum: Ascomycota.

Basidiospores

Sexual spores produced on a club-shaped basidium, such as those on mushroom gills. Associated phylum: Basidiomycota.

Zygospore

Sexual structure formed after compatible fungal hyphae fuse in the lecture's zygomycete example.

Sporangiospores and ascospores

Sporangiospores are asexual spores inside a sporangium. Ascospores are sexual spores inside an ascus.

Blastospore and conidium

A blastospore forms by budding. A conidium forms externally, often on a stalk. Both are asexual.

Zygomycosis

Fungal disease associated with molds such as Rhizopus. If asked for the general classification, answer mold. If asked for a representative genus, answer Rhizopus.

Tapeworms

Flatworms in phylum Platyhelminthes, class Cestoda. The scolex attaches to the host. A proglottid is a repeated body segment.

Monoecious and dioecious

Monoecious means one individual has both reproductive systems, as in a tapeworm. Dioecious means separate male and female individuals, as in Ascaris.

Endoparasites and ectoparasites

Endoparasites live inside the host, such as intestinal tapeworms. Ectoparasites live on the host's surface, such as fleas and lice.

Biological and mechanical vectors

A pathogen develops or multiplies inside a biological vector. A mechanical vector physically carries the pathogen from place to place.

Lichens as pioneer species

Lichens are among the first organisms to colonize exposed surfaces after a disturbance. They help weather rock and form soil.

Fruticose

Lichen growth form that branches like a small shrub or hangs in tassels.

Foliose

Lichen growth form with flat, leaflike lobes whose edges lift from the surface.

Crustose

Crustlike lichen growth form that sticks tightly to rock like a coat of paint.

Respiratory impacts

Bacterial examples include diphtheria and tuberculosis. Fungal examples include invasive mold disease and mold-triggered asthma.

Gastrointestinal impacts

Bacterial examples include cholera and H. pylori ulcers. Parasitic examples include intestinal tapeworms and flukes.

Beneficial microbial impacts

Pseudomonads recycle organic matter. Yeasts ferment sugars for industry. Paramecium serves as a model organism for teaching.

Five qualities of life

Metabolism, growth, responsiveness, control, and organization.

Viruses and living status

The lecture generally classifies viruses as nonliving because they lack independent metabolism and cellular growth and need a host cell to reproduce. They carry genetic information and evolve.

Viral classification

The three criteria are genome, particle morphology, and host.

Viral genome variations

DNA or RNA, single- or double-stranded, linear or circular, segmented or unsegmented, and positive or negative sense when applicable.

Viral morphology

Particle shapes include helical, polyhedral, complex, and binal (head and tail). A viral particle can be naked or enveloped.

Capsid, nucleocapsid, and envelope

Capsid = protein coat. Nucleocapsid = genome plus capsid. Envelope = outer lipid covering present in some viruses.

Host range and bacteriophages

Host range describes which hosts a virus can infect. A bacteriophage infects bacteria. Compatible receptors help determine which cells a virus can enter.

Positive-sense and negative-sense RNA

Positive-sense RNA can serve as messenger RNA. Negative-sense RNA must first be copied into complementary positive-sense mRNA before translation.

RNA copying and reverse transcription

Copying negative RNA into positive RNA is RNA → RNA and uses an RNA-dependent RNA polymerase. Reverse transcription is RNA → DNA.

Five lytic stages

Attachment → entry → synthesis → assembly → lysis (release).

Attachment and entry

In attachment, a tailed phage binds a receptor using its tail fibers. In entry, the genome passes into the bacterium while the capsid typically stays outside.

Synthesis and assembly

Synthesis makes viral genomes and proteins. Assembly puts those parts together into new viral particles.

Lysis

The infected bacterium bursts and dies, releasing newly assembled phages.

Phage growth curve axes

Horizontal axis = time. Vertical axis = number of infectious virions in the surrounding liquid.

Initial drop and low period

Free phage numbers drop as phages attach. The curve stays low while synthesis and assembly occur inside the cells.

Sharp rise and final plateau

Lysis releases new phages, causing the sharp rise. The count levels off once the infected cells finish releasing them.

Burst size and burst time

Burst size is the number of phages released per infected cell. Burst time is the interval from attachment to release. For 80 phages released after 25 minutes, size = 80 and time = 25 minutes.

Viral shape and host type

The lecture's bacterial example is a binal phage with a head and tail. Eukaryotic-host examples include helical, polyhedral, and complex viruses. The host cell is the one classified by whether it has a nucleus.

Lysogeny, prophage, and induction

During lysogeny, phage DNA persists as a prophage and can pass to daughter bacteria. Induction switches the phage back to productive replication.

Latency and provirus

Latency is a persistent animal-virus infection with little or no production of new particles. Integrated viral DNA is called a provirus. Some latent genomes remain separate from host chromosomes.

Low period of the lytic curve versus lysogeny

During the low period of the lytic curve, viral parts are being produced inside cells. During lysogeny, phage DNA persists and can pass to daughter bacteria as they divide.

Oncogenesis

The development of cancer. Viral integration or viral proteins can contribute by disrupting normal controls on cell division.

Proto-oncogene, oncogene, and tumor suppressor

A proto-oncogene normally promotes regulated growth. An oncogene drives excessive growth when abnormally activated. A tumor suppressor normally restrains growth or helps eliminate damaged cells.