Microbial Ecology
Contrast the relative rates of growth in a natural environment vs lab culture
Biofilms: what they are, generally how formed, and main types of issues they can cause for humans
Soils: note the variability of environmental conditions (water, O2) in both time and space (especially small spaces). Think about how this can impact microbial diversity and niches
Freshwater (lakes): importance of stratification, and what is the impact of eutrophication.
Review summer stratification profile and its impact on microbial communities especially with regard to hydrogen sulfide and oxygen
Marine habitat: what is primary productivity? What organisms in the upper ocean levels perform it and the need for nitrogen and phosphorous nutrients (not mentioned but iron is also important)
What can cause ocean dead zones?
Prochlorococcus as a principle primary producer in open ocean, Pelagibacter clade as a principle type of heterotrophic bacterium.
Role of heterotrophic bacteria and viruses in the carbon cycle of oceans
Connection between chemolithotrophs and life at deep sea hydrothermal vents
Microbial evolution and phylogeny – Chap 16 (13thed) or Chap 14 (12thed)
What was the likely metabolism of first primitive cells given conditions on early earth?
Review the concept/cause of Great Oxidation Event in earth history
Review the small subunit ribosomal RNA gene and use in molecular phylogeny construction, focus on the attributes that make this gene desirable
How does one use the 16S rRNA gene? The analytical methods (amplify, sequence, compare - review the animation on generating phylogenetic trees)
Basics of how to read a phylogenetic tree to infer relatedness among taxa; in the case of genetic sequence information that the distances refer to nucleotide differences between any two taxa.
Proteobacteria – Chap 17 (13thed) or Chap 15 (12thed)
General characteristics of proteobacteria: all gram negative, most commonly encountered, greatest metabolic diversity
Nitrifying bacteria: what is the process, its importance, and the difference between ammonia oxidation (Nitrosococcus) and nitrite oxidation (Nitrobacter)
Pseudomonas: nutritionally versatile, can degrade xenobiotics; P. aeurginosa is a possible nosocomial pathogen
Acetic acid bacteria:Acetobacter, may be found in alcoholic beverages (wine), make vinegar
Gram negative cocci (this is not too common): Neisseria, esp. N. gonorrhoeae which is a pathogen
Enteric bacteria: Enterobacteriaceae
Gram negative rods
Separation as mixed acid vsbutanediol fermenters
Main genera are Escherichia, Salmonella, Shigella for mixed acid, Enterobacter for butanediol (you can remember Serratia as example here since you worked with it)
Review role of LPS as endotoxin
Vibrio: Distinctive vibroid shape, aquatic habitat, V. cholera as an example
Gram negative spirilla: review Campylobacter and Helicobacter as examples
Gram positive and other bacteria – Chap 18 (13thed) or Chap 16 (12thed)
Firmicutes
Non-sporulatingGram positive
Staphyococcus vs. Micrococcus: facultative vs aerobe, S. aureus can be pathogen (incl. MRSA).
Lactic acid bacteria: note they are anaerobic, and their fermentation product. Which main groups are included?
Streptococci: incidence of hemolysis for some Streptococcus, types of hemolysis.
Review morphology of cells under microscope between Staph. and Streptococci
Importance of enterococci
Lactobacillusand Lacotcoccus: important in dairy
Listeria: L.monocytogenes cause of listeriosis, foodborne illness from processed food products
Sporulating Gram positive:
focus on Bacillus and Clostridium
why spores are important in soil
Bacillus: B. thuringiensis insect pathogen, Bt toxin; B. anthracis anthrax
Clostridium: obligate anaerobes, several pathogenic species All produce toxins
Mycoplasma: cells lack cell wall- so they therefore lack what? Peptidoglycan. Have critical structural role of sterols instead. Among smallest cells. These are primarily parasitic.
Actinobacteria:
Propionic acid bacteria: role in Swiss cheese, have secondary fermentation (what is it?)
Mycobacterium: acid fast, M. tuberculosis, causes tuberculosis, exhibits cord-like growth behavior.
Filamentous actinobacteriaàStreptomyces and Actinomyces: soil bacteria, mycelia similar to fungi. Be familiar with the very important role of Streptomyces in antibiotic production
Cyanobacteria: oxygenic photoautotrophs
Chlamydia: obligate parasites, poor metabolic capabilities, pathogenic nature of C. trachomatis
Spirochetes: gram negative, unique coiled shape. Treponemapallidum causes syphilis
Borellia causes Lyme disease
Viruses – Chap 9 (13th ed.) or Chap 10 (12th ed.)
Above all, try to understand how viruses reproduce in general, and therefore what their needs are to do this
Definitions of virus-related terminology: virus, viral particle/virion, capsid, capsomer, nucleocapsid, enveloped virus, helical vs. icosahedral, titer, plaque assay/plaques
Nature of viral envelopes, where does it come from?
The general role of virion enzymes - why they are needed?BYOE
The general phases of viral replication, and viral growth curve, including what happens in latent period
The 7 classes of viruses per the Baltimore Classification system
The difference between positive strand and negative strand RNA genomes, what it means in terms of protein expression
Understand the significance of RNA replicase (an RNA-dependent RNA polymerase), which types of viral life cycle would need this and for what?
The difference between virulent/lytic mode and temperate mode of bacteriophage life cycle, definition of lysogeny
Definitions of persistent infections, latent infections, and transformation
Retroviruses and the role of reverse transcriptase, just general process, including integration of viral dsDNA nucleic acid into the host genome
What a viroid and prion are
Viral diversity – Chap 21 (13th ed. ) or Chap 19 (12th ed.)
Phage MS-2: an RNA Bacteriophage of E. coli, small virion, small genome; and phi-X 174, a ssDNA Bacteriophage that makes a dsDNA replicative form to serve as mRNA template and to create more ssDNA genomes
Plus-strand RNA viruses of animals: genome can serve as mRNA; but need minus strand RNA for template to make new RNA genome. Ex. Enteroviruses,Flaviviruses. Be familiar a bit with
Negative-strand RNA viruses: need to copy the RNA genome into mRNA, use RNA replicase (viral RNA polymerase). Ex. influenza virus. Also, antigenic shift (allowed by recombination of genome segments) and antigenic drift processes in influenza.
Double-stranded RNA viruses in animals– Reoviruses, ex. Rotavirus
Double-stranded DNA viruses in animals –Herpes viruses are in this class. Key herpes viruses: Varicella-Zoster virus (chickenpox/shingles) and Herpes simplex virus.Also Papillomaviruses causing warts, possibly cancers
Retroviruses – already mentioned
Hepadnaviruses – dsDNA genome that replicates via an RNA intermediate. Hepatitis B is in this class. Thus, this virus also encodes a gene for reverse transcriptase.
Eukaryotes:
Key features of diplomonads (Giardia) and parabasalids (Trichomonas)
Euglenozoans: review Euglena and Trypanosomabrucei: African Sleeping Sickness
Alveolates: include ciliates, dinoflagellates, apicomplexans
Cilliates: ex. Paramecium
Dinoflagellates: mostly photoautotrophs, a primary cause of harmful algal blooms worldwide, including Florida Red Tide Karenia brevis. Dinoflagellates are also common algal symbiont inside coral polyp cells, which are lost during coral bleaching.
Apicomplexans: have a degenerate chloroplasts, know the three main pathogens Plasmodium (malaria), Toxoplasma (toxoplasmosis, cat litter), Eimeria (Coccidiosis)
Infectious Disease: person to person and vectorborne
Know the major respiratory bacteria and illness issues they cause:
Strep A (including TSS, Scarlet fever and Rheumatic fever and mechanism)
Strep pneumoniae (protected by capsule)
Mycobacterium tuberculosis (cord factor, persistence, dangerousness, how treated and difficulty of treatment)
Meningococcal (bacterial) meningitis (Neisseria) – who is more at risk, distinctive morphology
Pertussis
Measles
Know what causes the common cold
Influenza: review general virion structure and importance of HA and NA
Review antigenic shift and antigenic drift among influenza viruses, and the role recombination in animals can play in global pandemic emergence.
Staphylococcus aureus: review the major symptoms, virulence factors and antibiotic resistance
Familiarize with disease caused by hepatitis viruses A, B, and C.
Know the causative organisms, their attributes and characteristics of the major STDs: gonorrhea, syphilis, chlamydia, herpes simplex 2, HPV. I.e. for bacteria, know the diplococcus morphology of N. gonorrhoeae, spirochete shape of Treponema, intracellular pathogen characteristic of Chlamydia.
Review epidemiology and pathology of HIV/AIDS
Symptoms, and vector/cause of Lyme disease.
Arboviruses: Vector and incidence of West Nile fever, Eastern Equine Encephalitis.Also Flavivirus genus including Zika virus and Dengue. What are the symptoms and Zika’s possible link to birth defects.
Significance of mosquito control in controlling spread of these diseases
Know the organism and vector, and major symptoms of malaria (i.ered blood cells infected, causes fevers and chills)
Know cause of tetanus and how acquired
Ebola virus: causative virus, hemorrhagic fever, symptoms, therapy/treatment
Water and food borne disease will be on next exam