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 (13^thed) or Chap 14 (12^thed) 

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 (13^thed) or Chap 15 (12^thed) 

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 (13^thed) or Chap 16 (12^thed)

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 (13^th ed.) or Chap 10 (12^th 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 (13^th ed. ) or Chap 19 (12^th 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