HOW DOES ONE USE THE 16S RRNA GENE?

29 Jul HOW DOES ONE USE THE 16S RRNA GENE?

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 (13th ed) or Chap 14 (12th
ed)

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 (13th ed) or Chap 15 (12th ed)

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 vs butanediol 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 (13th ed) or Chap 16 (12th
ed)

Firmicutes

Non-sporulating Gram 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 actinobacteriaà Streptomyces 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. Treponema
pallidum 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 Trypanosoma brucei: 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.e red 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