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Microbiology 1 > Lecture #7 - Prokaryotic Diversity INTRO & PART I BACTERIAL DIVERSITY > Flashcards

Lecture #7 - Prokaryotic Diversity INTRO & PART I BACTERIAL DIVERSITY Flashcards

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1
Q

Two ways to describe microbial diversity:

A
  1. Phylogenetic diversity

2. Functional diversity

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2
Q

Phylogenetic diversity

A
  • Microbes are grouped into PHYLA based on evolutionary relationships
  • Most often based on 16S rRNA gene sequence

basically:

  • analyze 16S rRNA DNA sequence & est. a % homology
  • take multiple species (multiple genera) & putting them into 1 phylogenetic group based on what similarity they may have (NOT >97% within the gene)
  • focused on similarities that are much less but still lets them be placed into a single group
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3
Q
  1. Phylogenetic diversity

The RED DOTS represent the…

A

phyla only known from metagenome sequencing from diverse environmental samples (intersperced with the ones we can grow in each subcategory)

  • meaning, never seen (or grown) these organisms in a lab
  • don’t have much info, other than their genetics, that they exist
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4
Q

Phylogenetic diversity

The tree includes 92 named _____ phyla, 26 ____ phyla and all five of the ______ super groups

This tree represents microbial diversity based on 16S rRNA as of 2016

A

BACTERIAL

ARCHAEAL

EUKARYOTIC

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5
Q

What does…

The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic super groups

show us?

A

bacteria are MORE diverse - req’s us to put them in more groups to be able to keep them organized b/c that diversity will be rich

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6
Q
  1. Functional diversity
A
  • Groups microbes based on the activities they carry out

* Some functions appear to be performed in a single phylum only

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7
Q

Functional diversity

Groups microbes based on the activities they carry out (with ex)

A

think: grouping ppl who are vegetarian or like meat
- if 2 ppl are vegetarian it doesn’t mean same intellect, hobbies, ethnicity, hair colour etc.

Ex. Anoxygenic phototrophs: dispersed through several Phyla (formulate same coencentric circle)
- like photosynthesis that doesn’t produce O2

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8
Q

Where does O2 in photosyn. come from, what do you split?

If something is anoxygenic, what do you think about the e- donor?

A

SPLIT H20

not H20
- H2S - produce S compound rather than O2

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9
Q

What does Functional Diversity show us?

A

just b/c they all like to do this type of metabolism (ex: anoxygenic phototrophs), doesn’t mean anything about their genetic similarity b/c they’re pretty far apart from 1 another on the phylogenetic tree (so genetically they must have quite a bit of diversity)
- doesn’t make sense to put them in groups based off this, makes more sense to put them in groups based on genetics

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10
Q

Functional diversity

Some functions appear to be performed in a single phylum only (with ex)

A

Ex) oxygenic phototrophy
- splitting of H20, in order to generate e-‘s, & molecular O2

Simply by nature of where they sit on the phylogenetic tree, it’ll be a lil more representative of the genetic characteristics b/c its not anywhere else

  • probs b/c req’s a lot of machinery in the cell to do oxygenic photosyn.
  • get a bit more cohesiveness since there’s just 1
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11
Q

By comparing anoxygenic & oxygenic phototrophy, there’s an argument against grouping this according to function (______), but if you looked only at ______, maybe there’ll be an argument for (b/c…)

A

ANOXYGENIC PHOTOTROPHY

OXYGENIC PHOTOTROPHY

see it just within 1 partic. group

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12
Q

Most prokaryotes cannot be cultured in the lab (yet)

Some phyla…

Some are known only from…

A
  • take an sequence whole thing & notice a gene for H utilization or nitrification etc.
  • CAN’T give them N & watch what they do b/c we can’t grow them

…are well studied in lab

…16S sequences or metagenomic studies

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13
Q

Type Species have…

A

organisms of interest (well studied)

- we grow, study & identify

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14
Q

16S rRNA Gene Sequences have…

A

NOT been grown (NOT seen)

  • only known from METAGENOMIC SEQUENCING ANALYSIS
  • take sample & look through genetics in order to identify the 16S rRNA sequences that’re there & realizing its not a species seen before but it exists, so its its own species
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15
Q

Most phyla will contain ____ ____

A

MULTIPLE GENERA
- meaning not just genus mycobacterium
for ex:
- will be other genera found within the category

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16
Q

To be considered members of same species, you got greater than 97% homology in 16S rRNA gene.

BUT what do you figure within this Bacterial Phyla: Tenericutes, about the genera present? Do you figure closely related to 1 another 97% or no?

A

NOT REALLY - a lot of variation
- but, still same enough to be put in this category specifically

think: you & great aunt
- not as similar as you & sis
- but still from same lineage & as a result have more similarity than someone else

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17
Q

Bacterial Phyla: Tenericutes

A
  • The Mycoplasmas
  • Phylogenetically related to Gram positives, but they don’t have a cell wall (no PD, no lipotycholic acid, etc - lost gram + characteristics)
  • Gram stain NEGATIVE - *PINK STAIN much like EUKaryotes b/c ONLY plasma membrane
  • Often PLEOMORPHIC - many diff. shapes (NOT all bacilli, cocci, or spirilla)
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18
Q

Why would we call Bacterial Phyla: Tenericutes, pleomorphic?

A

NO CELL WALL - no thick rigid barrier that’ll confer a morphological det to outside of cell
- therefore, A LOT of FLEXibility in the structure

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19
Q

Bacterial Phyla: Tenericutes

Example:

A 
Mycoplasma genitalium (sexually transmitted infection - STI)
- can be asymptomatic, should be tested (chlamydia, gonerila all cause STI's)
  • Common cause of urethritis (inflammation of urethra) and pelvic inflammatory disease (PID)
  • First free-living bacterium to have it’s genome sequenced

• One of the smallest genomes known at 500 kbp (vs E. coli has million base pairs)
- think: pick 30 page recipe book to recopy & understand entire vs. 500 pages

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20
Q

Mycoplasma genitalium

A
  • Common cause of urethritis and pelvic inflammatory disease
  • First free-living bacterium to have it’s genome sequenced
  • One of the smallest genomes known at 500 kbp
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21
Q

Describe process of STI

A

When you get an STI, the organism gets deposited in vagina (normally mucus plug blocks opening to uterus in cervix - but in periods where ovulation is about to happen, the MUCUS PLUG IS SHED), so bacterium comes into uterus & then enters in FT

OUTCOME: immune system activates (v. aggressive)

  • sees what shouldn’t be there & goes after organism, which does a lot of damage to wall of FT
  • replace damage tissue with scar tissue inside body
  • egg ovulates from FT & sperm can still come & do fertilization, but egg can’t fit b/c has become so narrow & inflexible b/c of scar tissue
  • if you get fertilization in FT (diploid cell), starts cleavage division (becomes blastula) - (ampulla - where sperm & egg unite, egg starts dividing since its fertilized & diploid)
  • wanted to implant in uterus where its flexible & has nutrients & blood supply, but natural tendency is to implant in FT - called ectopic pregnany (FT will NOT be hospitable to host baby so BURTS & that bacteria gets released in pelvic cavity & is often a lethal condition (bacteria in sterile sites, haemorrhage)
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22
Q

Bacterial Phyla: Actinobacteria

A

• Second phylum of Gram POSITIVE bacteria – HIGH GC Gram positives

  • meaning, within its genetic material, it’ll have a lot of C & G
  • triple H-bonding – if heated, will be more resistant (stable) based on DNA sequence
    • BUT, still have to have stability of PL bilayer & of protein structure
  • just b/c DNA is thermostable, it doesn’t mean much of how rest of cell can cope when faced with heat
  • Includes CORYNEFORM BACTERIA
  • Club-shaped morphology
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23
Q

Bacterial Phyla: Actinobacteria

Example (Coryneform Bacteria):

A

Corynebacterium diphtheriae
- club shaped

• Produces an EXOTOXIN that INHIBITS PROTEIN SYNTHESIS

  • toxins that are proteins (built inside) secreted to the outside of a bug, to do whatever its specific for
  • protein syn is a BIG DEAL - so inability to make proteins will be lethal to the cell

• Causes tissue death in the respiratory tract - diphtheria
- as respiratory cells become parasitized in this way, they start to die & get replaced by (scar tissue), PSEUDOMEMBRANE FORMATION - impedes breathing - difficulty doing gas exchange

• Can lead to death by suffocation

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24
Q

What would we describe the effects of exotoxin as? (seen in Corynebacterium diphtheriae)

A

BACTERIOCIDAL - b/c cell can’t survive

Produces an EXOTOXIN that INHIBITS PROTEIN SYNTHESIS

  • toxins that are proteins (built inside) secreted to the outside of a bug, to do whatever its specific for
  • protein syn is a BIG DEAL - so inability to make proteins will be lethal to the cell
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25
Q

DPT (Diptheria DPT (Diptheria Pertussis Tetanus) Tetanus) vs. DTaPertussis

A

DPT (Diptheria Pertussis Tetanus)
- this component created a lot of side effect –> led to ppl not wanting to get vaccine

*3 toxoid vaccines (look like a bacterial toxin, but NOT)
- priming immune system against multiple things all @ same time
- produce an immune response against toxoid
- then works against toxin
(LESS PPL GET, MORE EFFECTIVE)

DTaPertussis
- acellular
(MORE PPL GET, LESS EFFECTIVE AS A VACCINE (DOESN’T WORK AS WELL))

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26
Q

Bacterial Phyla: Actinobacteria

Mycobacteria

A

Mycobacteria have a modified Gram POSITIVE cell wall
• Layer of MYCOLIC ACIDS outside the peptidoglycan layer
• Makes them ACID-FAST
- need another way to get gram stain
- treatment will also have to be diff. (diff. antibiotic)

acid fast stain result:

  • pink = carbol fuschin
  • blue = methylene blue
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27
Q

Bacterial Phyla: Actinobacteria

Mycobacteria Example:

A
  • Mycobacterium tuberculosis
  • SLOW growing (~ 24 hr/gen)
  • can get a test (swab of sputum) but won’t see growth for a long period of time on a petri dish
  • but would do genetic analysis, chest X-ray, manto test etc., in meantime in order to make a (+) diagnosis

• Colonies can take weeks to form on agar
medium (for conclusive (+) diagnosis)

• Cause of tuberculosis – slow, fatal respiratory disease
* in active cases vs. latent infection (substantial amount of ppl can become active cases)

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28
Q

Bacterial Phyla: Filamentous Actinobacteria

A
  • Gram (+) - NOT ENDOSPORES
  • Hyphae & Mycelia
    • repro. spores - conidia
  • OBLIGATE AEROBES
  • in aerated soils – geosmins (give soil its earthy smell)
  • produce substances that kill or inhibit growth of other microbes - antibiotics
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29
Q

Bacterial Phyla: Filamentous Actinobacteria

Example

A
  • Streptomyces griseus
  • Produces streptomycin: BROAD spectrum protein synthesis INHIBITOR active AGAINST Gram NEGATIVE bacteria
  • widely used antibiotic
  • not just targeting 1 partic. species (ex: Mycobacterium tuberculus only targets 1 partic. species (v. narrow spectrum)
  • narrow spectrum in the sense that its active against gram - bacteria
  • NOT gram +
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30
Q

Which of the following are true (thioglycolyte broth)?

Obligate aerobe (growing at top)

a) Streptomyces griseus
b) a member of the bacteriodetes phylum such as Bacteriodes spp.
c) using fermentation to produce ATP
d) cannot produce enzymes to remove ROS

A

a) Streptomyces griseus CORRECT
- an ex of obligate aerobes

b) a member of the bacteriodetes phylum such as Bacteriodes spp.
- obligate ANAEROBES - tube would have it down at bottom (far from O2)

c) using fermentation to produce ATP
- organism in q is engaging with aerobic respiration - using O2 & cellular respiration
- NOT fermentation b/c it would’ve been far away from O2 & this is close to O2 so means it must be using O2

d) cannot produce enzymes to remove ROS
- can tolerate O2, therefore means you must be able to deal with the toxic forms that accumulate
- so would need enzymes
(only obligate anaerobes or microaerophiles don’t produce them - steer clear of O2)

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31
Q

Bacterial Phyla: Bacteroidetes

A

• Large, heterogeneous phylum of Gram NEGATIVE bacteria
• Aerobes and anaerobes
- diversity with respect to O2 utilization

• FEW unifying characteristics
- genetically makes sense to put them here, but aside from that, diff. to group based on physical features or phenotypes

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32
Q

Bacterial Phyla: Bacteroidetes

Example:

A

Bacteroides (genus) thetaiotaomicron
• STRICT ANAEROBE - poisoned by presence of O2 (can’t tolerate it)

• NUMERICALLY DOMINANT microbe in the human large intestine

  • even if you got a lot of species diversity (lot of diff. organisms present within large intestine that collectively create your community within environment)
  • these organisms will still be most abundant numerically

• PRODUCES ENZYMES to DEGRADE POLYSACCHARIDES, greatly increasing the variety of plant polymers that can be digested in the human gut
- expansion of what is able to be digested

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33
Q

If you were left on own & didn’t have this organism (Bacteroides thetaiotaomicron) present in envir., you…

A

wouldn’t have been able to digest this sugar
- just been an expansion of what it is your able to digest, simply b/c of the presence of the bacteroides

  • (like adding a gene for carb digestion to your genome - not directly within the cell, but the sense that within your body, you now have an ability that you didn’t simply b/c of the physical presence of this organism)
  • like teaming up with architect
34
Q

Bacterial Phyla: Chlamydiae

A
  • Gram NEGATIVE cell wall type, but LACK peptidoglycan
  • OBLIGATE INTRACELLULAR PARASITES
  • NOT free living & reason why we still have not grown this in a lab -> still don’t know how to grow/culture it
  • use genetic analysis instead
    • SOUNDS SIMILAR TO VIRUS - involves the need to live on inside of cell (comparable to virus, but has BACTERIAL properties)
35
Q

Bacterial Phyla: Chlamydiae

Unique life-cycle with two types of cells:

A
  1. ELEMENTARY BODY
    • Small dense cell, resists drying
    - packed with IC material

• Allows infection of new host cells
*- INFECTIOUS FORM - going into new cells

Once it gets into cell that was uninfected, not naive anymore, it’s actually infected
2. RETICULATE BODY - in cell; infecting & replicating (but they themselves aren’t infected)
• LARGER vegetative cells - means *METABOLICALLY ACTIVE - therefore, ATP production protein synthesis etc. (multiplying so need to be making energy & protein & producing DNA)
• Multiply inside an existing host
but
*• Are NOT infective

  • cell is infected but RB are unable to infect (need elementary bodies to go in & turn naive cell into an infected cell)
36
Q

Bacterial Phyla: Chlamydiae

Example:

A

Chlamydia trachomatis (causes STI’s)

causes:
• Trachoma: infection of the EYE
- common in children by close interaction & can be spread to parents (partic. mother)
• Causes SCARRING and BLINDNESS
- as you continue to become infected, outcome is scar tissue formation (eye lashes are changed & will rub on surfaces of eye every blink)
- bad - opp. to scar surface & is diff. for you to see (cloudy & opacity)
- surgery req. to correct

37
Q

Why would a mother/female have a higher incidence of Chlamydias trachomatis infection in certain geographical areas based on a social factor?

A

more engagement with children (resp. with more duties)

38
Q

Bacterial Phyla: Chlamydiae can cause…

A

PID (pelvic inflammatory disease)
- capacity to move up to the FT’s - same way it causes damage to eye when immune system is activated, it’ll cause damage to FT’s for that reason

39
Q

How do STI’s travel?

A

STI’s travel in GROUPS, based on MODE by which they SPREAD

  • person who’s showing signs/symptoms of 1 partic. STI’s, you assume that its likely they have others
  • so use treatment that provides coverage over more than 1 STI
40
Q

What would be a key characteristic for the type of treatment that you need for Chlamydiae, where is the organism living?

A

INSIDE YOUR CELL

  • drugs used to treat chlamydia b/c of this unique attribute in the sense that it’s not free living but is hiding out inside of your cytoplasm must have GOOD TISSUE PENETRATION (meaning if the antibiotic doesn’t actually get into tissue, into cell it won’t be effective choice)
  • therefore, only certain antibiotics can be used & b/c of this unique attribute of chlamydia & b/c you like to use drugs that target potential STI’s in case they’re there - you wanna make sure it finds chlamydia most importantly & then the others will be targeted as well
41
Q

Bacterial Phyla: Planctomycetes

A
  • DON’T HAVE GRAM +/GRAM - CELL ARRANGEMENT
  • PROTEIN CELL WALL LIKE ARCHAEA (lack PD)

• BUDDING and APPENDAGED bacteria

  • stuck to a surface
  • like how organisms need to be attached in order to be able to persist & stay inside the body
  • in this case, even in the envir. the planctomycetes need to produce the stalk to attach physically to its surroundings
  • PROTEIN STALK used for attachment
  • LACK peptidoglycan in the cell wall
  • SOME have MEMBRANE-BOUND compartments inside the cell
42
Q

Bacterial Phyla: Planctomycetes

Example

A

Some have membrane-bound compartments (& mem. bound nucleoid) inside the cell

Example: Gemmata obscuriglobus

  • has protein in cell wall like archaea (even though its a bacterium)
  • has mem. bound compartments in the cell (like Euk’s even though its a bacterium) - PRETENDING
  • produces pili for exchange of genetic info & flagella

• Nuceoid is surrounded by a true unit membrane
* - sounds like a Euk, even though its A PROK

43
Q

Bacterial Phyla: Cyanobacteria

A
  • pleomorphic, large (unicellular, filamentous or branching fil)
  • unicellular, BUT form heterocysts
    • specialized N fixing cells (ANOXIC envir. –> cannot handle O2)
  • oxygenic photosyn. (harvest energy from light & produce O2)
  • autotrophs - fix CO2 (Calvin Cycle - in cytoplasm)
  • photosyn in thylakoids (store pigments like chlorophyll - increase SA)
  • cell walls
    • PD
    • gram (-)
  • widely distri.
  • self-sufficient –> lowest nutritional req.
    • primary producers
44
Q

Bacterial Phyla: Cyanobacteria are photosynthetic. If they’re photosynthetic, what are they making as a result of classical photosynthesis?

A

making O2

  • enzymes resp. for N fixing process can’t handle O2 - so by compartmentalizing this process, you keep it away from O2 (benefit)
  • organism will be able to achieve both tasks (oxygenic photosynthesis but also N-fixation)
45
Q

What is cytoplasm analogous to if we consider endosymbiotic theory?

A

STROMA - fluid filled region in middle is gonna be where Calvin cycle occurs in chloroplast
- analogous to cytoplasm which is where it occurs in cyanobacterium

46
Q

If Cyanobacteria are N fixing, have abundant C in form of CO2 & abundant sunlight, what would limit their growth?

A

PHOSPHOROUS most often limiting

47
Q

Bacterial Phyla: Cyanobacteria

Example:

A

Prochlorococcus

• One of the most abundant organisms on Earth

  • b/c:
  • SELF-SUFFICIENT
  • can live salt water, fresh water, land

• Accounts for ~ HALF OF PHOTOSYNTHESIS in the World’s OCEANS

  • huge representation respo. for a lot with respect to ocean production (i.e. primary production in the ocean that supplies other organisms that live there with C that they can use to build their own cell structure)
    • any organism that’s a chemoorganotroph, this guy is supplying
48
Q

Bacterial Phyla: Cyanobacteria

Toxic & Cyanobacterial Blooms

A

*GROWS UNHINGED (P can limit but for most part) until a certain level where it will produce toxin

Toxic Blooms produce toxins that effect the nervous system, the liver, the skin, etc.

  • NEUROTOXIN - has tropism for nervous tissue (causes NS damage)
  • contrast with endotoxin which have tropism for intestine
  • contrast with cytotoxin which have general tropism for cell

Experimental Lakes Area (Ontario): Lake 305, unfertilized
- NO N/P added “balanced community/balanced ecosystem”

Lake 227: cyanobacterial bloom after addition of phosphate
Because many cyanobacteria fix N2,
phosphate imbalance alone cause their blooms - respon. b/c provides P –> *nothing to limit them b/c so self-sufficient
- fertilized - nothing to limit growth or success of the cyanobacteria - will continue b/c of addition of P growing & growing –> cyanobacterial bloom
- provides P

49
Q

Bacterial Phyla: Proteobacteria

A
  • Includes many of the most commonly encountered bacteria
  • MOST METABOLICALLY DIVERSE phylum: (can use any source of energy within this group)
  • Chemolithotrophs
  • Chemoorganotrophs
  • Phototrophs
  • FACULTATIVE organisms that can SWITCH from one metabolic lifestyle to another (*ADAPTABLE)
    • think: transition to online learning (adapts vs. non-adaptable)
  • dance around anything thrown their way in order to ensure succes
  • v. little will serve to inhibit them (b/c adaptable)

LOOK ON SLIDE 21
major metabolisms - avail & possible for the organism in group

chemolithotrophy - all inorganic but organism can use to fill their energy req.

50
Q

What would these sub classes (Proteobacterial Classes - based on unique characteristics, genetics etc.) be analogous to?

A

species that weren’t identical (but same species b/c >97% similarity)

  • put into strains
  • do this to make sense of large group
51
Q

Bacterial Phyla: Proteobacteria

Divided into 6 classes:

A

(allowing a large amount of diversity to be organized into diff. groups)

• Alpha-, Beta-, Gamma-, are well studied with many important species
- easy to grow in lab - feed diff. things for success

• Delta-, Epsilon- are smaller classes but with a broad range of phenotypes
- even though they’re collectively smaller, they have opp. to produce a large amount of diff. things that will provide success to organism (diff. enzymes, survive under diff. conditions etc.)

• Zetaproteobacteria has barely been studied with only one known species: Mariprofundus ferrooxydans

  • taking iron & subjecting it to oxidation & will release energy
  • Fe2+ –> Fe3+
  • energy released (oxidation)
52
Q

Bacterial Phyla: Proteobacteria

Alphaproteobacteria

A

• Includes pathogens and non-pathogens (provides a lot of benefit)

53
Q

Bacterial Phyla: Proteobacteria

Alphaproteobacteria

Example of a non-pathogen:

A

• Rhizobium leguminosarum

  • lives in nodules on plant root
  • plant passes sugar down & so the bacterium gets a nutrient source & C source
  • @ the same time, the rhizobium passes a utilizable form of N
  • 2 NH3 from N2
  • symbiotic relationship (+/+) b/c both members benefit
• Forms root nodules on legume plants
• Symbiotic relationship (+/+)
• Bacterium fixes nitrogen
into a bioavailable form
• Plant provides nutrients and a home for the bacteria
54
Q

If you removed the rhizobium from the root nodules, the outcome would be that…

A

the plant would be deficient in N (generally)
- organisms are dependent & req. it to make sure the plant is able to be strong & successful & have all organic molecules it req’s within the structure

55
Q

Bacterial Phyla: Proteobacteria

Alphaproteobacteria

Example of a pathogen:

A

• Rickettsia rickettsii
- mitochondria was thought to evolve from Rickettsia (endosymbiotic theory)

• OBLIGATE INTRACELLULAR PATHOGEN
- explains how it ended up inside of a cell to begin with - in order to evolve & become a mitochondrian

• CARRIED BY INSECTS and TRANSMITTED BY insect BITES
= vector based transmission

• CAUSES Rocky Mountain spotted fever

• PHYLOGENETICALLY Rickettsia is the CLOSEST RELATIVE TO the EUKARYOTIC MITOCHONDRION
- just like how cyanobacteria has evidence to suggest that it’s the chloroplast origin

56
Q

Bacterial Phyla: Proteobacteria

Betaproteobacteria

A

• METABOLICALLY DIVERSE

  • provides additional evidence to suggest that we shouldn’t use functional diversity to classify organisms
  • b/c just b/c they do 1 type of metabolism, doesn’t necessarily mean that they’ll all gonna do that type of metabolism

• SOME are PATHOGENS and SOME are NON- PATHOGENS

57
Q

Bacterial Phyla: Proteobacteria

Betaproteobacteria

Examples:

A

• Neisseria mucosa
- kinda like normal flora
• NON-PATHogenic commensal (no harm) of the human body: LIVES ON MUCOUS MEMBRANES (& has modes by which it can attach so it doesn’t get flushed)
- keeps harmful bact out of body
- probs provides benefit if only b/c of microbial antagonism; competition exclusion that keeps other harmful bact out of our body

• Neisseria gonorrhoeae
• PATHogenic: CAUSES GONORRHEA
- stick to mucoual sites to
- but add. characteristics allow opp. to cause disease
- in females it can cause PID (like mycoplasmic genitalia)
- transmitted by sexual mode (usually travel in packs)

58
Q

Bacterial Phyla: Proteobacteria

Gammaproteobacteria

A

• METABOLICALLY and ECOLOGICALLY DIVERSE
- expect a lot of metabolism & have ability to live in a lot of habitats

• MANY GROW WELL in the lab and have become important research models
- with basic nutrient requirements (as long as you provide them with some source of C & N etc.)

59
Q

Bacterial Phyla: Proteobacteria

Gammaproteobacteria

Examples: Escherichia coli

A

• Escherichia coli

• Gram negative, rod shaped, FACULTATIVE AEROBES (switch depending on if O2 is avail. to use aerobic or anaerobic metabolism)
• MOTILE by means of PERITRICHOUS FLAGELLA
- can swim from A –> B

• FERMENTS LACTOSE to a mixture of acids and alcohols

  • an ex of anaerobic metabolism
    • but get DIFF fermatative endproducts produced depending on mode of fermentation that the organism uses
  • can use DIFFERENTIAL growth media that will allow you opp. to enumerate the organism on a GM plate & use a pH indicator which will pick up the presence of acid (colour indicator that the organism is there)
  • if it’s not fermenting & producing acid, it won’t produce that pH rxn with the indicator & it will be diff. colour of colonies growing on the plate

• RESIDENT OF the LARGE INTESTINE of warm-blooded animals

  • us, cows, etc.
  • meaning it…

• Serves as an important INDICATOR OF FECAL CONTAMINATION
- ex: E. coli present in ground beef is an indication that fecal matter has been added accidently

60
Q

Bacterial Phyla: Proteobacteria

Gammaproteobacteria

Example Pseudomonas aeruginosa:

A

Pseudomonas aeruginosa

  • Gram (-), rod, motile; POLAR flagella
  • NON-lactose fermenter
  • RESISTANT to many antibiotics & disinfectants
  • OPPORTUNISTIC pathogen; COWARD (preys on weak) causes infection in immunocompromised patients
  • -> RT infections in cystic fibrosis patients
61
Q

Bacterial Phyla: Proteobacteria

Deltaproteobacteria

A

Contains many species with strange behavior

62
Q

Bacterial Phyla: Proteobacteria

Deltaproteobacteria

Example:

A

Myxococcus xanthus

• GLIDING MOTILITY

  • REQUIRES CONTACT constantly within a solid surface
  • CAN’T be free moving (not gonna swim from 1 location to another)
  • will find a surface, secrete slime & then glide over that surface or use protein attachments
  • LOT MORE RESTRICTED

• PREDATORY: RELEASES EXOENZYMES (toxic to organisms within immediate surroundings) to lyse other bacteria for nutrients

  • outcome: nutrients left over as a result of bacterial destruction can then be used for the purposes of nutrients
  • organism digested it & now has C, ATP source, supply of N (everything an organism needs to be able to support it’s own growth will be present there)

• WHEN STARVED (not a lot of nutrients avail) the cells MIGRATE TOGETHER to forms complex multicellular FRUITING BODIES
- has opp. to support 1 another (like a pop. - group of identical members of a species, inhabiting a certain area)
- close to 1 another - fairly organized structure
• Individual cells differentiate into MYXOSPORES for dispersal
- diff from endospores that protect against environmental extremes
- IMP. FOR REPRODUCTIVE DISPERSIAL (beneficial to organism)
- to allow it to move to a # of diff. locations so it won’t be stuck or isolated in 1 partic. region
- if it doesn’t have a lot of nutrients where it is, it’ll distribute itself in this protective structure & find other environments that might be located nearby that might provide them with protection

63
Q

Bacterial Phyla: Proteobacteria

Deltaproteobacteria

Example: Bdellovibrio bacteriovorus

A

Bdellovibrio bacteriovorus

  • vibrio - v-shaped (add. morphological feature to cocci, bacilla, spirochete, sprilla)
  • continues with the pattern of hunting other organisms
  • CURVED, HIGHLY MOTILE (FLAGELLA) PREDATOR of other Proteobacteria and Gram negative bacteria
  • PENETRATES the CELL WALL and MULTIPLES IN the PERIPLASM

• PARASITIC: uses macromolecules obtained directly from the host
+/-
- think: someone comes to your house & the person living there temporarily leaves groceries in yard
- they’ll go through grocery bag & take whatever they’ll like to satisfy themselves
- disadv. to you who intended to eat the food & spent money & effort

64
Q

Bacterial Phyla: Proteobacteria

Deltaproteobacteria

Example: Bdellovibrio bacteriovorus

CYCLE

A
  1. Bdellovibrio
    - free, motile
    - flagella
  2. Attachment
    - binds to prey
  3. Prey periplasmic space (gets in)
    - ABC transporters
    - nutrient accumulation site - b/c nutrients come in through the outer mem non-specifically using those porins
    - once organism accumulates within that region - there’s a lot of nutrients that starts there, that’ll eventually be taken in to the cytoplasm using ABC transporters & other transporters that have a high level of specificity
  4. Elongation of Bdellovibrio inside the bdelloplast
    - once it penetrates, it has the capacity to be able to go through reproduction in this region (40-60 mins)
    - prey cytoplasm
    - shrinks cytoplasm
    - organism is now bigger & occupying a greater amount of space
    - shrunk cell to facilitate its own reproduction
  5. Prey lysis (2.5-4 h postattachment)
    - gets released
  6. Release of progeny
65
Q

Bacterial Phyla: Proteobacteria

Epsilonproteobacteria

A
  • A SMALL class
  • Famous for a FEW MICROAEROPHILIC, SPIRILLUM shaped pathogens
  • req. O2 but are poison by it
  • localize themselves within a portion of the tube that’ll allow them the best opp./chance for survival
66
Q

Bacterial Phyla: Proteobacteria

Epsilonproteobacteria

Example:

A

Campylobacter jejuni

  • Frequently transmitted in UNDER-COOKED CHICKEN
  • One of the most COMMON CAUSES of FOOD-BORNE ILLNESS

• CAUSES GASTROENTERITIS (stomach, intestine inflammation) and BLOOD DIARRHEA
- inflammatory response results in tissue damage, which in turn leads to bloody diarrhea

67
Q

Bacterial Phyla: Firmicutes

A

• One of two phyla with Gram positive cell walls

    • LOW GC Gram positives
    • DNA WOULD BE LESS THERMOSTABLE (easier to denature DNA that has fewer H-bonds)
  • but not hyperthermophilic so it wouldn’t matter

• Includes lactic acid bacteria

    • Aerotolerant anaerobes that produce lactic acid as an end product of fermentation (ONLY)
  • tolerate O2 - but organism can’t use it b/c it doesn’t have an ETC (meaning only mode of energy prod. will be fermentation)
  • since organism only have fermentation (diff. varieties), but lactic acid bact specifically produce lactic acid waste which acidifies things
  • Includes many NON-lactic acid bacteria
  • Endospore forming Firmicutes
68
Q

Bacterial Phyla: Firmicutes

LACTIC Acid Bacteria Examples

A

Aerotolerant anaerobes that produce lactic acid as an end product of fermentation

• Lactobacillus delbrueckii

  • part of starter culture
  • add it to the milk & lactobacillus (concerned for its own well-being, will start to metabolize)
  • outcome: going to be producing lactic acid as waste product, acidifies milk which causes change in texture (proteins start to unraval, chemical contribution will be diff)
  • tanginess comes from acidity of this accumulation
  • end product =
  • YOGURT PRODUCTION
  • also present in female vaginal envir.
  • vaginal chemistry changes (after puberty it starts to accumulate glycogen which selects for certain flora including lactobacillus)
  • idea is to protect against STI’s b/c its now in anticipation of it becoming an active area for repro. & as a conseq. you end up with acidification to a pH ~4.5 from the lactobacillus (sperm need to be protective against)

• Streptococcus pyogenes
- Cause of strep throat, scarlet fever and the flesh eating disease

69
Q

How is it that you can develop strep throat from Streptococcus pyogenes, but also develop scarlet fever or flesh eating disease?

A
  • DIFFERENCE IN STRAIN
  • diff genetics that they harbour in their host cell, that allows them the opp. to produce toxin
  • those toxins & exoenzymes are able to cut through human tissue
  • they’ll produce an enzyme like collaganease which will cut collagen & promote spread through CT’s to other regions on the inside of the body
    • if the organism can make those enzymes, it can do things like flesh eating disease, if the organism can’t then it might still have genetic similarity to be streptococcus pyrogenes but won’t be present all of the time
  • need to consider are own suceptability - if not in good state of health when picked up infection then outcome is you can suffer from more severe consequences b/c you’re vulnerable
70
Q

Bacterial Phyla: Firmicutes
• Includes many non-lactic acid bacteria (diff. based on O2 req)

Example: Staphylococcus aureus

A

• FACULTATIVE AEROBE that forms characteristic grape-like clusters
• Lives ON SKIN (normal member of your FLORA)
• HALOTOLERANT
- b/c skin has b/t 3-5% NaCl [ ] (high component to 0.9% ECF)
- indicates halotolerant (opp. to hold water content as it lives on skin)
- Can be isolated using media with HIGH NaCl (Ex: mannitol salt agar): produces acids-YELLOW
- selective - growing b/c it can tolerate salt, other organism who can’t, will not
- & can add diff. indicators, such that this organism which produces acid will react with pH indicator to produce a yellow colouration

• Frequent cause of NOSOCOMIAL infections

  • organism is acquired THROUGH HOSPITALIZATION
  • tend to prey on weak ppl b/c it understands there’s vulnerability present there
  • found a lot within INNER NOSTRIL (in a lot of ppl, but not everyone & TRANSIENT (comes & goes)
  • MRSA is resistant to a lot of antibiotics
  • imp. b/c if spread in hospital setting there isn’t much avail to treat the organism
71
Q

MRSA

A
  • MRSA is resistant to a lot of antibiotics

- imp. b/c if spread in hospital setting there isn’t much avail to treat the organism

72
Q

Bacterial Phyla: Firmicutes
• Includes many non-lactic acid bacteria (diff. based on O2 req)

Example: Staphylococcus epidermidis

A

• Normal commensal on skin

• Can be distinguished on mannitol salts agar: NO acid production-PINK
- will produce a diff colour - still grow b/c its a commensal on skin & can handle presence of salt but can’t produce acid through metabolism (can be treated with antibiotic that works against it)

73
Q

Bacterial Phyla: Firmicutes

Endospore forming Firmicutes

A

make sense b/c its a Gram + group

• The best studied genera of endospore formers are:
• Bacillus – aerobic endospore formers (req’s O2)
• Clostridium – strictly anaerobic endospore formers
- * in airs that are not well aerated b/c O2 will be lethal to them so they have to find like anaerobic pockets to thrive

  • shows no correlation b/c O2 req’s & types of organism or spore formation they have

• Endospore formers are found primarily in SOIL

• Most are NON-PATHogenic (ex) saprophytic soil organisms
- living naturally in soil, unable to cause disease
• Some can be dangerous pathogens
- but if they find conditions that’ll be hospitable to their survival, they’ll gladly have the opp to go on & form an endospore to support they’re ability to survive during that time until they find conditions that’ll be more favourable for their survival

74
Q

Bacterial Phyla: Firmicutes

Example: Bacillus subtilis

A

(harmless)

Aerobic endospore forming

• Important lab bacterium used as a model for:
- easy to grow & good if we’re looking for a spore to study
• GRAM POSITIVE cell structure and genetics
• Cell division and differentiation into endospores

75
Q

Bacillus anthracis species

A

causes anthrax (harmful)

  • form spores
  • bioterrism threat - can be distributed & diseminated to individuals in a spore form which then goes into body to become vegetative & causes serious often life threatening disease
76
Q

Bacterial Phyla: Firmicutes

Example: Clostridium botulinum

A

Strictly anaerobic endospore forming

• STRICT ANAEROBE with a fermentative metabolism
- specifically chose fermentation

• Lives in tiny ANOXIC POCKETS in the SOIL
- any aerated parts will be devastating b/c it can’t produce enzymes to be able to tolerate that O2

• Secretes a variety of EXOENZYMES to DEGRADE PLANT MATERIAL

  • go on & digest carb
  • outcome: nutrients are now monomeric (small & easily absorbed)
  • organism can now pick them up to interior of body which allows them the opp. to use that nutrient to support their own growth & metabolism

• Can also grow in ANAEROBIC CANNED FOODS

• Produces a deadly neurotoxin - *PRODUCES BOTOX - v. potent neurotoxin that interferes with activity @ NMJ - can’t tell a partic. cell (muscle fiber) to contract - FLACCID PARALYSIS
- bad b/c diaphragm is part of 2 main respiratory muscles & if it can’t contract, you sufficate to death (therefore, botox & tetanus toxic are lethal when RELEASED SYSTEMICALLY opposed to locally)
• When consumed causes botulism

• Proper canning procedures must either:
• Reach temp above 120°C to destroy endospores
OR
• Include enough acid or sugar to prevent germination
- make sure envir is HYPERTONIC ENOUGH, that the cell will not have enough water to become vegetative to stay quite in a spore or to add acid so the pH isn’t okay for the organism

77
Q

Hyperthermophilic Bacteria

A

most classificed as thermophilic b/c they like hot temps but more intermediate than excessively high

There are several deeply branching phyla (form an evolutionary standpoint, they go FAR down in history) that consist of hyperthermophilic bacteria
• Suggests that the last universal common ancestor (LUCA) may have been a hyperthermophile
- makes sense b/c conditions in early earth were v. hot
- so the organisms that were able to evolve under those conditions would’ve needed to be able to handle that excessively high temp

78
Q

Hyperthermophilic/Thermophiles also Bacteria

Two famous species:

A
  1. Thermus aquaticus

2. Deinococcus radiodurans

79
Q

Hyperthermophilic/Thermophiles also Bacteria

  1. Thermus aquaticus
A

• A thermophilic chemoorganoheterotroph
- likes high temp & uses organic chemicals for energy & uses organic C to satisfy its C req.

• Source of temperature stable enzymes: Taq DNA polymerase

    • use in order to do PCR
  • take DNA & subject it to high temp & that serves to separate the strands (like how we’d use enzymes to accomplish this)
  • allows opp. for primers to adhere & Taq polymerase elongates DNA, in order to produce 2 copies of DNA from what started with 1
  • then high temp separates them with a thermocycler (opens it up, lets Taq polymerase synthesize using primers avail. that you provided in the system) & continues again & again
  • outcome: amplifying the genetic material that you have the opp. to make use of (study, identification of infectious material etc.)
  • point is it can handle high temp which you need to use to separate DNA strands if its outside a cell
  • inside a cell, normal enzymes can accomplish this under cellular temp (37.5 degrees celsius)
  • Allows DNA synthesis reactions in the lab to be carried out quickly at high temperatures
  • An essential tool for polymerase chain reaction (PCR)
80
Q

Hyperthermophilic/Thermophiles also Bacteria

  1. Deinococcus radiodurans
A

• EXTREMELY RESISTANT TO RADIATION

  • Highly effective DNA repair mechanisms (allow it to be able to accomplish this)
  • as there DNA experience from things like radiation, the organism can go through & make changes according to where those mutations have been introduced & then DNA’s back to normal
  • having this sufficient repair mech. makes the organism more or less invincible to normal radiation damage

• Forms PAIRS or TETRADS

  • in doing so, have power in #’s & that’s when they can start repair process
  • think: when stressed, better with others
  • In RESPONSE TO massive DNA DAMAGE NUCLEOIDS from TWO cells CAN FUSE to facilitate repair
  • Has a GRAM NEGATIVE cell wall type BUT STAINS Gram POSITIVE because of THICK peptidoglycan
81
Q

Hyperthermophilic/Thermophiles also Bacteria

  1. Deinococcus radiodurans

Why would it have a thick layer of peptidoglycan?

A

more resistant - got a sort of cage protection outside the cell that’s thicker & more capable

Microbiology 1 (15 decks)

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