Lecture #7 - Prokaryotic Diversity INTRO & PART I BACTERIAL DIVERSITY Flashcards
Two ways to describe microbial diversity:
- Phylogenetic diversity
2. Functional diversity
Phylogenetic diversity
- 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
- Phylogenetic diversity
The RED DOTS represent the…
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
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
BACTERIAL
ARCHAEAL
EUKARYOTIC
What does…
The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic super groups
show us?
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
- Functional diversity
- Groups microbes based on the activities they carry out
* Some functions appear to be performed in a single phylum only
Functional diversity
Groups microbes based on the activities they carry out (with ex)
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
Where does O2 in photosyn. come from, what do you split?
If something is anoxygenic, what do you think about the e- donor?
SPLIT H20
not H20
- H2S - produce S compound rather than O2
What does Functional Diversity show us?
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
Functional diversity
Some functions appear to be performed in a single phylum only (with ex)
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
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…)
ANOXYGENIC PHOTOTROPHY
OXYGENIC PHOTOTROPHY
see it just within 1 partic. group
Most prokaryotes cannot be cultured in the lab (yet)
Some phyla…
Some are known only from…
- 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
Type Species have…
organisms of interest (well studied)
- we grow, study & identify
16S rRNA Gene Sequences have…
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
Most phyla will contain ____ ____
MULTIPLE GENERA
- meaning not just genus mycobacterium
for ex:
- will be other genera found within the category
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?
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
Bacterial Phyla: Tenericutes
- 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)
Why would we call Bacterial Phyla: Tenericutes, pleomorphic?
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
Bacterial Phyla: Tenericutes
Example:
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
Mycoplasma genitalium
- 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
Describe process of STI
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)
Bacterial Phyla: Actinobacteria
• 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
Bacterial Phyla: Actinobacteria
Example (Coryneform Bacteria):
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
What would we describe the effects of exotoxin as? (seen in Corynebacterium diphtheriae)
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
DPT (Diptheria DPT (Diptheria Pertussis Tetanus) Tetanus) vs. DTaPertussis
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))
Bacterial Phyla: Actinobacteria
Mycobacteria
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
Bacterial Phyla: Actinobacteria
Mycobacteria Example:
- 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)
Bacterial Phyla: Filamentous Actinobacteria
- 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
Bacterial Phyla: Filamentous Actinobacteria
Example
- 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 +
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) 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)
Bacterial Phyla: Bacteroidetes
• 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
Bacterial Phyla: Bacteroidetes
Example:
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