Download Currenty we have three DOMAINS Who are these organisms

Currenty we have three DOMAINS
Who are these organisms?
Prokaryotes here are….?
Bacteria
Archaea
Common ancestor
of all species living
today
Eukarya
We are going to be very bad biologists and lump
Archaea and Bacteria together and talk about them
as if they are very similar.
Figure 24.18
Euryarchaeotes
Crenarchaeotes
UNIVERSAL
ANCESTOR
Nanoarchaeotes
Proteobacteria
Bacteria
Spirochetes
Cyanobacteria
Gram-positive
bacteria
Domain Bacteria
Chlamydias
Prokaryotes
Archaea
Domain Archaea
Korarchaeotes
Domain
Eukarya
Eukaryotes
Figure 24.18
Euryarchaeotes
Crenarchaeotes
UNIVERSAL
ANCESTOR
Nanoarchaeotes
Domain Archaea
Korarchaeotes
Domain
Eukarya
Eukaryotes
Proteobacteria
Spirochetes
Cyanobacteria
Gram-positive
bacteria
Domain Bacteria
Chlamydias
3 Domains? 2 Domains?
Proceedings National Academy of Sciences 2015 May
26;112(21):6670-5. doi: 10.1073/pnas.1420858112. Epub 2015
May 11.
The two-domain tree of life is linked to a new root for the
Archaea.
root of the Archaea that lies within the Euryarchaeota, challenging
the traditional topology of the archaeal tree. Therefore, if we are
to embrace an archaeal origin for eukaryotes, our view of the
evolution of the third domain of life will have to be profoundly
reconsidered, as will many areas of investigation aimed at
inferring ancestral characteristics of early life and Earth.
Precambrian (Evolution of life to 500mya)
Paleozoic (500-250mya)
Mesozoic (250-about 65mya)
Cenozoic (65mya-present)
Precambrian (Evolution of life to 500mya)
Evolution of Prokaryotes (when?)
TODAY we will talk about diversity of
Prokaryotes around on earth today!
Evolution of Eukaryotes
Paleozoic
Evolution of lots of bigger things…
Mesozoic
Dinosaurs and lots of other things…
Cenozoic
Evolution of many seed plants and flowering
plants
Evolution of mammals
PROKARYOTES are Everywhere!
(Remember we are loosely grouping Bacteria and
Archaea here)
500 species in mouth (300 described and named)
Total number of bacterial cells in/on the human host
out-number host cells by at least 100-fold.
In the gut alone, the bacterial population is ~ 100
trillion and is composed of between 500 and 1,000
different species
(http://www.nature.com/ajgsup/journal/v1/n1/pdf/ajgsup20126a.pdf)
8-13km=Upper Troposphere
Microbiome of the upper troposphere: Species composition and
prevalence, effects of tropical storms, and atmospheric implications
( Science Magazine-January 2013)
……airborne microorganisms above the oceans remain essentially
uncharacterized, as most work to date is restricted to samples taken near
the Earth’s surface. Here we report on the microbiome of low- and
high-altitude air masses sampled ……before, during, and after two
major tropical hurricanes, Earl and Karl. Quantitative PCR and
microscopy revealed that viable bacterial cells represented on
average around 20% of the total …... The samples from the two
hurricanes were characterized by significantly different bacterial
communities, revealing that hurricanes aerosolize a large amount of
new cells. Nonetheless, 17 bacterial taxa, ….were found in all samples,
indicating that these organisms possess traits that allow survival in the
troposphere. The findings presented here suggest that the microbiome is
a dynamic and underappreciated aspect of the upper troposphere with
potentially important impacts on the hydrological cycle, clouds, and
Extremely important!
Some nasty…
• During 14th c Black Death or Bubonic plague killed 25%
of population..
(other diseases tuberculosis, cholera, Lyme etc )
But most are beneficial…..
• Mutualisms- generate nutrients that we need in our gut
• Nutrient cycling-decomposers..
Archaea
Thermophiles
Halophiles
Methanogens
https://www.uni-due.de/biofilm-centre/archaea/
Thermophiles..
•  The current record is …..Pyrodictium occultum,
survived 121 C (250 F) for an hour.
•  Some living at 170 C (338 F) around volcanic vents
in ocean (J. Parkes).
•  Early life on Earth –hyperthermophile?
Extreme Halophiles
• Tolerate salt concentrations
exceeding 15%
• Most are photosynthetic
autotrophs but not using
chlorophyll
• Use bacteriorhodopsin
(which uses all light except
for purple, making the cells
appear purple).
Methanogens-common in many areas
Release methane
Why do we hear about methane these days?
Anaerobic
Wetland soils, bottom of lakes
In gut of cattle, termites and humans…
In sewage treatment facilities
Methanogens in Human Health and Disease
Mark Pimentel MD1, et al. (2012)1GI Motility Program, Cedars-Sinai
Medical Center, Los Angeles, California, USA
There is growing evidence that host/microbial interactions within the gut can have a profound
impact on human health and disease; in fact, the intestinal microflora have been shown to
influence the innate physiology, biochemistry, immunology, maturation of the vasculature, and
gene expression in a host. Although most research has focused on gut bacteria, current
evidence suggests that the Archaea—an ancient domain of single-celled organisms—are
resident within the gut in high numbers, and have direct and indirect effects on the host.
In particular, the methanogens are an essential component of luminal intestinal microbial
ecosystems. Methanogens oxidize hydrogen to produce methane and ensure more complete
fermentation of carbohydrate substrates, leading to higher production and adsorption of shortchain fatty acids, which may lead to obesity. Methane, the key product of carbohydrate
fermentation by the methanogens, has long been thought to produce no ill effects in humans
aside from gaseous distention. However, recent evidence has linked methane production to
the pathogenesis of constipation and irritable bowel syndrome (IBS), as well as obesity. In
particular, a significant percentage of patients with IBS and constipation excrete methane,
suggesting an overabundance of methanogenic archaea in their gut. Methane by itself may
influence intestinal transit and pH and facilitate development of constipation. If methane has a
direct or indirect effect on intestinal transit, attempting to manipulate methanogenic flora may
serve as a novel therapeutic option. Thus, understanding methanogens and their role in gut
function/dysfunction is vital to our understanding of human health and disease.
Behavior
1.  Getting around..
Flagellum or flagella
Analogous or homologous?
Secrete mucous (chemicals-ooze around)
Figure 24.10
Flagellum
Filament
Hook
Motor
Cell wall
Plasma
membrane
Rod
Peptidoglycan
layer
20 nm
Fimbriae?
Gonorrhea bacterium uses these
2. Show photo, chemo, geotaxis.
3. Endospores-packages chromosome in tough
coat (Anthrax)
4. Bacteriocins
chemical “weapons” that kill or inhibit other bacteria
Galvez A, Lopez RL, Abriouel H, Valdivia E, Omar NB.
Crit Rev Biotechnol. 2008;28(2):125-52.
Area de Microbiologia, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain. [email protected]
Bacteriocins are antimicrobial peptides or proteins produced by
strains of diverse bacterial species. The antimicrobial activity of
this group of natural substances against foodborne pathogenic, as
well as spoilage bacteria, has raised considerable interest for their
application in food preservation. Application of bacteriocins may
help reduce the use of chemical preservatives and/or the intensity of heat and
other physical treatments, satisfying the demands of consumers for foods that are fresh tasting, ready to eat, and lightly
preserved. In recent years, considerable effort has been made to develop food applications for many different bacteriocins
and bacteriocinogenic strains. Depending on the raw materials, processing conditions, distribution, and consumption, the
different types of foods offer a great variety of scenarios where food poisoning, pathogenic, or spoilage bacteria may
proliferate. Therefore, the effectiveness of bacteriocins requires careful testing in the food systems for which they are
intended to be applied against the selected target bacteria. This and other issues on application of bacteriocins in foods of
dairy, meat, seafood, and vegetable origins are addressed in this review.
5. Quorum sensing
Release and detect chemical pheromones to gauge
their population density
When lots of neighbors (a quorum) a group behavior is
triggered …..
bioluminesce
attack
Bacterium that causes Cholera does this
6. Individually, in strings, small clumps and in
colonies-Biofilms!
Typically multispecies mats stuck to a solid surface.
Harmful in some cases (Cystic fibrosis).
Kolenbrander, P. Andersen, R. Blehert, D. Palmer, R. Microbiol Mol Biol Rev. 2002 September;
66(3): 486–505.
Communication among Oral Bacteria
Development of the oral microbial community involves competition as well
as cooperation among the 500 species that compose this community.
Sequential changes in populations of bacteria associated with tooth
eruption as well as with caries development and periodontal disease states
are known.
Temporal changes in populations of bacteria on tooth surfaces after
professional cleaning are ordered and sequential. Such sequential changes
must occur through attachment and growth of different bacterial species.
With the attachment of each new cell type, a nascent surface is presented
for the attachment of other kinds of bacteria, resulting in a progression of
nascent surfaces and concomitant changes in species diversity .
Such coordination indicates communication. In the absence of
communication, these orderly changes would be random. Due to the
dynamics of growth and adherence, the bacterial populations in the oral
cavity are constantly changing, even during the intervals between normal
daily oral hygiene treatments. It is unlikely that the various species within
oral biofilms function as independent, discrete constituents; rather, these
organisms function as a coordinated community that uses intra- and
interspecies communication.
7. Reproduction
Binary fission-what is that?
No sexual reproduction (a Eukaryotic thing)
So where does new genetic variation come from?
mutation
(obviously Eukaryotes experience mutations too)
In addition to mutation there are other “styles”
of recombination (mixing genomes)
Conjugation-use pili to pull each other
together
Get together share a plasmid
Transformation
Pick up “naked DNA”
Transduction
Phage infection (bacteriophages)
All of these processes are…
Lateral Gene Transfer…
Also called Horizontal gene transfer…
So this is not like us…… we have vertical
transmission!
8. Genome
1/1000 as much DNA as eukaryotes
• One double stranded circular DNA molecule
• Additional PLASMIDS
• These two parts replicate (make copies of
themselves) independently
Figure 24.12
Chromosome
Plasmids
Ruptured E. coli
1 µm
9. Nutrition (focus on energy source)
Actually just know that they are photosynthetic (autotrophs), able to
extract energy from inorganic deep sea vent gasses (like hydrogen
sulfide) and eat things (heterotrophic like us)!
There are some cool things in this table but probably too much for us
right now!
10. Nutrient Cycling
Elements move between biological and physical
parts of ecosystems
“Legumes add nitrogen to the soil”
Rhizobium species fix nitrogen (each legume may
have its own).
Uptake of K by plants (mg)
Even non-legumes do better in soils with some
strains of bacteria added
1.0
0.8
0.6
0.4
0.2
0
Figure 24.22
Seedlings growing in the lab
No
Strain 1 Strain 2 Strain 3
bacteria
Soil treatment
11. Humans…..
• Many are mutualistic
(vitamins in gut)
• Many are commensal
(neither hurt nor harm us)
• Others are parasitic
(neg. effects on us-Lyme disease,
Salmonella-”food poisoning”)
Normal flora-keep out disease causing bacteria
What about E. coli….
Text- strain 0157:H7
About ¼ of its genes came in through transduction as compared to
non pathogenic strain.
Which is? (phage)
These genes code for adhesive fimbraie that help it stick to your gut
wall.
Shiga toxin-producing Escherichia coli O26
Random addition #1 Gram staining..
Purple positive (have larger quantities of
peptidoglycan in cell wall-considered simpler)
Gram negative pink (more complex outer
membrane-more dangerous -more resistant to
antibiotics)
Random addition #2 The largest prokaryote, next to
a fruit fly-almost 1mm in diameter.
Sulfur Pearl (Thiomargarita namibiensis) from
Namibia, inhabits the sediments along the west coast
of Africa. (microbe garden website)
Random addition #3 Bloom of cyanobacteria
MN Pollution Control Agency
Severe blue-green algal blooms typically occur on lakes with
poor water quality (high in nutrients), and look like green
paint, pea soup, or a thick green cake (see photo gallery
below for examples). HAB often result in extremely low
water clarity (less than 1 foot). There is no visual way to
predict the toxicity of an algal bloom
Random addition #4
We use these organisms-Bioremediation!
Random addition #5 Mutualism: bacterial
“headlights”
Random addition #6 tubeworms !
• no mouths, no stomachs, and no intestines
• bodies house billions of bacteria that feed
them
(convert hydrogen sulfide
from the hydrothermal
vents into molecules that
serve as usable nutrients)
• eight feet long