A.  The early life and the Diversification of Prokaryotes (Ch24) continued….

What topics have we covered so far... We still need to talk about...

What did we used to think? (you might remember I drew a sketch on the board)

Bacteria

Common ancestor of all species living today

Archaea

Eukarya

Currenty we have three DOMAINS Who are these organisms?Who are the Prokaryotes in this phylogeny….?

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

UNIVERSAL ANCESTOR

Dom

ain Eukarya

Gram-positive bacteria

Cyanobacteria

Spirochetes

Chlamydias

Proteobacteria

Nanoarchaeotes

Crenarchaeotes

Euryarchaeotes

Korarchaeotes

Eukaryotes

Dom

ain Archaea

Dom

ain Bacteria

Archaea

Bacteria

Prokaryotes

Figure 24.18

UNIVERSAL ANCESTOR

Dom

ain Eukarya

Gram-positive bacteria

Cyanobacteria

Spirochetes

Chlamydias

Proteobacteria

Nanoarchaeotes

Crenarchaeotes

Euryarchaeotes

Korarchaeotes

Eukaryotes

Dom

ain Archaea

Dom

ain Bacteria

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.

It currently appears that the “root of the Archaea … 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.

Bacteria

Common ancestor of all species living today

Archaea

Eukarya

Currenty we have three DOMAINS Who are these organisms?Who are the Prokaryotes in this phylogeny….?

We are going to be very bad biologists and lump Archaea and Bacteria together and talk about them as if they are very similar.

TODAY we will talk about diversity of Prokaryotes around on earth today!

Archaea Thermophiles

HalophilesMethanogens

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 DiseaseMark Pimentel MD1, et al. (2012)1GI Motility Program, Cedars-Sinai Medical Center, Los Angeles, California, USAThere 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 short-chain 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.

Bacteria

Bacteria are everywhere

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 500 and 1,000 different species (http://www.nature.com/ajgsup/journal/v1/n1/pdf/ajgsup20126a.pdf)

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..

Behavior

1.  Getting around..

Flagellum or flagella

Analogous or homologous?

Secrete mucous (chemicals-ooze around)

Figure 24.10

Flagellum

Filament 20 nm

Hook Motor Cell wall

Rod Peptidoglycan layer

Plasma membrane

These are probably not flagella but fimbriaeBacterium that causes gonorrhea uses these to stick to tissues

2. Show photo, chemo, geotaxis.

3. Endospores-packages chromosome in tough coat (Anthrax)

Monique, Mehek, and Tess

Bacterial Adaptation● The water inside of a bacterial cell can act as a gel, solid, or liquid● Spores can intentionally freeze and immobilize water○ DNA is preserved○ Reproduction can

continuehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187170/

http://www.manchester.ac.uk/discover/news/scientists-discover-hazardous-waste-eating-bacteria/

4. Bacteriocinschemical “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. agalvez@ujaen.es

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 …..

bioluminesceattack

Bacterium that causes Cholera does this

Annalise, Danielle, Kellyhttps://owlcation.com/stem/Unusual-Bacteria-Strange-Facts-About-Fascinating-Microbes

Bacteria can communicate with each other and coordinate their actions. Some bacteria can also survive extreme environmental conditions that would be fatal to human

● Halophilic bacteria live in salty environments● Salinibacter ruber is a rod-shaped, orange-red bacterium that grows best when it's living

in ponds that contain 20% to 30% salt. (Seawater contains about 3.5% salt by weight.)

Bacteria Communication with Eukaryotic Cells

●  http://science.sciencemag.org/content/358/6359/77.6●  http://discovermagazine.com/2008/dec/28-20-things-you-didn2019t-know-about-bacteria

Bacteria communicate with host by excreting small molecules that a human cell can receive

Can alter glucose metabolism in a similar way as diabetes treatment

140 genesTested on mice, mice without these bacteria need to eat 40% more food if they didn’t have these bacteria

Cameron, Hunter, Jack, Olaf

6. Individually, in strings, small clumps and in colonies-Biofilms!Typically multispecies mats stuck to a solid surface.

Harmful in some cases (Cystic fibrosis).

Communication among Oral Bacteria Kolenbrander, P. Andersen, R. Blehert, D. Palmer, R. Microbiol Mol Biol Rev. 2002 September; 66(3): 486–505.

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. ReproductionBinary 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

TransformationPick up “naked DNA”

TransductionPhage infection (bacteriophages)

All of these processes are…

Lateral Gene Transfer…

Also called Horizontal Gene Gransfer (HGT)…

So this is not like us…… we have vertical transmission!

What about E. coli….Text covers strain 0157:H7 About ¼ of its genes came in through transduction as compared to non pathogenic strain.Transduction is? (phage) These genes code for (make) adhesive fimbraie that help it stick to your gut wall.

Shiga toxin-producing Escherichia coli O26

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

Plasmids

1 µm

Chromosome

Ruptured E. coli

9. Nutrition (focus on energy source)Actually just know that…•  Some are photosynthetic (are autotrophs), •  Some are able to extract energy from inorganic deep sea vent

gasses (like hydrogen sulfide)•  Some eat things (heterotrophic like us)!There are some cool things in this table but I am not going to focus on it right now!

Kind of like Plants

Kind of like Us Animals

Getting energy from inorganic chemicals but building their carbon bodies with CO2 etc..

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).

Figure 24.22

Seedlings growing in the lab

Soil treatment

Upt

ake

of K

by

plan

ts (m

g)

Strain 1 Strain 2 Strain 3 No bacteria

1.0

0.8

0.6

0.4

0.2

0

Even non-legumes do better in soils with some strains of bacteria added

11. Humans…..

• Many are mutualistic

(vitamins in gut)

• Many are commensal

(neither hurt nor harm us)

• Others are parasitic

(neg. effects on us)

Ex. Lyme disease, Ex. Salmonella-”food poisoning”

Normal flora-keep out disease causing bacteria!

The following slides also have some interesting information, definitely look over.

You should have a good understanding of the amazing abilities of bacteria (and archaea)!

Bacteria Radiation Resistance

-Geobacter thrive where there is radiation in the soil, so scientists working to clean up the Chernobyl use them to clean up the soil. When the bacteria intake metals, they produce electricity and then attach the extra electrons to those metals, which makes the metals less soluble and so removes the uranium from the groundwater.

-Deinococcus radiodurans is an extremophilic bacteria, which is cool because it is super resistant to acidic, cold, dehydrated, and vacuum like environments, in addition to being one of the most resistant bacteria to ionizing radiation. It also is able to repair single and double stranded DNA, and it has been used to study how cell death correlates with radiation-induced protein damage, rather than DNA damage, in both robust and standard species

Hannah Haglund, Margot, Maggie

Stephanie, Annie, LailaGeobacter Metallireducens●  Rod-shaped and gram-negative●  Conductive pili●  Anaerobic respiration

○  Acetate oxidation by reducing metals like iron, manganese, plutonium, uranium●  Geobacter species were the only known source of protein nanowires. Protein nanowires are

useful in the conversion of wastes to methane and electricity.●  Geobacter metallireducens, was the first organism found to oxidize organic compounds to

carbon dioxide with iron oxide as the electron acceptor. In other words, Geobacter metallireducens gains its energy by using iron oxide (an abundant rust-like mineral in soils and sediments) in the same way that humans use oxygen.

●  Geobacter species can destroy petroleum contaminants in polluted groundwater by oxidizing these compounds to harmless carbon dioxide and can remove radioactive metal contaminants from groundwater.

●  Metal-breathing microbes: rely on dissolved metals like we do with oxygen

Lucia, Jiyayi, and Poonam https://www.newyorker.com/magazine/2015/12/07/bacteria-on-the-brain

+ Enterobacter aerogenes (fecal bacteria) + Is it ethical? This protocol was not tested in a laboratory & not approved by the Food and Drug Administration… + The bacteria infect the bone flap

+  Tumor cells are killed by bacterial infection + Glioblastoma tumors

+ Malignant tumor affecting +  the brain or spine

Emily and Allie●  In Death Valley, bacteria found trapped

within the fluid filled pockets in salt crystals.●  The bacteria found was 34,000 years old.●  The bacteria was considered to be in a sort

of hibernation state.●  They believed they were able to live 34,000

years because they were trapped with algae called Dunaliella that could have acted as their food source.

http://www.dailymail.co.uk/sciencetech/article-1347528/The-34-000-year-old-bacteria-thats-alive.html

Bridget, Sydney, Boithatelo, Brandon

Some Civil War soldiers had wounds that glowed in the dark because of a bioluminescent bacteria that was puked up by nematodes. These bacteria actually killed off other pathogens and made the survival rate of those soldiers higher.

http://www.kickassfacts.com/30-interesting-facts-about-bacteria/

Jay, Amrit, Rosy, Weema Magnetospirillum magneticum is a free-living bacteria which has the ability to actively take in iron, convert it to magnetic magnetite, align it like a backbone along its body, and travel through its environment using magnetic fields. http://www.kickassfacts.com/30-interesting-facts-about-bacteria/

jf

Ziqi, Sean

Bacteria has sort of consciousness. They can orient themselves, react to the environment, and even organise themselves into structure.

Exp:Myxococcus xanthus, bacteria that blob together, rolling around as a pack, devouring other bacteria.source:https://www.astrobio.net/origin-and-evolution-of-life/bacterial-intelligence/

“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

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 thatserve as usable nutrients)

• eight feet long

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)