Molecular Biosciences 305: The Diversity of Prokaryotic ...c... · Molecular Biosciences 305: The...

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Molecular Biosciences 305: The Diversity of Prokaryotic Organisms Lecture 25 [Consetta Helmick]

Slide # 1 Slide Title: WSU Online Title Slide Title: The Diversity of Prokaryotic Organisms Instructor: Consetta Helmick online.wsu.edu Audio: [Music]

Slide # 2 Slide Title: The Diversity of Prokaryotic Organisms The Diversity of Prokaryotic Organisms Audio: Lecture two the diversity of prokaryotic organisms. Eventually in this section we will be talking about metabolism and the different pathways that bacteria use and the only pathway that eukaryotic cells use. But to understand this we also have to look at the diversity of prokaryotic organisms. They are so adaptable we can find them at a variety of temperatures, pH, oxygen requirements, and now in a number of different places where they can use different food sources.

Slide # 3 Slide Title: Slide 3 Diversity of Prokaryotes

Scientists just beginning to understand vast diversity of microbial life

Only ~6,000 of estimated million species of prokaryotes described 950 genera

Vast majority have not been isolated

New molecular techniques aiding in discovery, characterization [Image of a prokaryote] Audio: Scientists have just begun to understand the vast diversity of microbial life. Only 6,000 of an estimated million species of prokaryotes have been described, 950 genera. The vast majority

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have been isolated but because of new molecular techniques aiding in the discovery of characteristics of these organisms our numbers will increase greatly. Plus we will be able to use these organisms in a number of beneficial ways for human medicine, genetic information, a variety of things that could be very important.

Slide # 4 Slide Title: Slide 4 Diversity of Prokaryotes

Prokaryotes are metabolically diverse Numerous approaches to harvest energy to produce ATP

[Table 11.1] Audio: If we look at table 11.1 we’ll see there is a vast number of organisms that are categorized based again on their nutritional needs. Prokaryotes are metabolically diverse so there are numerous ways or approaches that these organisms can use to harvest energy and to produce ATP. This table plus the rest of these lectures would be very wise to understand again for maybe future test questions.

Slide # 5 Slide Title: Slide 5 Anaerobic Chemotrophs

Atmosphere anoxic for first ~1.5 billion years that prokaryotes inhabited earth Early chemotrophs likely used anaerobic respiration

- Terminal electron acceptors like abundant CO2 or S Others may have used fermentation

- Passed electrons to organic molecule like pyruvate

Today anaerobic habitats common Aerobes contribute by depleting O2 Mud, tightly packed soil limit diffusion of gases Aquatic environments can become limiting Human body (especially intestinal tract)

- Also anaerobic microenvironments in skin, oral cavity Audio: The first category we will talk about is the anaerobic chemotrophs. You’ve got to realize 1.5 billion years ago there wasn’t a lot of oxygen probably in the earth. And these organisms had to learn how to adapt without oxygen. So we have a number of true anaerobes. So the early chemotrophs likely used anaerobic respiration. Their terminal electron acceptor probably was again carbon dioxide or sulfur. Many of them probably did a process of fermentation. They

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were able to pass electrons to organic molecules like pyruvate. Today’s anaerobes actually habitate a number of different areas. They are areas where there is a deplete of oxygen. An example is mud, tightly packed soil which has limited diffuse of gas. Aquatic environments can become very, very limited. The human body, think about your own intestinal tract. There isn’t a lot of oxygen down in your large intestine. Now remember you have about 500 species of organisms living in the large intestine itself. You also have a variety of anaerobic organisms that live in the skin and the oral cavity. So these organisms have adapted a beautiful way to produce energy, survive, metabolize, and again doing it without the presence of oxygen.


Anaerobic Chemolithotrophs (continued…) Methanogens are group of methane-producing archaea

- Oxidize H2 gas to generate ATP o Alternatives include formate, methanol, acetate

- CO2 as terminal electron acceptor o Smaller energy yield than other electron acceptors

- Very sensitive to O2 - Sewage, swamps, marine sediments, rice paddies, digestive tracts - Cows produce ~10 ft3/day

4 H2 + CO2 → CH4 + 2 H2O (energy source) (terminal electron acceptor) [Images of chemotrophs] Audio: Another group of our anaerobic chemotrophs is our anaerobic chemolithotrophs. These are our methanogen organisms. These are the organisms that produce methane. Our archaea species are involved in this. They can oxidize hydrogen gas to generate ATP. Alternate forms include formate, methanol, and acetate. Carbon dioxide is the terminal electron acceptor. Very small yields of oxygen compared to other electron acceptors but these organisms seem to do just fine. They are extremely sensitive to oxygen, will die in the presence of oxygen. We find them in areas such as sewage, swamps, marine sediment, rice paddies, again digestive tracts. The rumen of a cow is loaded with organisms that produce again methane or methane gas. So what we have is cows can produce 10 cubic foot of methane per day by again using the food that the cows have eaten, then they use again the carbon dioxide as the terminal electron acceptor and one of the byproducts is methane gas.

Slide # 7 Slide Title: Slide 7

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Anaerobic Chemotrophs

Anaerobic Chemoorganotrophs – Respiration Chemoorganotrophs oxidize organic compounds (e.g., glucose) to obtain energy

- Anaerobes often use sulfur, sulfate as electron acceptor Sulfur- and Sulfate-Reducing Bacteria

- Produce hydrogen sulfide (rotten-egg smell) - H2S is corrosive to metals - Important in sulfur cycle - At least a dozen recognized genera

o Desulfovibrio most studied o Gram-negative curved rods

- Some archaea organic compounds + S → CO2 + H2S (energy source) (terminal electron acceptor) Audio: Another category of our anaerobic chemotrophs are anaerobic chemoorganotrophs respiration. Chemoorganotrophs oxidize organic compounds, such as glucose, to obtain energy. Anaerobically they also use sulfur. Sulfur can be their electron acceptor. Sulfur and sulfate-reducing bacteria. These organisms produce hydrogen sulfide and this is what gives that rotten-egg smell. So if you have ever been to a geyser there is probably again sulfur reducing bacteria living in that geyser. The sulfuric acid is also corrosive to metals. This particular organism is very important to the sulfur cycle. If you think about it sulfur is required for protein folding, correct structure of protein, disulfide bonds, and again has also been recognized as a genera. So the desulfovibrios have been studies, they are gram-negative curved rods, some of them are also found in the archaea species; are groups which are the organisms that withstand very high temperatures.


Anaerobic Chemoorganotrophs – Fermentation Numerous anaerobic bacteria ferment

- ATP via substrate-level phosphorylation - Many different organic energy sources, end products glucose → pyruvate → lactic acid (energy source) (terminal electron acceptor)

Clostridium are Gram-positive, endospore-forming rods - Common in soils; vegetative cells live in anaerobic microenvironments created by aerobes consuming O2 - Endospores tolerate O2, survive long periods of heat, drying, chemicals, irradiation;

o Germinate when conditions improve

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- Diverse metabolism; some cause diseases Audio: The anaerobic chemoorganotrophs can also do fermentation. Numerous anaerobes bacteria ferment. ATP is obtained via substrate-level phosphorylation. Many different organic energy sources have different end products. So if you go from glucose to pyruvate to lactic acid. And if we think about lactic acid we talked about a number of products that are produced from lactic acid fermentation in our previous section. The clostridium species are gram-positive. They are endospore-forming rods, very common in soils. This endospore stage can withstand long term survivability in very harsh environments. It can survive without the presence of oxygen. Clostridium species are actually true anaerobes. They will die in the presence of oxygen. The endospores that are produced again we mentioned before have been found in mummy tombs. You put them into the right environment, they come back to life. They can withstand long periods of heat, drying, chemicals, and even irradiation. When conditions improve, when the organism knows it’s time to come back to life, germination will occur and we get a diverse metabolic activity occurring and some of these can cause disease such as frost bite, gangrene, clostridium difficilis is one we are having problems with now in intestinal diseases.


Anaerobic Chemoorganotrophs – Fermentation Lactic Acid Bacteria: produce lactic acid

- Most can grow in aerobic environments; only ferment - Lack catalase - Streptococcus inhabit oral cavity; normal microbiota

o Some pathogenic (e.g., β-hemolytic S. pyogenes) [Images of cocci] Audio: Anaerobic chemoorganotrophs again fermentation lactic acid bacteria. These organisms produce lactic acid. So we go from glucose to pyruvate to lactic acid. Most can grow in aerobic environments and only ferment. They lack catalase. Streptococcus inhabits your mouth, it is a normal flora organism. Some pathogen organisms such as Beta-hemolytic Streptococcus pyogenes is also a lactic acid producer. And this is the organism that would again cause strep throat. The two illustrations again are showing you the classic cocci structure of these organisms that we find in very long chains.


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Anaerobic Chemotrophs

Anaerobic Chemoorganotrophs – Fermentation Lactic Acid Bacteria (continued…)

- Lactococcus species used to make cheese, yogurt - Enterococcus inhabit human, animal intestinal tract - Lactobacillus rod-shaped, common in mouth, vagina

o Break down glycogen deposited in vaginal lining o Resulting low pH helps prevent vaginal infection o Also present in decomposing materials o Important in production of fermented foods

[Image of chemotrophs] Audio: As we mentioned in section two when we talked about food production lactic acid bacteria. Lactococcus species again used to make cheese, yogurt. Enterococcus inhabits the human and animal intestinal tract. Lactobacillus are rod-shaped, common in the mouth and vagina. They break down glycogen, deposit it the vaginal lining and again can lead to lowering the pH of that area which can prevent vaginal infections. So it is a very nice relationship with this organism. Also present in decomposing material. Important in the production of fermented foods such as sour kraut, pickles, these type of items because of again the lactic acid production.

Slide # 11 Slide Title: Slide 11 Anoxygenic Phototrophs

Earliest photosynthesizers likely anoxygenic phototrophs Use hydrogen sulfide or organic compounds (not water) to make NADPH; do not

generate O2 Modern-day phylogenetically diverse

- Live in bogs, lakes, upper layers of mud - Little or no O2, but light penetrates - Different photosystems that plants, algae, cyanobacteria

o Use unique bacteriochlorophyll o Absorb wavelengths that penetrate deeper

6 CO2 + 12 H2S → C6H12O6 + 12 S + 6 H2O (carbon source) (electron source)

Audio: Because of the diversity of our prokaryotes a number of them can also be phototrophic. Photosynthesis producers or use the process of photosynthesis to produce their food products and again their energy. So the earliest photosynthesizers were likely called anoxygenic phototrophs. They probably used hydrogen sulfide or an organic compound, not water, to make NADPH but did not generate oxygen. Modern day again diversity we find these organisms live in

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bogs, lakes, upper layers of mud where there is little or no oxygen but light can penetrate. Different photosystems than plants, algae, and cyanobacteria. They use a unique bacteriochlorophyll to absorb wavelengths and eventually again through the process of photosynthesis.


Purple Bacteria Purple Sulfur Bacteria (continued…)

- Representatives include Chromatium, Thiospirillum, Thiodictyon

[Images of bacteria] Audio: A group of the anoxygenic phototrophs are purple bacteria, purple sulfur bacteria. Represented in this group of organisms we find the chromatium and the thiodictyon organisms. A lot of times if you have been around a bog or a lake that has that pretty purple color to it we always assume it is algae but more than likely it is actually purple sulfur bacteria that is present in that particular area.


Purple Bacteria (continued…) Purple Non-Sulfur Bacteria

- Moist soils, bogs, paddy fields - Preferentially use organic molecules instead of H2S as source of electrons - Lack gas vesicles - May store sulfur; granules form outside cell - Remarkably diverse metabolism

o Many use H2 or H2S (like purple sulfur bacteria) o Most can grow aerobically in absence of light using chemotrophic

metabolism - Representatives include Rhodobacter, Rhodopseudomonas

Audio: The purple non-sulfur bacteria, again these are ones that we find in soils, bogs, paddy fields. Preferably use organic molecules instead of hydrogen sulfide as a source of their electrons. They lack gas vesicles and oxygen would probably be damaging. They store sulfur, granules form outside the cells. Remarkable diversity in metabolism. Many use again hydrogen or

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hydrogen sulfide like purple sulfur bacteria. They can grow aerobically in the presence of light using chemotrophic metabolism. So a number of these organisms are ones that we find are called Rhodobacteria or Rhodopseudomonas.


Green Bacteria Gram-negative; typically green or brownish Green Sulfur Bacteria:

- Habitats similar to purple sulfur bacteria - Form granules outside of cell - Accessory pigments located in chlorosomes - Lack flagella - May have gas vesicles - Strict anaerobes - None are chemotrophic - Representatives include Chlorobium, Pelodictyon

[Image of bacteria] Audio: Another category of our anoxygenic phototrophs is the green bacteria. These are typically a gram-negative; typically a green or literally a brownish color. Green sulfur bacteria habitats similar to the purple sulfur bacteria so bogs, stagnant areas. They also form granules outside of the cell. They have an accessory pigment located in the chlorosomes. They lack a flagella, many have gas vesicles, they are strict anaerobes, none are chemotrophs, and organisms that represent this group are called the Chlorobiums or the Pelodictyon.

Slide # 15 Slide Title: Slide 15 Oxygenic Phototrophs

Cyanobacteria (continued…) Morphologically diverse Unicellular: cocci, rods, spiral Multicellular: filamentous associations: trichomes

- May be in sheath - Motile trichomes glide as unit

May have gas vesicles for vertical movement in water [Images of phototrophs]

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Audio: Another group of the oxygenic phototrophs are the cyanobacteria. These are some of the most morphologically diverse organisms. They can be unicellular, they can be cocci, they can be rods, they can be spirals. They can be multicellular. They can have a filamentous type appearance to them. They can have a sheath, they can have trichomes glide that act as units. Many have gas vesicles for vertical movement in water.


Cyanobacteria (continued…) Large numbers can accumulate in freshwater habitats

- Called a bloom - Sunny, hot weather can lyse cells, create scum

Photosystems like those in chloroplasts of algae, plants, which evolved from ancestral cyanobacteria

Also have phycobiliproteins - Absorb additional wavelengths

[Image of a bloom] Audio: The cyanobacteria again can accumulate in large numbers in fresh water habitats. And when we have large numbers of cyanobacteria again we always assume it is algae but it is not. This is called a bloom. Sunny, hot weather can lyse cells; it can create scum. If you have ever been to the river in July when it is hot and the water is very stagnant you might find this slimy component actually in the water. Photosystems like those in chloroplasts of algae plants which evolved from ancestral cyanobacteria. So the cyanobacteria was actually ahead of the plants when it came to the process of photosynthesis.


Cyanobacteria (continued…) Nitrogen-fixing cyanobacteria critical ecologically

- Incorporate N2 and CO2 into organic material o Form usable by other organisms

- Nitrogenase destroyed by O2, must be protected o Anabaena form specialized heterocysts o Lack photosystem II

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o A. azollae fixes N2 in special sac of fern o Synechococcus fix N2 in dark

[Image of heterocyst] Audio: From an ecological standpoint cyanobacteria is probably extremely diverse because they can also do nitrogen fixing. They can incorporate nitrogen and carbon dioxide into organic material. This form is unusable for other organisms. Nitrogenase destroyed by oxygen must be protected. So our anabaena form specialized in heterocysts, they lack photosystem II, even though we see with photosynthesis we have photosystem II, photosystem I. These organisms again have developed a very specific way of fixing nitrogen and being a photosynthetic organism without the same processes that we would see in a plant.

Slide # 18 Slide Title: Slide 18 Aerobic Chemolithotrophs

Aerobic chemolithotrophs gain energy by oxidizing reduced inorganic chemicals Sulfur-oxidizing bacteria: Gram-negative rods, spirals

- Energy from oxidation of sulfur, sulfur compounds including H2S, thiosulfate - Important in sulfur cycle - Filamentous and unicellular lifestyles

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. S + 1 ½ O2 + H2O → H2SO4 (energy source) (terminal electron acceptor) Audio: Our aerobic. Remember the term aerobic means requires oxygen. So we have our aerobic chemolithotrophs. Our aerobic chemolithotrophs gain oxygen by oxidating reduced inorganic chemicals. Sulfur oxidizing bacteria, they are usually a gram-negative rod, they can be spiral. Energy from oxidation is sulfur, sulfur compounds including again hydrogen sulfide or thiosulfate. Important in the sulfur cycle. You will be going through nutrient cycles in a little bit. Remember sulfur is an important component for protein folding, disulfide bonds in any life form. These can also be filamentous and unicellular lifestyles. If we look at the illustration below we have sulfur as again our electron terminal which is going to produce water and then hydrogen sulfide.


Aerobic chemolithotrophs (continued…)

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Filamentous Sulfur Oxidizers - Beggiatoa, Thiothrix: sulfur springs, sewage-polluted waters, surface of marine and freshwater sediments - Store sulfur as intracellular granules - Beggiatoa filaments move by gliding motility - Thiothrix filaments immobile; progeny cells detach, move via gliding motility

[Images of chemolithotrophs] Audio: Some of our aerobic chemolithotrophs again as sulfur oxidizers have a variety of unique structures. They are found in sulfur springs, again that gas, that rotten-egg smell, sewage polluted waters, surfaces of marine and fresh water sediments. They can store sulfur as an intracellular granule inside the cell itself. Some of them have filaments that they can use for movement by gliding through material.


Aerobic chemolithotrophs (continued…) Unicellular Sulfur Oxidizers

- Acidithiobacillus: terrestrial and aquatic habitats - Oxidize metal sulfides, can be used for bioleaching

o E.g., oxidation of gold sulfide produces sulfuric acid; lower pH converts metal to soluble form

- Can oxidize sulfur in fuels to sulfate; removal helps prevent acid rain - Can produce damaging acid runoff as low as pH 1.0

[Image of terrain] Audio: We also have unicellular sulfur oxidizers that are used in a variety of ways. Our acidithiobacillus, these are organisms that are terrestrial and inhabit aquatic habitats. They oxidize metal sulfides. So they can be used for what is called bioleaching. We use a number of organisms to leach out gold, mercury by using again these organisms. So the oxidation of gold sulfide produces sulfuric acid. Lower pH converts metal to a soluble form. The oxidized sulfur is fuel to sulfate; removal helps prevent acid rain. It can produce damaging acid runoff as low as again pH 1. So in areas where we use this organism for bioleaching there has been a huge controversy on the destruction that is occurring to natural habitats.


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Aerobic Chemolithotrophs

Aerobic chemolithotrophs (continued…) Nitrifiers are diverse group of Gram-negatives

- Oxidize inorganic nitrogen compounds for energy - Concern to farmers using ammonium nitrogen - Can deplete water of O2 if wastes high in ammonia - Two groups; usually grow in close association

o Ammonia oxidizers: Nitrosomonas, Nitrosococcus Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. NH4

+ + 1 ½ O2 → NO2- + H2O + 2 H+

(energy source) (terminal electron acceptor) o Nitrite oxidizers: Nitrobacter, Nitrococcus Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. NO2

- + ½ O2 → NO3-

(energy source) (terminal electron acceptor) Audio: The next area of aerobic chemolithotrophs is very important to farmers. They are very important to plants in general. These are the nitrifiers. They are a very diverse group of gram-negatives. They oxidize inorganic nitrogen compounds for energy. Concerns to farmers using again ammonium nitrate. They can deplete water of oxygen if waste is high in ammonium. Two groups usually grow in close association, our ammonia oxidizers, our nitrosomonas and our nitrococcus, and our also nitric oxidizers which are our nitrobacter and our nitrococcus.


Aerobic chemolithotrophs (continued…) Hydrogen-Oxidizing Bacteria

- Aquifex, Hydrogenobactera among few hydrogen-oxidizing bacteria that are obligate chemolithotrophs - Thermophillic; typically inhabit hot springs - Some Aquifex have maximum growth at 95oC - Deeply branching in phylogenetic tree, believed one of earliest bacterial forms to exist on earth

o O2 requirements low, possibly available early on in certain niches due to photochemical processes that split water

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2 + ½ O2 → H2O

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(energy source) (terminal electron acceptor) Audio: Another of our aerobic chemolithotrophs is our hydrogen oxidizing bacteria. Aquifex again are among the few hydrogen-oxidizing bacteria that are obligate chemolithotrophs. They are usually found in hot springs. They can be found in temperatures as high as 95 degrees Centigrade. They have a deeply branching phylogenetic tree believed to be one of the earliest forms of bacteria that existed on the earth. Oxygen requirements are low possibly because of available oxygen at certain times during their development was not available due to photochemical processes that split water. So we have hydrogen plus our electron acceptor again producing water.

Slide # 23 Slide Title: Slide 23 Aerobic Chemoorganotrophs

Aerobic chemoorganotrophs oxidize organic compounds for energy organic compounds + O2 → CO2 + H2O (energy source) (terminal electron acceptor)

Some inhabit specific environments, others ubiquitous Obligate Aerobes Micrococcus: Gram-positive cocci

- Found in soil, dust particles, inanimate objects, skin - Pigmented colonies - Tolerate dry, salty conditions

[Image of cocci] Audio: Our aerobic chemoautotrophs oxidize organic compounds for energy. So we have an organic compound, oxygen is going to be our final electron acceptor, we are going to produce carbon dioxide and water as byproducts and the production of energy. These inhabit some very specific environments. Some are ubiquitous, we find them everywhere. We have our obligate aerobes and our most common species is micrococcus. It is a gram positive coccus found in soils, dust particles, innate objects, skin. They have pigmented yellow colonies. They can tolerate dry, salty conditions. If any of you have ever set up bacterial cultures and you get an air contaminant, little, tiny yellow colonies, more than likely that is micrococcus.


Obligate Aerobes

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Mycobacterium are acid-fast bacteria Mycolic acid in cell wall prevents Gram-staining Special staining used; resist destaining Generally pleomorphic rods Notable pathogens: M. tuberculosis, M. leprae More resistant to disinfectants, differ in susceptibility to antimicrobial drugs Related Nocardia species also acid-fast

Audio: Another aerobic chemoautotroph is the obligate aerobes is mycobacterium. Mycobacterium again are acid-fast bacteria. They have a mycolic acid in the cell wall that prevents gram staining. So you have to use a special procedure to stain for them called acid-fast because you have to actually etch the mycolic acid in the cell wall to get the stain in. They have a pleomorphic shape which means they are not a true gram-positive or, excuse me, cocci or rod. They have unusual shapes. A number of them can cause disease but we have notable pathogens Mycococcus tuberculosis causes tuberculosis, Mycococcus leprae which causes leprosy. Most are resistant to disinfectants because again that tough mycolic acid in the cell wall. Different susceptibility to antimicrobial drugs. Other related species in this area are nocardia species which is also acid-fast.


Obligate Aerobes (continued…)

Pseudomonas: Gram-negative rods; oxidase positive Motile by polar flagella; often produce pigments Most are strict aerobes; no fermentation Extreme metabolic diversity important in degradation

- Ability sometimes from plasmids Widespread: soil, water Most harmless Some pathogens:

P. aeruginosa common opportunistic pathogen

[Image of petrie dishes] Audio: Another aerobic chemoorganotroph is our obligate aerobes is pseudomonas. Pseudomonas is a gram-negative rod, oxidase positive, it is motile by a polar flagella, often produces pigment, most are strict aerobes, no fermentation is going to occur. A lot of metabolic diversity important in these organisms. Sometimes they can gain a plasmid. They are found widespread in soil, water. Most are harmless, some are pathogenic. Pseudomonas aeruginosa is our most

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common one that is an opportunistic organism. This is an organism that we are having a lot of issues with in hospitals. We have a lot of issues with this organism in burn victims because once it gets into the correct environment it starts releasing those exotoxins, makes the host its environment and causes a huge amount of damage. So this is one we are still trying to figure out how to combat in a number of situations.


Obligate Aerobes (continued…)

Family Enterobacteriaceae: enterics or enterobacteria are Gram-negative rods typically found in intestinal tract of humans, other animals; some thrive in soil

Facultative anaerobes that ferment glucose Normal intestinal microbiota include Enterobacter, Klebsiella, Proteus, most E.

coli strains Those that cause diarrheal disease include Shigella, Salmonella enteric, and some

E. coli strains Life-threatening systemic diseases include typhoid fever (Salmonella enterica

serotype Thyphi) and bubonic and pneumonic plague (Yersinia pestis) Lactose fermenters termed coliforms

Audio: Another obligate aerobe is in the family Enterobacteriaceae. These are enterics or enterobacters. They are gram-negative rods typically found in the intestinal tract of humans and other animals but they can thrive in soil also. They can be a facultative anaerobe that ferments glucose. Facultative anaerobe means that it can be alive in the presence or lack of oxygen. It can usually flip either way. Normal intestine organisms includes Enterobacter, Klebsiella, Proteus, and most of our E. coli strands. Those that cause diarrhea specifically are going to be Shigella, our Salmonella species, and a number of our E. coli strands. They can produce life-threatening systematic diseases including typhoid fever, bubonic plague, again Yersinia pestis and again the 0157 strain of E. coli.

Slide # 27 Slide Title: Slide 27 Ecophysiological Diversity [Table 11.2] Audio: Besides again organisms needing specific food sources, carbon sources, or specific electron acceptors at the end of their energy metabolism we have a number of organisms that we find in

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very ecophysiological diverse areas. So we have organisms that thrive in terrestrial environments, aquatic environments. So we are going to be going over a number of these.

Slide # 28 Slide Title: Slide 28 Thriving in Terrestrial Environments

Soils pose variety of challenges Wet and dry, warm and cold, abundant to sparse nutrients Bacteria that from a resting stage Endospore-formers most resistant to environmental extremes

- Bacillus, Clostridium most common - Gram-positive rods - Bacillus include obligate and facultative anaerobes - Some medically important: B. anthracis

[Images of bacteria] Audio: Organisms that can thrive in soil, a terrestrial environment. Soil is probably one of the most harsh environments you ever want to think about. Sometimes there is not a lot of water, drastic pH changes depending on oxygen, probably not a lot of food either. So organisms that thrive in soil have developed again over time to adapt to their environment. Because again those challenges. It can be wet, dry, warm, cold, abundant to sparse and again nutrients. A lot of the organisms we find in soil might be in a resting stage endospore producers. Our Clostridium species and our Bacillus species. Most of these organisms can be gram-positive rods. Bacillus can be an obligate or facultative anaerobe. A number of them are medically important. Bacillus anthracis, the organism that causes anthrax, Clostridium again botulinum, Clostridium tetani, Clostridium perfringens. These are all organisms again that can be medically important.


Bacteria that form a resting stage (continued…)

Myxobacteria: group of aerobic Gram-negative rods that includes Chondromyces, Myxococcus, Stigmaterlla

Favorable conditions: secrete slime layer, form swarm Nutrients depleted: cells congregate into fruiting body

- Cells differentiate, form dormant microcysts - Microcysts resist heat, drying, radiation

Degraders of complex organic substances

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[Images of bacteria] Audio: We also have other organisms again bacteria in the resting stage in soils. We have our myxobacteria, a group of aerobic gram-negative rods that include again Myxococcus and Stigmaterlla. Favorable conditions again when things are good, life is good, they will secrete a slime layer. They will form a swarming type growth on surfaces of the dirt, people, again or nutrient plates. When they are nutrient depleted they will again conjugate into what are called fruiting bodies. Cells differentiate, form dormant microcysts. Microcysts resist heat, drying, and radiation. So and degraders of complex organic substances. So again a very interesting organism that we find in soil that has adapted beautifully to that harsh environment.


Bacteria that form a resting stage (continued…)

Streptomyces: aerobic Gram-positive bacteria Growth resembles fungi: form mass of branching hyphae called mycelium Chains of spores (conidia) develop at tips Conidia resistant to drying; easily spread by air currents Produce extracellular enzymes; also geosmins, medically useful antibiotics

including streptomycin, tetracycline, erythromycin [Image of bacteria] Audio: Other organisms that can thrive in soil are the streptomycin species. These are an aerobic gram-positive bacteria. Their growth resembles fungi, forms a mass with branching hyphae called mycelium. Chains of spores can develop at the tips. Resistant to drying, spread by air currents, produce extracellular enzymes. Very helpful in antibiotics. A lot of our antibiotics came from our streptomycin species including streptomycin, tetracycline, and erythromycin.


Bacteria That Associate with Plants (continued…)

Rhizobia: Gram-negative rods that often fix nitrogen Includes Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium,

Azorhizobium Live in nodules on roots of legumes Plants synthesize leghemoglobin, which binds and controls O2 level to yield

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microaerobic conditions Allows bacteria to fix nitrogen

[Images of rhizobia] Audio: Other soil organisms have wonderful associations with plants. Plants have to have nitrogen but they cannot fix atmospheric nitrogen. Plants produce proteins, carbon, hydrogen, oxygen, and nitrogen. So a lot of our soil bacteria work in association with the nodules on the roots of plants to fix the nitrogen. So rhizobia species are gram-negative rods that often fix nitrogen. These organisms live in the nodules of the roots of usually legumes. Legumes are things like garbanzo beans, chick peas, peas, lentils, these types of plants. A lot of times around on the Palouse you’ll see rotational crops where they’ll plant wheat, barley, and then peas or lentils or garbanzos. What they are doing is they are allowing these plants to put nitrogen back into the soil for the next crop to actually use the nitrogen and recharging the soil with these organisms.

Slide # 32 Slide Title: Slide 32 Thriving in Aquatic Environments

Aquatic environments lack steady nutrient supply Sheathed bacteria form chains of cells within tube

- Sheaths protect, help bacteria attach to solid objects - Often seen streaming from rocks in water polluted by nutrient-rich effluents; may clog pipes - Include Gram-negative rods Sphaerotilus, Leptothrix - Motile swarmer cells exit open end of sheath, move to new surface, attach

[Image of sheathed bacteria] Audio: There is a wide variety of organisms that live in aquatic environments. Like I said before sometimes you get that slimy things that look like algae blooms but it is really bacteria. So these organisms again can live in these areas. They can live in aquatic environments that lack a stead nutrient supply. These are sheathed bacteria. They form chains of cells within tubes, the sheath pocket. It helps the bacteria attach to solid objects. Often seen streaming from rocks in water polluted areas by nutrient rich effluence. Again they clog pipes. You may see this again in down from sewage treatment plants or again areas where pollutants are very, very high. They include the gram-negative rods. These are motile swarmer cells exit open ended at the sheath, move to new surface, and then again attach. Talk about a fascinating system for motility of these particular organisms.

Slide # 33

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Slide Title: Slide 33 Thriving in Aquatic Environments

Bacteria That Derive Nutrients from Other Organisms

Bdellovibrio: highly motile Gram-negative curved rods Prey on E. coli and other Gram-negatives Strikes forcefully; prey propelled short distance Parasite attaches, rotates, secretes digestive enzymes; forms hole in cell wall of

prey [Image and diagram of Bdellovibrio] Audio: And we also have other aquatic organisms that derive nutrients from other organisms. It is almost a parasitic relationship if you think about it. They prey on E. coli and other gram-negative organisms. They are usually a highly motile gram-negative curved rod. The striking force is that they can prey, their prey can propel short distances. They almost have like a parasitic attack. They rotate, secrete digestive enzymes, form holes in the cell wall of prey, and then feed on them. We don’t think a lot of times of bacteria being parasitic. We think of them causing diseases but actually attacking other bacteria for food, like I said, is an amazing system.


Bacteria That Derive Nutrients from Other Organisms

Bioluminescent bacteria: Photobacterium, Vibrio Symbiotic relationship with certain fish, squid Help with camouflage, confuse predators and prey Gram-negative rods (Vibrio are curved rods) Facultative anaerobes; not all are bioluminescent

- Some pathogenic: V. cholera; V. parahaemolyticus

[Images of bacteria and a fish] Audio: We also have other aquatic organisms that can derive nutrients from other organisms. We’ve got bioluminescent bacteria, some of our vibrio species. It is a symbiotic relationship with certain fish and squid. Help with camouflage, confuse predators and prey. It is a gram-negative rod, vibrios are curved, they are a facultative anaerobe, some are pathogenic. Vibrio cholera causes cholera but when they are in a relationship with these animals, fish and squid, they emit a wonderful defense mechanism for these fish.

Slide # 35

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Slide Title: Slide 35 Thriving in Aquatic Environments

Bacteria That Move by Unusual Mechanisms

Spirochetes: group of Gram-negatives with spiral shape Flexible cell wall Endoflagella or axial filament contained within periplasm allows corkscrew-like

motion Able to move through viscous environments like mud Spirochaeta thrive in muds, anaerobic waters Leptospira are aerobes; some free-living, others inhabit animals

- L. interrogans causes leptospirosis

[Image of spirochetes] Audio: We also have aquatic organisms or bacteria that move by unusual mechanisms, our spirochetes. These are gram-negative organisms with a spiral shaped structure to them. They have a flexible cell wall. They have an endoflagella or axial flagella which actually looks like somebody took a piece of thread and threaded it through the cell wall of the organism itself. They have a corkscrew like motion. Their ability to move through thick environments like mud, they can move through tissue, a number of these can be pathogenic. We find them in muddy areas, anaerobic waters. They can also again produce leptospira, which is an aerobe, in some free-living and others inhabit animals. They can cause leptospirosis which is a pathogen of humans and a number of animals.


Bacteria That Form Storage Granules

Spirillum: Gram-negative spiral-shaped microaerophilic bacteria S. volutans stores phosphate as volutin granules

- Metachromatic granules

Sulfur-Oxidizing, Nitrate-Reducing Marine Bacteria Some store sulfur (energy source) and nitrate (terminal electron acceptor),

which may not coexist Thioploca species form long sheaths; cells shuttle between sulfur-rich sediments

and nitrate-rich water Thiomargarita namibiensis cells have nitrate storage vacuole occupying ~ 98% of

cell; cell diameter can reach ¾ mm

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Audio: Other aquatic environment adaptations is that we have bacteria that form storage granules. The spirillum, gram-negative, spiral shaped microaerophilic bacteria. They can store phosphate. They can store metachromatic granules. A number of our sulfur-oxidizing, nitrate-reducing marine bacteria store some sulfate, sulfur again for energy source and nitrate terminal electron acceptor. They have a wonderful way of adapting to their environment. Some of them form long sheaths, the cells shuttle between sulfur-rich sediments and nitrate-rich sediments. So you talk about an organism that can switch its final electron acceptor from sulfate to nitrate. They are just like I said unbelievable. Some of them have nitrogen or nitrate storage capability that can occupy up to 98 percent of the cell. The cells can reach huge diameters because again all the storage of the nitrates.

Slide # 37 Slide Title: Slide 37 Archaea That Thrive in Extreme Conditions

Characterized Archaea thrive in extremes High heat, acidity, alkalinity, salinity Methanogens are exception

[Table 11.4] Audio: As we continue with our diversity of prokaryotes we also have to talk about organisms that can thrive in extreme conditions, the Archaea. These organisms have been found in high heat, acidity, alkalinity, and salinity. If we look at table 11.4 it gives us the categories of organisms that we are going to find in the Archaea area and some of the extreme areas that they will be found.


Extreme Halophiles: salt lakes, soda lakes, brines Most can grow in 32% NaCl; require at least 9% NaCl Produce pigments; seen as red patches on salted fish, pink blooms in salt water

ponds Aerobic or facultatively anaerobic chemoheterotrophs Some obtain additional energy from light via bacteriorhodopsin, which expels

protons from cell - Proton gradient can drive flagella, ATP synthesis

Variety of shapes: rods, cocci, discs, triangles Includes Halobacterium, Halorubrum, Natronobacterium, Natronococcus

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[Image of halophile environment] Audio: In this category we have our extreme halophiles. These are found in salt lakes, soda lakes, brine. Most can grow in up to again 32 percent sodium chloride. Some require at least 9 percent sodium chloride just to exist. Some can produce pigments seen as red patches on salted fish, pink blooms in salt water ponds. They can be aerobic, facultative anaerobes, chemoheterotrophs. Some obtain additional energy from light. Some have a photo gradient that can drive the flagella. ATP synthesis, a variety of shapes: rods, cocci, discs. So there are a number of organisms that fall into this category and again adapted to extreme, extreme salty conditions.


Extreme Thermophiles Found near volcanic vents and fissures that release sulfurous gases, other hot

vapors - Believed to closely mimic earth’s early environment

Others in hydrothermal vents in deep sea, hot springs Methane-Generating Hyperthermophiles

- Methanothermus species grow optimally at 84oC, as high as 97oC - Oxidize H2 using CO2 as terminal electron acceptor

Audio: We also have our extreme thermophiles. These are organisms that we find in volcanic vents down in the ocean. These are organisms that we find in volcanoes. They release sulfurous gas and other hot vapors. They are believed to closely mimic the earth’s early environment. Others can be found in hydrothermal vents, in deep seas, hot springs. We have methane generating hyperthermophiles. Organisms like this can be found in the geysers at Yellowstone. They oxidize hydrogen using carbon dioxide as the terminal electron acceptor. They can be found in temperatures of 84 degrees Centigrade up to 97 degrees Centigrade. A number of these organisms right now are being studied because of their ability to produce enzymes at such high temperatures where we would think proteins would be denatured. So this is a huge area of exploration right now in a lot of research areas.


Extreme Thermophiles (continued…)

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Sulfur-Reducing Hyperthermophiles - Obligate anaerobes; oxidize organic compounds, H2 - Sulfur as terminal electron acceptor; generate H2S - Sulfur hot springs, hydrothermal vents - Pyrolobus fumarii from “black smoker” 3,650 m deep in Atlantic Ocean; grows between 90-113oC - Pyrodictium occultum cannot grow below 82oC; 105oC is optimum - “Strain 121” grows at 121oC; related to Pyrodictium

[Image of thermophiles] Audio: Also with our extreme thermophiles we have sulfur reducing myperthermophiles. These are obligate anaerobes. They oxidate organic compounds such as hydrogen. Sulfur is the terminal electron acceptor; generates hydrogen sulfide. We are going to find these in sulfur hot springs, hydrothermic vents. A lot of these like I said are found in a lot of extremely, extremely harsh extreme temperatures. And like I said before these organisms that are being looked at right now because of their adaptability in such extreme areas.


Extreme Thermophiles (continued…) Nanoarchaea: Nanoarcheota is new phylum

- Nanoarchaeum equitans grows as 400 nm spheres attached to sulfur-reducing hyperthermophile Ignococcus, presumably parasitizing

Sulfur Oxidizers: Sulfolobus species at surface of acidic sulfur-containing hot springs - Obligate aerobes - Oxidize sulfur compounds - Generate sulfuric acid - Thermoacidophilic: grow above 50oC and pH 1-6

[Image of thermophile terrain] Audio: Also with our extreme thermophiles we have our sulfur-oxidizers. These are organisms that again are found in sulfur containing hot springs. The thing about these organisms too is they generate sulfuric acid. Besides being in extremely high temperatures they can grow in pHs anywhere between 1 and 6 pH. They are an obligate aerobe. So again hot springs, places like this, you are going to find these organisms. Later on we will be talking about using sulfur, nitrogen, nitrate, a number of different elements again for the electron acceptor for these organisms in extreme environments.

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