molecular biosciences 305: microbial ecology part 1 ...c141).pdf · ammonia, sulfates, phosphates,...

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Molecular Biosciences 305: Microbial Ecology Part 1 Lecture 26 [Consetta Helmick]

Slide #: 1 Slide Title: WSU Online Title Slide Title: Microbial Ecology Part 1 Instructor: Consetta Helmick online.wsu.edu Audio: [Music]

Slide #: 2 Slide Title: Microbial Ecology Part 1

Microbial Ecology o Food Chain o Aquatic Habitats o Terrestrial Habitats

Nutrient Cycles Audio: Lecture three, microbial ecology: the food chain, aquatic habitats, terrestrial habitats, and the nutrients cycles.

Slide #: 3 Slide Title: Slide 3

Microbes cycle nutrients, maintain fertile soil, and decompose wastes and other pollutants - Without, we would quickly become buried by the tons of wastes we generate, and nutrients would be depleted

Yet, less than 1% have been successfully grown in culture Even if we could cultivate all, laboratory conditions may not accurately reflect

real role in environment - Grown in pure cultures under controlled conditions - In nature, organisms grow as members of mixed communities under often changing conditions - Nutrients usually in short supply

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[Image of farmland] Audio: A lot of time when we think about microorganisms or microbes we always think of disease, but less than one percent of all our organisms cause disease. It is because microbes in the soil, in the water, on your skin, normal flora organisms that we have the ability to recycle nutrients. We find organisms in water environments, soil environments, and because of these organisms, they can decompose waste, they can get rid of pollutants for us, and if it wasn’t for these organisms, then again, we would be in a world of hurt. We would be up to our eye teeth literally in carcasses. A number of them also are going to be involved in the nutrients cycle, such as carbon, nitrogen, phosphorous, sulfur. If you remember, plants cannot fix nitrogen. It’s a relationship between the organisms in the soil and on the root nodule that allows them to do this. Because of this unusual relationship we have with these organisms, we can grow crops, we can decompose material (plant material, animal material), and we can recycle our nutrients.


Ecology is study of relationships of organisms - To each other, and to their environment

Living organisms interact with each other in symbiotic relationships: commensalism, mutualism, parasitism

- Organisms in given area, the community, interact with each other, non-living environment to form ecosystem

Major ecosystems include oceans, rivers and lakes, deserts, marshes, grassland, forests, tundra

Region of earth inhabited by living organisms is biosphere - Within the biosphere, ecosystems vary both in biodiversity (number, variety of species and their distribution) and biomass (weight of all organisms) - Microorganisms play a major role in most ecosystems; role an organism plays is its ecological niche

Audio: Ecology is the study of a relationship of organisms. We always think about like the bunny and the grasslands, but microorganisms have their own ecology also. They live in a relationship with their host, such as relationships as commensalism, mutualism, and parasitism- ones that we’ve talked about before. Organisms produce a given community. They interact with nonliving environments to form an ecosystem. Major ecosystems include oceans, rivers, lakes, deserts, marshes, grasslands, forests, tundra, your skin. These organisms inhabited these areas, it is because of the relationship with this we get a biodiversity, large number of variety of species, their

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distribution, exactly what they can do. They play a major role in ecosystems. They play a major role in ecological niches.


Ecology is study of relationships of organisms o Microenvironment- the environment immediately surrounding an individual-

is most relevant to that cell Difficult to measure, since most microbes so small Macroenvironment more readily measured, but may be different

Consider bacterial cells living within a biofilm

Growth of aerobic organisms can deplete O2, create microzones where obligate anaerobes can grow

Fermenters can produce organic acids that may be metabolized by other organisms; various growth factors can also be transferred between organisms

Thus, microbes unexpected in a macroenvironment might thrive in the microenvironment

Audio: When we think of ecology also we always think of macroenvironments, the large environment, the bunny and the grassland, the raptor that feeds on the bunny, but we also have what are called microenvironments, and these are things that immediately surround an individual and is most relevant to the cell. Difficult to measure sometimes because microbes are so small, but when we look at the relationship between our organisms and their environment, remember the biofilm. The biofilm is a little ecosystem. Organisms attach to a surface via the pili, the fibrion, the slime layer, the capsule, the flagella, and then another organism attaches and then another organism attaches, and they’re capturing food and water and every nutrient that they require, so these little biofilms are little, again, little ecosystems, and those ecosystems again serve a very important purpose. Not all organisms require oxygen, so an ecosystem could be an anaerobic environment. Fermenters can produce organic acids that can metabolize other organisms, growth factors can be made between organisms, environments can be changed, think about the growth curve. So these microenvironments are just as important as the macroenvironments, and the organisms just thrive, and they can change those microenvironments to meet their THIR requirements.

Slide #: 6 Slide Title: Food Chain Food Chain

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Nutrient Acquisition o Organisms categorized according to their trophic level

Source of food; intimately related to nutrient cycling o Three general trophic levels: primary producers, consumers, and decomposers

[Diagram of food chain] Audio: The food chain; who eats whom is basically the food chain. So organisms, again, acquire nutrition at different levels, so organisms are categorized according to their trophic level. The source of food, the relationship with nutrient cycling, and there are three general trophic levels when we think about the food chain. The primary producers, the consumers, and the decomposers. So if you look at the illustration below, the sun, again, is stimulating the producers, plant material, algae, photosynthesis occurs, those organisms grow. Then something’s going to feed on the producers. It could be a primary consumer, it could be an insect, it could be a cow, it could be a sheep. Then we’re going to have our consumers again feeding on our primary consumers, our secondary consumers, our tertiary consumers, so who eats whom. And eventually everything dies, ashes to ashes, dust to dust. Everything has to die. When it gets back into the soil or water system then we have our decomposers. And our decomposers are going to break that material down, release those nutrients, and the whole process starts again.

Slide #: 7 Slide Title: Who Eats Whom Who Eats Whom

Primary producers are autotrophs o Convert CO2 into organic material o Photoautotrophs us sunlight for energy o Chemolithoautotrophs oxidize inorganic chemicals o Serve as food source for consumers, decomposers

Consumers are heterotrophs o Use organic materials; rely on activities of autotrophs o Herbivores eat plants or algae, are primary consumers o Carnivores that eat herbivores are secondary consumers; those that eat other

carnivores are tertiary consumers o Chain of consumption is food chain; interacting food chains are a food web

Audio: Who eats whom? Primary producers are autotrophs. They convert carbon dioxide into organic material. Photoautotrophs use sunlight for energy- process of photosynthesis. Our chemolithoautotrophs oxidize inorganic chemicals, again, that serve as a food source for consumers and decomposers. Consumers are heterotrophs. They use organic material, rely

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on activities of the autotrophs. Herbivores eat plant or algae, our primary consumers. An insect could be a primary consumers. Carnivores, they eat the herbivores, are secondary consumers. Those that eat the other carnivores are tertiary consumers. Chains of consumption is the food chain. Interacting food chains are what are called food webs.

Slide #: 8 Slide Title: Food Chain

Decomposers are heterotrophs that digest remains of primary producers and consumers

o Fresh or partially decomposed organic matter (including carcasses, excreta, plant litter) is detritus

o Specialize in digesting complex materials such as cellulose, converting into small molecules more easily used by other organisms

o Complete breakdown of organic molecules into inorganic molecules such as ammonia, sulfates, phosphates, carbon dioxide is called mineralization

o Microorganisms, especially bacteria and fungi, play a major role in decomposition due to ubiquity and unique metabolic capabilities

Audio: As we continue with the food chain, the decomposers are heterotrophs that digest remains of primary producers and consumers. Ashes to ashes, dust to dust. Fresh or partially decomposed organic matter, including carcasses, excrement, plant litter, again, is debris. These organisms specialize in digesting complex materials, such as cellulose, converting it to small molecules making it easier for other organisms to use or we can get complete breakdown of the organic material into inorganic materials, such as ammonia, sulfur, phosphates, carbon dioxide, and this is called mineralization. Microorganisms, especially bacteria and fungi, play a major role in decomposition to their ubiquity and unique metabolic capabilities. They’re found everywhere. They can utilize almost everything. They can be found in almost any pH. They can be found at almost any temperature, any oxygen requirement, and any nutritional requirement. Extremely, extremely diverse.


Bacteria in Low-Nutrient Environments o Common in nature; include lakes, rivers, streams

Microorganisms that can grow in dilute aqueous solutions are widespread; most grow in biofilms

Microbes can even grow in distilled-water reservoirs (e.g., in laboratories, pulmonary mist therapy units in hospitals)

Extract trace nutrients absorbed by water from air or adsorbed onto the biofilm

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Growth is slow but can reach 107 per milliliter; not high enough to result in cloudy solution, so he goes unnoticed

Can have serious health consequences, impact success of laboratory experiments

Organisms that grow in dilute environments contain highly efficient transport systems for nutrient uptake

Audio: A lot of our organisms live in very low nutrient environments. Common in lakes, streams, rivers, soil. Microorganisms that can grow in dilute aqueous solutions are widespread. Most begin growing in biofilms. That biofilm allows them to trap their food source, create a little ecosystem, everybody’s protected, and they continue to thrive. Microbes can even grow in distilled water reservoirs. We see this a lot of time in laboratories. You’ll see a pink or red growth inside your tubing or your water column or your water filter. More than likely that’s going to be pseudomonas or seratia. If we have little yellow colonies somewhere, again, it could be micrococcus. The thing is this, again, that they have the ability to go everywhere, so they can grow quickly, they can grow slow, but they can reach 107 per million or higher concentrations that don’t even go unnoticed. Can cause serious health consequences and impact success of laboratory experiments, so you always have to be checking your equipment: tubing, distillers, all of these things, filters. In hospital situations, kidney dialysis tubing, any kind of tubing that has moisture in it organisms, again, could grow. Organisms that grow in dilute environment contain highly efficient transport systems for the uptake of nutrients, and they also use different final electron acceptors in their metabolism, which we’ll be seeing in the next lecture.


Microbial Competition and Antagonism o Competition fierce, results quickly evident

Ability to compete related to rate of multiplication, also ability to withstand adverse environmental conditions

Because of logarithmic growth, small differences in generation times quickly produce very large differences in total numbers of cells

o Antagonism also helps determine community makeup Some microbes resort to chemical warfare, produce antimicrobials

Bacteriocins kill closely related strains [Image of the growth of bacteria] Audio: You have to go back and think about the growth curve. When we talked about the growth curve, remember we said the lag phase, the log phase, the stationary phase, and the death

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phase, and during each one of those phases organisms are competing for nutrients, oxygen, pH, whatever, again, that organism requires. Then they have the ability also to create secondary metabolites, the antibiotics, the exoenzymes, so now, again, if you think about this from an ecosystem, this is a competitive fierce, extremely harsh, violent environment that organisms, again, live in, and so they have the ability to adapt and then they have the ability to, again, change their environment (think about the milk growth curve), so that they can, again, get what they require. Some microbes resort to chemical warfare, literally. They can produce, again, antibiotics, exoenzymes, bacteriocidins (it means to kill- closely related strains). Our streptomycin organisms produce our streptomycin antibiotics that we use in medicine all the time. Fungus that grows on certain foods, the penicillin fungus, again, produces penicillin. It wasn’t produced for our benefit; these were produced, again, so that the organisms could survive in their environments.


Microorganisms and Environmental Changes o Environmental changes often alter communities

Organisms adapted to live in one environment likely not well suited to a different one

External sources can change Growth, metabolism of organisms can also alter

Nutrients become depleted, wastes accumulate

Can bring about succession of bacterial species

Succession in raw milk is example [Graph of time and acidity and number of organisms] Audio: If we think about the growth curve, now apply it to a container of milk. Microorganisms can environmentally change their environment and then again select for or select against different organisms. If you take a container of milk, leave it in your fridge for a little bit longer than it’s supposed to be, it’s going to change over time. If we look at the illustration below, what we’ll see is that in that container of milk we will have our lactobacillus species reacting first. They’re going to use the lactose, they’re going to use the food supply, they’re going to produce byproducts, they’re going to change the pH. Changing the pH is going to select for lactobacillus species, and, again, this is the organism we use in the production of yogurt- that’s why yogurt has a little bit of a sharp taste to it, and then as those organisms use up those food sources and, again, die off, pHs are going to change, and then we’re going to wind up selecting for our yeast and our molds, our proteins are going to curdle, you drink that milk it tastes disgusting, and then eventually we’re going to select for our putrefying bacteria or our spoilage bacteria, and by that time your milk is pretty much toast, so you’re looking at about two weeks down the road. But you can do this with any organism, you can do this

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with any environment that’s going to change over time because organisms that are surviving are selecting literally for another organism, so if you look at that illustration, those four growth curves are literally what is going on in a container of raw milk.


Microbial Communities o Often grow as biofilms attached to solid substrates or at air-water interfaces

Microbial mat is a specific type: thick, dense, highly organized structure composed of distinct layers

Colors frequently correspond with microbial groups

Photosynthetic cyanobacteria (green)

Anoxygenic phototrophic purple sulfur bacteria (pink)

Obligate anaerobic sulfate-reducers (black) Many locations; hot springs near Yellowstone extensively studied

[Image of microbial groups in microbial mat] Audio: Besides organisms growing, again, in a liquid environment they can also grow in a solid environment. They can produce solid biofilms either on air or, again, water. We get these microbial mats, and they’re a specific thick, dense, highly organized structure composed of distinctive layers. If you look at the illustration here, this is a winagasky column, this is something that’s very common that you can do in a lab- you put in soil, you put in different types of substrates, and, again, look at it over time. And so what we see is that you’ll get different colors. Organisms can produce a number of pigments, which also, again, show us in our blooms and our diseases, so some of the organisms that produce color are the cyanobacteria, photosynthetic bacteria, they’re going to produce a green color, our anoxygenic phototrophic purple sulfur bacteria, again, is that pink layer, and then our obligate anaerobes also produce, again, sulfur, so our sulfur reducing, and we will wind up with the black layer, so by looking at these, again, columns and things like this, we can get an idea of what organisms are going to be in that location. Any locations, hot springs near Yellowstone, have been extremely studied because of the temperature. Remember archaea species, and then if we look at the Great Salt Lakes, also, again, because of that extreme salt, which is our halophilics, and so our organisms are selecting for very distinctive locations, but they have the ability to survive in these locations because of their diversity.

Slide #: 13 Slide Title: Aquatic Habitats

Marine environments cover >70% of earth o Most abundant aquatic habitat; ~95% of global water

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Freshwater environments (lakes, rivers) only a fraction o Deep lakes, oceans have characteristic zones

Uppermost layer supports growth of photosynthetic microorganisms including algae, cyanobacteria

Organic material they synthesize gradually descends, is metabolized by heterotrophs

Audio: Let’s look at some specific, again, microbial ecology environments. Our aquatic habitats- marine environments cover 70% of the Earth. Most aquatic habitats, 95% of global water. Fresh water environments, lakes, rivers, are only a fraction, but you have the ocean, stagnant water, ponds- all these different types of things. In deep lakes, oceans have a characteristic zone: upper layer supports growth of photosynthetic microbes including algae and cyanobacteria. As the sunlight dissipates, we’re going to get selection of different organisms. As oxygen temperature and food requirements change, again, we’ll select for very specific organisms.


Deep lakes, oceans (continued…) o Number of microbes influenced by nutrient content

Oligotrophic (nutrient poor) waters limit growth of autotrophs due to lack of inorganic nutrients

Especially phosphate, nitrate, iron Eutrophic (nutrient rich) waters encourage growth of autotrophs,

which produce organic compounds that foster growth of heterotrophs in lower layers

Heterotrophs consumer O2, can deplete, leave water hypoxic, lead to death of aquatic animals

[Image of cows on pasture] Audio: If we continue looking at our aquatic environments, the number of microbes influenced by nutrient content are oligotrophic (our nutrient poor waters) limit growth of autotrophs due to lack of inorganic nutrients especially phosphorous and nitrogen and iron. Our eutrophics (nitrogen rich waters) encourage growth of autotrophs, which reduce organic compounds that foster growth of heterotrophs in lower layers. So our heterotrophs consume oxygen but can deplete, leave water hypoxic, which can lead to death of aquatic animals, fish, insects, and a number of other things. So by the organisms growing into that area too fast, too high, we’re going to change the dynamics, release or take up the saturated oxygen, and then we’re going to select for a different population of organisms, and we may kill a number of the

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eukaryotic organisms that require the oxygen.

Slide #: 15 Slide Title: Aquatic Habitats

Marine environments o Ranges from deep sea to shallower coastal regions

Deep sea nutrient poor; nutrients may be abundant in coastal regions due to runoff from the land

Seawater contains ~3.5% salt vs. ~0.05% in freshwater

Seawater supports growth of halophilic organisms

Temperatures vary widely at surface, generally decrease with depth to about 2˚C in deeper waters

Typically oligotrophic; lack of nutrients limits growth

Limited organic material produced by photosynthetic organisms is quickly consumed as it descends

o Few nutrients reach sediments below o Even in deep sea, marine water O2-saturated due to

mixing from tides, currents, wind action Audio: In our marine environments, again, we have to look at a little bit different because now we’re dealing with maybe salt concentrations- can range from deep sea to shallower coastal regions, estuaries. Deep sea nutrients are poor. Nutrients may be abundant in coastal regions due to runoff from, again, land and agricultural areas. Seawater contains 3.5 to salt versus 0.05 in freshwater. Seawater supports growth of, again, halophile organisms that select for the high salt concentrations, temperatures can vary at the surface generally decreasing with depth about 2 degrees in deeper water, so now we’re selecting for organisms that like a cooler environment, so when you think about your marine environments, your estuaries versus your ocean, think about what those organisms are requiring. Typically the oligotrophics lack of nutrient limit growth. Limited organic material produced by, again, photosynthetic organisms is quickly consumed as it descends. Few nutrients reach sediments. Even in deep seas, marine water oxygen saturate due to mixing from tides, currents, and wind action, but again, as you get deeper into those areas, we’re going to see a shift in oxygen areas. One of the things we’re seeing now especially in freshwater streams is the ability for E. coli to survive. We find it in sediment but remember E. coli can be a facultative anaerobe, so it can be an anaerobe, a facultative anaerobe, and it can adapt in a number of environments.


Marine Environments (continued…)

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o Ecology of inshore areas less stable than deep seas Can be dramatically affected by nutrient-rich runoff Example is dead zone (e.g., in Gulf of Mexico, elsewhere)

Mississippi River carries nutrients from agricultural, industrial, and urbanized areas out into the Gulf

Algae, cyanobacteria flourish in spring, summer

Heterotrophs metabolize the organic compounds, consume dissolved O2, turn region hypoxic

[Diagram of a marine environment with nutrient-rich water and affected organisms] Audio: Marine environments. Ecology of inshore areas is less stable than deep seas, so you get a lot of mixing of nutrients, you get nutrients coming in from runoff, from either sewage treatment plants or agriculture, and this can have a huge impact, again, on those areas. For example, the dead zone: The Gulf of Mexico and other places. Mississippi River carries nutrients from agricultural land, industrial, and urban areas out to the Gulf. The Gulf doesn’t have a lot of mixing, it’s not extremely deep, the temperatures are going to be a bit more stable, so you’re going to select for certain organisms. You’re going to get mainly your algae, your cyanobacterias flourish, again, in the spring and the summer because if you think about agricultural practices and temperatures and sunlight. The heterotrophs metabolize the organic compounds, consume dissolved oxygen, and turn the area, again, into hypoxic, and hypoxic means without oxygen, so you can create a dead zone. Organisms can’t thrive there; eukaryotes can’t thrive there, again, because of the lack of saturated oxygen or the dynamics have changed.

Slide #: 17 Slide Title: Terrestrial Habitats

Human interest in soil microbiology stems partly from useful chemicals synthesized by microbes

o Over 500 different antibiotic substances produced by species of Streptomyces >50 have applications in medicine, agriculture, industry Pharmaceutical industry has tested many thousands of soil

microorganisms looking for useful antibiotics Soil microbes investigated for ability to degrade toxic chemicals

(bioremediation) Soil probably has greatest range of biosynthetic and biodegradative

capabilities Audio: Terrestrial habitats. Soil- best thing to think about. Human interest in soil microbiology has escalated. Stems partly from the useful chemicals synthesized by the microbes themselves.

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Pharmaceutical companies are not investing a lot of money into new antibiotics. Time, resources, turnover, payback is just not there. Plus with the number of our antibiotic resistant organisms, we really have nothing again to treat them with, so there’s a new shift to actually looking at soil organisms because a number of our antibiotics can do come from, again, our soil organisms, and if you think about the harsh environment that soil lives in—dry, temperature-dependent, pH, nutrient-dependent—we have a huge number of organisms that have to produce either secondary metabolites, antibiotics, or exoenzymes to survive. Could we tap into those? Could we go back and look for new antibiotics? And that’s exactly what, again, we’re starting to do. So there are over 500 different antibiotic substances produced by the species of streptomycin. Again you use streptomycin drugs all the time when you go to the doctor. Over 50 have applications in medicine, agriculture, and industry. Pharmaceutical industry has tested many thousands of soil microorganisms looking for useful antibiotics, again, looking back at our soils. Soil microbes investigated for ability to degrade toxin chemicals, even the process of bioremediation. We have a lot of contaminated soil out there from smelters, silver, mining, mercury, lead- how do we clean up our soil? Could we actually add an organism in there that would help clean up the process- huge research area. Soil probably has the greatest range of biosynthetic and biogradative capabilities, and so now we’re going back again and tapping into these areas and seeing what we can find.

Slide #: 18 Slide Title: Biogeochemical Cycling and Energy Flow

Elements have three purposes in metabolism o Biosynthesis (biomass production)

Required for all organisms; many different pathways o Energy source

Reduced carbon compounds such as sugars, lipids, amino acids used by chemoorganotrophs

Chemolithotrophs can use reduced inorganic molecules such as hydrogen sulfide (H2S), ammonia (NH3), and hydrogen gas (H2)

o Terminal electron acceptor In aerobic conditions, O2 is used In anaerobic conditions, some prokaryotes can use nitrate (NO3-),

nitrate (NO2-), sulfate (SO4

-), or carbon dioxide (CO2) Audio: When we think also about these microbial ecology, we got to think of biogeochemical cycling and energy flow or the nutrients cycle. Elements have three purposes in metabolism. First, biosynthesis, biomass production. Required for all organisms. Many different pathways, so to produce things again you have to have those elements present. Again, 25 different elements for all life forms to produce and continue life.

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Energy source. You got to reduce carbon compounds, such as sugars, lipids, amino acids, again, into energy, into byproducts, again, that we can use, into nucleic acids, into lipids, into amino acids, and then, again, energy. Chemolithotrophs can use reduced inorganic molecules, such as hydrogen sulfide, ammonia, and hydrogen gas, so they have the ability to tap into a different resource than eukaryotic cells. We can, again, only use oxygen for energy production. Terminal electron acceptor or the final electron acceptor is the end of the electron transport chain. In aerobic conditions, oxygen. In a eukaryotic cell you have to have oxygen at the end of your electron transport chain to make ATP, but we have a number of organisms that can use different electron acceptors at the end of their electron transport chain. In an anaerobic condition, we have some prokaryotes that can use nitrates, nitrites, sulfate, or carbon dioxide, and when we get into our next set of material on energy metabolism, we’ll be looking into those final electron acceptors and seeing how organisms use them.


Carbon Cycle o Carbon fixation is fundamental aspect

Without primary producers, no other organisms could exist o Respiration and Fermentation

Organic material consumed by heterotrophs for energy source and biosynthesis

CO2 produced Carbon travels through food chain

[Diagram of the carbon cycle] Audio: Next we’ll be talking about a number of the nutrients cycles. We’ll start with carbon. Carbon fixation is a fundamental aspect. Without primary producers no other organisms could, again, exist. Respiration and fermentation. Organic material consumed by heterotrophs for energy source and biosynthesis, again, produces carbon dioxide. Carbon travels through the food chain. If you look at the illustration to the right and know this illustration to the right, it shows you, again, all the processes of the carbon cycle from the aerobic again to the anaerobic and then a number of the byproducts that are produced through this is methane. We have a real problem with methane and methane gas destroying our ozone. So, again, we’re trying to figure out how to decrease the production of methane especially in ruminant animals by, again, changing their diets and, again, seeing if we can get different organisms that don’t produce so much methane, so be sure, again, to understand this process.

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Carbon Cycle (continued…) o Decomposers degrade detritus o Rapidly multiplying bacteria often play dominant role in degrading sugars,

amino acids, proteins o Only certain fungi degrade lignin

Aerobic conditions required, so wood at bottom of marshes resists decay

o O2 supply strongly affects carbon cycle Allows degradation of some, helps determine types of carbon-

containing gases produced [Image of a fungus] Audio: Okay, let’s talk a little bit more about the carbon cycle. Okay, decomposers degrade debris. Rapid multiplying bacteria often play a dominant role in degrading sugars, amino acids, and proteins. Carcass decomposing: ashes to ashes, dust to dust. Only certain fungi degrade lignin. Aerobic conditions are required so wood at the bottom of the marshes resist decay, so that’s why a lot of times when you see logs and stuff in sediment in environments where there isn’t a lot of oxygen, they look the same way as when they fell into that area because the fungi and things like this cannot decay them. Oxygen supplies strongly affects carbon cycle. It allows degradation of some, helps determine types of carbon gasses that are going to be produced. Again, example would be methane.


Methanogenesis and Methane Oxidation o In anaerobic environments, CO2 used by methanogens

These archaea obtain energy by oxidation of hydrogen gas, using CO2 as terminal electron acceptor

Generate methane (CH4)

Methane enters atmosphere, is oxidized by ultraviolet light and chemical ions, forms carbon monoxide (CO) and CO2

Microorganisms called methylotrophs can use methane as an energy source, oxidizing it to produce CO2

Audio: I keep coming back to methane because, again, we do have organisms that produce methane

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gas. We have our methanogenesis and methane oxidizers. In an anaerobic environment, carbon dioxide is used by methanogens. These archaea obtain energy by oxidation of hydrogen gasses using carbon dioxide as their final electron acceptor, but they generate methane. Methane enters the atmosphere, is oxidized by ultraviolet light, and chemical ions form carbon monoxide and, again, carbon dioxide. So we’re destroying our ozone by, again, a number of these methane producers. Microorganisms called methylotrophs can use methane as an energy source, oxidizing it to produce carbon dioxide. Alright let’s look at the rumen of a cow, a deer, an elk. For that animal to process cellulose, the cell wall, there are billions of organisms living in the rumen as one of their byproducts as they are breaking down that cellulose, again, which is glucose linked to glucose linked to glucose, then the byproducts they’re producing is methane or methane gas. So it’s been theorized or thought that the number of dairies we have could be actually impacting methane production and, again, impacting our ozone. You as a eukaryote, you also produce methane as you’re processing a number of these carbon structures again also. So what do we do? How do we combat it? So, again, we look at our gasses, we look at our animals, we look at our cars, again, trying to get rid of carbon dioxide production. We plant plants along highways now or at long freeways because they’ll capture the carbon dioxide and use it in photosynthesis, so if you think about the dynamics of how to combat just methane, like I said, go back and look around you, and you’ll come up with a number of examples where we use microorganisms, different techniques, different ecosystems, to work on this problem of methane.


Nitrogen Cycle o Component of proteins and nucleic acids o Nitrogen fixation

N2 is reduced to ammonia (NH3) Can be incorporated into cellular material Enzyme complex nitrogenase catalyzes Requires tremendous energy since N2 has very stable triple bond

[Diagram of nitrogen cycle] Audio: Nitrogen cycle. Why is nitrogen so important? Lipids are made of carbon, hydrogen, oxygen. Sugars are made up of carbon, hydrogen, oxygen. Proteins are made of carbon, hydrogen, oxygen, and nitrogen. Without the nitrogen you would not be producing the amino acids and you would not be, again, producing polypeptide chains or, again, proteins. So nitrogen is a component of proteins and our nucleic acids, so we have nitrogen fixation. Nitrogen is

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reduced to ammonia (NH3). It can be incorporated into cellular material, enzyme complexes (nitrogenase catalyzes it), again, requires tenuous energy since nitrogen has very stable, again, triple bonds. If you look at the illustration again on the nitrogen cycle, you have atmospheric nitrogen that is going to be put into the soil, be captured by organisms by various specific populations of organisms, make the nitrogen available to bacterium, make the nitrogen available, again, to plants, so that the plants can take up the nitrogen, produce the proteins that they require, plants are primary producers, our primary consumer comes along, eats the plant, they obtain the nitrogen as they’re eating the plant, secondary consumer comes along and eats the primary consumer, and then, again, we’re passing on nitrogen, all the nutrients, all the energy, and the cycle, again, continues.

Slide #: 23 Slide Title: Mutualistic Relationships Between Microorganisms and Eukaryotes [Diagram of relationship between microorganisms and eukaryotes] Audio: The relationship between bacteria and nodules and plants is a very mutualistic relationship because plants cannot fix nitrogen, they cannot fix atmospheric nitrogen. They get the nitrogen from the soil and from the plants that live in their nodules that have the ability to take the nitrogen from decomposing animals and atmospheric nitrogen and to make it into a form that is useable for the plant because a plant also produces, again, proteins, we never think about proteins and plants, but they produce enzymes, they have transport proteins in their membranes, they have structural proteins, there’s a lot of components in a plant that is protein based, so this relationship between microorganisms, the root nodules, and the plant themselves is a wonderful example of a mutualistic relationship


Nitrogen Cycle (continued…) o Atmosphere consists of ~80% nitrogen gas

Relatively few organisms can fix nitrogen

All are prokaryotes; called diazotrophs Some are free-living, such as members of Azotobacter

Heterotrophic, aerobic, Gram-negative rods; may be main suppliers of fixed nitrogen in ecosystems lacking plants with nitrogen-fixing symbionts (e.g., grasslands)

Dominant free-living anaerobic soil diazotrophs are members of genus Clostridium

Certain cyanobacteria are diazotrophs; use both nitrogen and carbon from atmosphere

Symbiotic diazotrophs form relationships with higher organisms,

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especially plants Audio: If we go into the nitrogen cycle in a little bit more detail, okay, atmospheric nitrogen is about 80% gas. Relatively few organisms can fix nitrogen. All prokaryotes are called diazotrophs. Some are free-living, such as the members of the azotobacteria. They’re heterotrophic, aerobic, gram-negative rods that, again, can fix nitrogen in ecosystems, and they can allow that nitrogen to be available to plants so they, again, have this wonderful mutualistic relationship. Certain bacteria, again, have the ability to fix nitrogen and carbon from, again, the atmosphere. So when we see this relationship between the diazotrophics with the relationship with higher organisms especially plants, it is a wonderful symbiotic relationship.


Nitrogen Cycle (continued…) o Ammonification and Decomposition

Ammonification is decomposition process that converts organic nitrogen into ammonia (NH3)

In alkaline environments, gaseous ammonia may enter atmosphere; in neutral environments, ammonium (NH4

+) is formed, adheres to negatively charged particles

Wide variety of microbes degrade proteins, among most common nitrogen-containing compounds

Secrete proteolytic enzymes to break proteins into short peptides or amino acids

Products are transported into cell

Amino groups are removed, releasing ammonium Audio: Also we have the ammonification and decomposition. Ammonification is a decomposition process that converts organic nitrogen into ammonia (NH3). In alkaline environments, gaseous ammonia may enter the atmosphere. In neutral environments, ammonium (NH4) is formed; adheres to negatively-charged particles. A wide variety of microbes degrade proteins. Among most contain nitrogen-containing proteins. They can secrete a proteolytic enzyme to break proteins into short peptides of amino acids. Products are transported into the cell. The amino groups are removed, releasing, again, ammonium.


Nitrogen Cycle (continued…) o Nitrification

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Process that oxidizes ammonium (NH4+) to nitrate (NO3

-) Group of obligate aerobic bacteria known as nitrifiers accomplish in

cooperative two-step process

Use ammonium and nitrite (NO2-) as energy sources

Does not occur in anaerobic environments Nitrification has important consequences for agriculture

Farmers often apply ammonium-containing compounds as fertilizers; positive charge adheres to negatively charged soil particles

Nitrification converts to nitrate: readily used by plants, but leaches from soil by rainwater, contaminates water

Nitrite is toxic, can combine with hemoglobin of blood Audio: Nitrification: process that oxidizes ammonium into nitrate. Groups of obligate aerobic bacteria, such as nitrifiers, accomplish this feat in a cooperative two-step process. They use ammonium and nitrite as energy sources, final electron acceptors, but it does not occur in an anaerobic environment. Nitrification has an important consequence, again, for agricultures. Farmers apply ammonium-containing compounds as fertilizer, so to crops to, again, to get the plants to take up the nitrogen for better growth. Nitrification occurs to nitrate readily used by plants but leaches from the soil by rainwater contaminates water systems, so we can get, again, algae blooms, we could get blooms of material in water systems, from nitrogen fertilizers. If you think of high concentrations of blooms, bacteria, then we deplete the oxygen in the water and then we can now be killing organisms and winding with a hypoxic environment. Nitrogen is toxic, again, it can combine with hemoglobin of the blood and cause other issues.


Nitrogen Cycle (continued…) o Denitrification

Reduction of nitrate (NO3-) to gaseous forms such as nitrous oxide (N2O) and molecular nitrogen (N2)

Happens when prokaryotes anaerobically respire, use nitrate as terminal electron acceptor

Can have negative environmental, economic impacts

Under anaerobic conditions in wet soils, denitrifying bacteria reduce the oxidized nitrogen compounds in fertilizers, release gaseous nitrogen into atmosphere

May represent 80% of nitrogen lost from fertilized soils in some areas

Nitrous oxide contributes to global warming

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Useful in wastewater treatment in removing nitrogen Audio: As we continue with the nitrogen cycle, denitrification, reduction of nitrate to gaseous forms, such as nitrous oxide and molecular nitrogen. Happens when prokaryotes anaerobically respire. They use nitrate as their terminal electron acceptor so that they can produce energy. Under anaerobic conditions in wet soils, denitrifying bacteria reduce the oxidized nitrogen compounds in fertilizers, release gaseous nitrate into the atmosphere. It can represent almost 80% of nitrogen lost from fertilized soils in some area. Nitrous oxide also contributes to global warming, again, changing of our ozone layer. It is useful in water treatment plants and removing nitrogen. We’ll be getting into water treatment plants in our last lecture.


Sulfur Cycle o Sulfur found in all living matter, mainly in amino acids methionine, cysteine

Key steps of sulfur cycle depend on prokaryotes o Sulfur Assimilation and Decomposition

Most plants, microbes assimilate as sulfate (SO42-), reduce to form

biomass Decomposition releases hydrogen sulfide (H2S)

[Image of the sulfur cycle] Audio: The sulfur cycle: sulfur is found in all living matter especially amino acids methionine and cysteine. It’s part of the amino acid structure. Disulfide bonds allow for the protein structure itself, so key steps of sulfur cycle depends, again, on prokaryotes. Sulfur assimilation and decomposition: most plants, microbes assimilate as sulfate reduce to form biomass. Decomposition releases hydrogen sulfide, and then we get the salts for gas being released and we get the rotten egg smell. So the sulfur cycle in organisms is crucial for all life forms because we have to have that sulfur in our amino acids and our protein structures to, again, produce our proteins and produce the correct shape. Again, look at the sulfur cycle. Be familiar with it.


Sulfur Cycle (continued…) o Sulfur Oxidation

Hydrogen sulfide (H2S) and elemental sulfur (S0) can serve as energy source for certain chemolithotrophs

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Beggiatoa, Thiothrix, Thiobacillus oxidize to sulfate

Anaerobic marine prokaryotes Thioploca, Thiomargarita namibiensis use energy source and terminal electron acceptor found in different locations

Photosynthetic green and purple sulfur bacteria anaerobically oxidize to sulfate

Sulfur Reduction

Sulfur- and sulfate- reducing bacteria, archaea use as a terminal electron acceptor, reduce to hydrogen sulfide (H2S); unpleasant odor, reacts with metals

Audio: Sulfur oxidation: hydrogen sulfide and elemental sulfur can serve as energy sources for certain chemolithotrophs, so we have these, again, as our final electron acceptors. Some of your photosynthetic green and purple sulfur bacteria anaerobically oxidize, again, to sulfate. Sulfur reduction: sulfur and sulfate-reducing bacteria. The archaea uses, again, electron acceptors, reduce hydrogen sulfide, which causes that rotten egg smell again that can react with metals, it can cause it to look rusty, it can cause it to break down, kind of gives an orange-yellow color to it, again, are all produced by certain bacteria.


Phosphorus Cycle and Other Cycles o Phosphorous is component of nucleic acids, phospholipids, ATP

Most plants, microbes take up as orthophosphate (PO43)

Algae, cyanobacteria limited in many aquatic environments by low concentrations of phosphorous

Addition from other sources (agricultural runoff, phosphate-containing detergents, wastewater) can result in eutrophication

Other important elements including iron, calcium, zinc, manganese, cobalt, and mercury also recycled by microorganisms

Many prokaryotes have plasmids coding for enzymes that carry out oxidation of metallic ions

Audio: Phosphorous cycle and other cycles, again, phosphorous is a component of nucleic acids, phospholipids, and ATP (adenosine triphosphate). Most plants microbes take up, again, orthophosphate from the soil and, again, through the process of, again, nitrogen cycling. Algae, cyanobacteria limited in many aquatic environments by low concentrations of phosphorous. Additional forms of sources, again, come from agricultural runoff, phosphate-containing detergents, wastewater, can, again, result in, again, algae blooms, which can contaminate water systems, deplete oxygen, and, again, we wind up with a dead area. So this

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is one of the reasons we got away from phosphorous detergents and laundry soaps especially if you have a sewage treatment plant nearby or, again, or a septic tank, you could overload your septic tank with phosphorous and then kill off the organisms in your septic tank that are breaking down the material that come from your house, so, again, the phosphorous cycle is the leaching of soil, material coming from runoff, and, again, continuing with the cycle and think back again on your food chain. Also, again, farmers add phosphorous a lot of times to their fertilizer, it’s very important plant production, but they also, again, have to regulate the amount. Think about spring runoff and what could get into a water system. Other important elements include iron cycle, calcium, zinc, magnesium, cobalt, mercury, are also recycled from microorganisms. Some prokaryotes have plasmids coding for enzymes that carry down oxidation of metallic ions. A lot of these organisms, again, are used in bioremediation trying to figure out how to clean up our soils that have been contaminated by lead, mercury, and zinc, but these are also all very important elements in all life forms, so, again, recycling of these nutrients is essential for all life.


Energy Sources for Ecosystems o Chemotrophs harvest energy trapped in chemical bonds

ATP is generated, but portion of energy is lost as heat Energy continuously lost from biological systems

Must be replaced o Photosynthesis converts radiant energy (sunlight) to chemical energy in the

form of chemical bonds Available for chemoorganotrophs Requirement for light traditionally explained why life not equally

abundant everywhere Discovery of different types of communities far removed from sunlight,

including near hydrothermal vents and within rocks, has dramatically altered this idea

These communities rely on chemolithoautotrophs Audio: Energy sources of ecosystems because we will be getting into metabolism here shortly. Chemotrophs harvest energy trapped in chemical bonds. ATP is generated, but a portion of energy is lost as heat. Energy consistently, again, lost from biological systems must be replaced. So we take ATP, we break up a higher energy bond, we now have ADP plus a phosphate bond, we have to reattach that phosphate bond to produce ATP. It’s a cyclic event. Photosynthesis converts radiant energy (sunlight) to chemical energy in the form of, again, chemical bonds. This is going to be available for our chemoautotrophs. Requirement for light traditionally explained why life is not abundant in other areas, again, because of photosynthetic activities. We see there’s a wide variety of organisms that can be involved in

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this, and then if we think about our food chain, most of our producers are photosynthetic producers, and then our primary consumers, our secondary consumers, our tertiary consumers, our decomposers and our cycle.

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