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78 Cards in this Set

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  • Back

What is the relationship between populations, guilds, and communities?

Communities are sets of guilds

Guilds are sets of metabolically related populations

Populations are the progeny of an individual cell

What are the 2 main focuses of microbial ecology?

1) Study of biodiversity of microorganisms and their interactions

2) Study the activities of microorganisms and their effects on the ecosystem

It is a study of them in their niche envrionment

What is biochemical cycling? What is responsible for this cycling?

It is the turnover of carbon, nitrogen, and sulfur which is only possible due to the activites of microorganisms

Soil and ____ is the principal habitat for the majority of microorganisms. Where within the soil can we find these microorganisms. Microorganisms have been found in what type of rock and where?

Water. Most microorganisms are in soil and sediments found in a thin layer within a few feet of the surface. Living microorganisms (bacteria) have been found in porous rock formations thousands of feet below the surface of the earth.

Where does the concentration of microorganisms never drop below 10^5 cells/ml? Where are the highest concentrations of microorganisms found in this particular environment?

Microorganisms in bodies of water such as lakes or oceans are concentrated at the surface and at the very bottom, in the few inches just above the mud.

The lowest concentrations of microorganisms in open sea-water never drop below about 10^5cells per ml.

When microorganisms are found in the _____, they are considered accidental wanderers which can be blown to heights exceeding 20,000 ft.


What 6 factors defines a microenvironmental niche?

1) pH

2) Temperature

3) Pressure

4) Light

5) Water availability

6) Oxygen

What are the 2 characteristics of a microenvironment?

1) Microscopic at the micron level

2) Steep gradients with extreme changes in physiological parameters

What do the benefits of living with a biofilm have in common with the properties of a surface as it relates to a microbial habitat?

1) They both Immobilize diverse microorganisms to allow bulk liquid flow for transport of nutrients and waste products

2) They both confer protection from damage by toxins, biocides, other organisms, and antibiotics

What benefit does living within a biofilm differ confer that the properties of a surface as it relates to a microbial habitat cannot provide and vice versa?

Biofilm: Buffer against changes to the 6 factors that defines a microenvironmental

Surface: Can concentrate and also act as nutrients

Most microorganisms in the environment exist as _______, such that 60% of all bacterial infections in humans are caused by _____

biofilms, biofilms!

What is reductive cell division and it's function?

Bacteria's ability to “tune down” metabolically by increasing their surface-to-volume ratio by reductivecell division

What is the relationship between environmental and laboratory growth rates for microorganisms

Growth rates of microorganisms in the environment are typically only 1%-10% of those achieved in the laboratory

Different organisms compete for niche's and can inhibit the growth of competitive organisms through the products of toxic substances such as?

Acids, antibiotics, bacteriocins

Define syntrophic consortia. Give an example.

In some situations, microorganisms are involved in cross feeding, stimulating the growth of a neighbor by metabolizing one or more of its waste products. Cross-feeding in bacterial communities is known as syntrophic consortia. Ex: The oxidation of ammonia to nitrate by one organism, and the reduction of nitrate to ammonia by another.

How can we give an organisms a selective advantage in a mixed sample?

We can grow it in an enrichment culture which is made by duplicating the environmental conditions where an organism is naturally found and then “spiking” the medium with one or more nutrients.

Give an example of a sample that confers a selective advantage to cellulose degrading organisms?

If we wish to select for cellulose degrading microorganisms, we can take a sample of mud, put it in a tube and add paper to the tube.

Once an organisms is grown in an enrichment culture, what 2 ways we can isolate a pure culture of it?

1) Dilution to extinction

2) Streak plating

How can we use dilution to extinction to isolate an organism?

We need an enrichment culture so that the predominant microorganism present will be the target rather than a contaminant. We then perform dilution to extinction via serial dilutions to find the lowest dilution of sample where the microorganism where still grow. The final dilution will have the predominant organism of the enrichment culture, eliminating all others and allowing isolation.

What are the 3 ways to reveal the presence of individual cells when we have non-culturable organisms?

1) Acridine Organce nucleic acid staining

2) LIVE/DEAD Bac light to distinguish between live and dead bacteria

3) Direct Cell count by counting stained organisms

How can we discriminate between actively growing and non-growing bacteria? What is the mechanism of action for this?

We can use acridine orange nucleic acid stain. Acridine Orange intercalates into the major groove of DNA and RNA and fluoresces orange upon binding of single stranded nucleic acid or green upon binding of double stranded nucleic acid.

What flourescence color would we expect to predominate in a live sample stained with Acridine Orange and why?

We would expect to see orange fluorescence predominate in live cells since actively growing cells contain large amounts of single stranded RNA and AO fluoresces orange when binding single stranded nucleic acid. Actively growing cells contain large amounts of RNA, whereas dead cells contain no RNA.

Acridine Orange and the LIVE/DEAD Baclight both can distinguish between live and dead cells. How do these methods differ?

Acridine Orange distinguishes between growing and non-growing cells based upon nucleic acid activity, whereas the LIVE/DEAD Baclight detects the presence of an intact cytoplasmic membrane to distinguish between live/dead cells

What is the 3 steps for Direct Cell Count?

1) Cells are fluorescently stained

2) Cells are attachment onto a filter membrane

3) Membrane is viewed under microscope and counted

What is the formula for calculating the total number of cells from a Direct Cell Count?

Total cell count = (number of cells in the observed area) * number of observed areas that fit into 1ml of the original sample

Acridine Orange, LIVE/DEAD Baclight, and Direct Cell count reveal the presence of cells without culturing, but does not distinguish between types of cells. What are 3 ways that we can use to determine the types of cells in a sample without culturing the sample.

1) Flourescence labeled antibodies

2) FISH Probing


What are the 2 uses of flourescence labeled antibodies when working with unculturable cell samples?

1) Quantification

2) Evaluate which cells/groups of cells carry a particular antigen from an environmental sample

How can we run a PCR on an individual bacterium in a single sample when there are many different taxonomic groups present? What is the point of this?

In Situ Reverse-Transcriptase PCR. RT-PCR is used in order to amplify specific mRNA in a sample to determine whether a particular gene is being transcribed in a bacterium(without having to culture the bacteria)

How can we seperate an individual bateria from an uncultured sample?

Optical Tweezers + FISH

What are the 3 major zones in a body of water. What would we expect to find in each zone?

1) Oxic zone: Chemoorganotrophic bacteria

2) Photic zone: Cyanobacteria, algae,

3) Anoxic zone: 4 guilds of bacteria

What kind of bacteria do we find in the 4 guilds found in community 3 of a body of water, the sedimentary anoxic zone?

Guild 1: Methanogenenic + Hemoacetogenic bacteria

Guild 2: 2 types of Sulfur reducing bacteria

Guild 3: Denitrifying bacteria + ferric iron-reducing bacteria

Guild 4: Fermentative bacteria

Where do we find bacteria that use CO2 as a reactant in their metabolism in a body of water? What are their products?

- We find them in the sedimentary anoxic zone

- Both methanogenic and homoacetogenic bacteria use CO2 as a reagent

- Methanogenic produces CH4 methane

- Homoacetogenic produces acetate

What do the 2 types of sulfur reducing bacteria have in common? What are their substrates for this reduction? Where are they found in a body of water?

Both produce H2S

One of them reduces SO4 -2 sulfate whereas the other uses elemental sulfur

They are found in the anoxic zone, in the sediment layer, in community 3

What is the predominant chemical reaction that occurs in the oxic zone? What kind of bacteria are responsible for this?

Chemoorganotrophic bacteria

C6H12O6 + 6 O2 --> 6 CO2 + 6 H20

What is the predominant chemical reaction that occurs in the photic zone? What kind of bacteria are responsible for this? What other bacteria do we find in this zone? How do they differ?

Cyanobacteria and Algae

6 CO2 + 6 H20 --> C6H12O6 + 6 O2

We also find green and purple sulfur or non-sulfur bacteria which uses sulfur as a reagent for photosynthesis instead of water

Where do find denitrifying bacteria together with ferric iron-reducing bacteria? What are their respective reactions?

Guild 3 in the anoxic zone in the sediments

NO3 - --> N2

Fe 3+ --> Fe2+

What form of intercellular communication can we block to prevent biofilm formation? How can we disrupt a mature biofilm?

Block biofilm formation by addition of quorum sensing blocker

Disrupt mature biofilm by addition of dispersion inducer

What chemical exchange occurs between the anaerobic layer of water and the anaerobic sediment? How does this exchange occur?

H2S is produced in the water layer and exchanged for SO4 -2 from the sedimentary layer

This occurs because the photosynthetic purple bacteria in the anaerobic zone reduce hydrogen sulfide or elemental sulfur and produce sulfate as their byproduct for use by bacteria in the anaerobic sediment layer.

The rate of sulfate reduction is dependent on the availability of __. We measure this through the use of what radioactive isotope?

Concentration of the product is dependent on the presence of H2. We use sulfur 35 isotope to measure formation of hydrogen sulfide (H2S)

The rate of methanogenesis is dependent on the availability of __. We measure this through the use of what radioactive isotope?

Methanoic acid CH3COO- via the Carbon 14 radioisotope

What is the function of an oxygen electrode? How does it work?

Measures oxygen levels using the net reaction: O2 + 4 e− --> 2 H2O → 4 OH−

Platinum rod functions as cathode when voltage is applied. Oxygen is reduced to H2O at gold surface generating a current which can be measured

What do we use to detect nitrate? How does this sensor work?

Biological microsensor. Denitrifying bacteria convert NO3- to N20 which is further reduced to N2 at the cathode where it is detected.

The use of microelectrodes allows for development of depth profiles for O2, pH, and H2S respectively. What trend do we see using microelectrodes in soil. At what layer do in water do we see a similar inversion of oxygen and hydrogen sulfide concentration?

At the surface of the soil is the highest concentration of O2 and highest (basic) pH with no hydrogen sulfide present. Oxygen and pH decrease as we go deeper as hydrogen sulfide increases in concentration. Oxygen concentration is inverse to Hydrogen sulfide concentration just under the surface of the soil. This trend occurs at the thermocline in water

What radioisotopes do we use to measure protein synthesis and DNA replication respectively which is also growth rate.

35 radioisotope of sulfur via Sulfur-methionine is used to measure protein synthesis whereas tritiated hydrogen-thymidine is used to measure DNA replication

Comparing the ratio of ___ to ___ enables us to determine whether the substance is of biological origin or geological origin. Which isotope would we expect to find in higher concentration in organic and inorganic substances respectively? Why would we expect this trend?

C-13 to C-12. Organic derived compounds should have higher concentrations of C-12 rather than the stable C13 because metabolic pathways preferentially incorporate the lighter isotope due to it's lower inertia

What are the 3 main terrestrial soil environments? How do we derive these respectively?

1) Mineral soils derived from weathering of rocks and other inorganics

2) Organic soils derived from sedimentation in bogs and marshes

3) Rhyzosphere is the habitat surrounding the roots of a plant

In the terrestrial soil microenvironment, where does the predominant microbial activity?

Most extensive microbial activity occurs on the surfaces of soil particles(biofilms), usually within the rhizosphere.

What are the 4 ingredients of a soil aggregate?

Combination of organic material, mineral water, water and microorganisms

There are both aerobic and anaerobic zones in aquatic environment. What microorganisms would we find there respectively?

Aerobic zones: Cyanobacteria and Algae

Anaerobic zones: Anoxygenic phototrophic bacteria

Why do we find less relative photosynthetic activity in open oceans vs inshore environments?

Open oceans generally have low concentrations of irons needed for the iron-porphyrin portion of chlorophyll

What is the dominant oxygenic phototroph and possibly the most abundant microorganism on earth?


Why would we expect to find different bacteria at different levels in a lake?

Lakes often stratify and different bacteria are found at different levels depending on their metabolic activity.

What is the geological reason for the formation of hydrothermal vents?

Hot basalt and magma near the sea floor cause the floor to slowly drift apart

What are the 2 types of hydrothermal vents? Describe their temperatures and flow rates.

1) Warm vents: 6-23* C with low flow rates

2) Hot vents: 270-380* C with high flow rates

Describe what compounds we would expect to find in the environments surrounding hydrothermal vents? What is the predominant metabolic activity here?

Richin CO3 2-and HCO3- (from CO2), and O2, but contains very low amounts of organic material. Chemolithotrophic activity of bacteria living in or adjacentto the vents predominates

How do tube worms survive in the inorganic hydrothermal vent environment?

Tubeworms contain symbiotic sulfur oxidizing autotrophs in their gastrointestinal tracts. The tube worm blood transports O2, CO2 and H2S to the symbiotic bacteria, which provide the tube worms with reduced carbon for energy production and biosynthesis.

What is the largest carbon reservoir and what is the most rapid means of carbon turnover?

The earths crust is the largest reservoir and the most rapid means of carbon turnover involves CO2 from the atmosphere. CO2 is removed from the atmosphere and aquatic habitats photosynthetic organisms and is returned to the atmosphere by respiration of animals and chemoorganotrophic microbes.

What are the 2 main processes to fix carbon? What organisms are primarily responsible for this terrestrially and aquatically respectively?

1) Photosynthesis by higher plants on land and microbial algae/bacteria in the water

2) Chemolithotrophy

In order for carbon to be fixed by phototrophs, the rat of photosynthesis must _____ the rate of respiration


Photosynthetically fixed carbon is eventually degraded to ultimately form ____ or ____. Methane is eventually oxidized to ____ to feed to cycle

CO2 or CH4. CH4 is eventually oxidized to CO2 by methanotrophs

The major reservoir of nitrogen on earth is the _____. Nitrogense enzyme converts nitrogen to the more useable form ____. The enzyme is deactivated by ___. The principle nitrogen fixing bacteria is ____ found in symbiotic relationships with legumes.

Atmosphere, NH3, Oxygen, Rhizobium

Theanaerobic process of nitrogen fixation is possible due to theproduction of _______,a protein synthesized partly by the plant and partly by the bacteria,which combines with oxygen in much the same way as hemoglobin does inour blood. _____ regulates the concentration of _____ within the root nodule.

leghemoglobin, leghemoglobin, oxygen

Muchof the sulfur of Earth is found in _____ and _____ in the form of ______ minerals. The largest reservoir of sulfur (as sulfate)exists in the ____

sediments and rocks, sulfate, oceans

Why is sulfur cycling so complex?

Variety of oxidation states of sulfur and is also brought about geochemically

What are the 3 dominant oxidation states of sulfur found in significant quantities in nature? Give examples of sulfur in these compounds

-2 (HS- sulfide), 0 (elemental), and +6 (sulfate SO4 2-)

The Ferric (+3) iron ion is commonly found in ______ soils, ____, and in anoxic lake sediments. What oxidation state or iron would we expect to find in iron rich oxic environments? How do we cycle between these oxidation states?

Waterlogged soils and bogs. Iron-oxidizing bacteria convert Ferrous (+2) iron to Ferric (+3) iron

What is the most common form of iron available for use as an energy source for iron oxidizing bacteria? How does this effect water pH and what is the mechanism of this pH change?

Iron pyrite (FeS2) is the most common form. It's oxidation leads to the production of H2SO4 which breaks down into SO4 2- and H+. This occurs when bacteria oxidize Fe2+ to Fe3+ which then spontaneously reacts with FeS2 and oxidizes HS-to form sulfuric acid (H2SO4)

What is the fawlty towers hydrothermal complex?

array of black smokers, that spew out superheated mineral-rich water

What is the net equation for the oxic phase of the nitrogen cycle and what are the intermediates? What forms of nitrogen are used to assimilate into proteins?

Net equation is generation of Nitrate from elemental nitrogen

Intermediates are ammonia and nitrite

N2 --> NH3 (ammonia)

NH3 --> NO2- (nitrite)

NO2- --> NO3- (Nitrate)

NO3- and NH3 can then be assimilated into proteins as NH2

What is the net equation for the anoxic phase of the nitrogen cycle and what are the intermediates?

Net equation is reduction of NO3- (nitrate) to NH3 (ammonia)

Intermediates are NO2, NO, N2O, and N2

1)NO3- (nitrate) to NO2- (nitrite)

2) Denitrification of nitrite to NO, N2O, or N2

3) Nitrogen fixation of denitrification products to NH3

What are the 4 forms of sulfur found in the sulfur cycle? What is it called when we incorporate and remove sulfur into proteins respectively?

1) Elemental sulfur

2) SO4 2-

3) SH

4) H2S

Incorporate via assimilative sulfate reduction and remove via desulfurylation

What are the processes of the sulfur cycle?

1) Assimilative and Dissimilative sulfate reduction

3) Desulfurylation

4) Sulfur disproportionation

5) Dissimilative (elemental sulfur/sulfate) reduction

What form of sulfur is incorporated into proteins and what is the sulfur product when we remove it from proteins?

Sulfate SO4 2- is used for assimilative sulfate reduction into proteins as an SH groups and the product of desulfurylation is hydrogen sulfide H2S

How does the oxic and anoxc dissimilative reduction of sulfur compare and contrast?

Both forms generate hydrogen sulfide from sulfate or elemental sulfur

Oxic reagent: Sulfate SO4 2-

Anoxic reagent: Hydrogen sulfide H2S

What form of sulfur is used to generate sulfate in the sulfur cycle?

What form of sulfur is used to regenerate elemental sulfur in the sulfur cycle?

What form of sulfur is used to regenerate elemental hydrogen sulfide in the sulfur cycle?

-Sulfhydryl regenerates hydrogen sulfide

-Hydrogen sulfide regenerates elemental sulfur

-Elemental sulfur generates sulfate and hydrogen sulfide

How do we generate elemental iron? Can elemental iron become Fe2+ and Fe3+ by direct conversion?

Smelting of ores generates elemental iron

Fe3+ --> Elemental iron

Fe2+ <--> Elemental iron

How do we cycle between Fe2+ and Fe3+?

Bacterial/chemical redox

Fe2+ oxidation generates Fe3+

Fe3+ reduction generates Fe2+

How does elemental sulfur in an oxic environment differ from elemental sulfur in an anoxic environment relative to the types of reactions it can undergo. What is the name for the reaction that anoxic sulfur can undergo?

Oxic sulfur can only become sulfate

Anoxic sulfur can become sulfate OR hydrogen sulfide via sulfur disproportionation