MAME Midterm

Chapters 1 and 2, FINKEL readings, Ch. 14 excerpts, intro material, kids readings, climate change article, all HW and quiz questions

Provide the value for N and for P based on this table.

N = 22.86

P = 9.01

In a sentence or two in your own words, tell me how the elemental ratio of C to N (C:N) in exponentially-growing isolate #1 compares to that of the Redfield ratio hypothesis (0.5 pt). Bonus points (+0.5) for providing context with respect to the textbook Figure 2.4.

The exponentially-growing culture #1 has a relatively high number of N in the macromolecules that are primarily made up of CHNOPS, where the fast growth culture C:N is 106/22 = 4.8, compared to what would be expected by Redfield, where C:N would be 106/16 = 6.625.

Bonus:

This C:N ratio <<6.625 is likely due to a higher number of N-rich protein molecules per cell in the fast culture (grey bars) compared to # of molecules in more slowly growing oceanic plankton cells (black bars), as shown in the textbook Figure 2.4, which provides the # of macromolecules per cell in these two different scenarios (fast growth vs slow growth). In the “proteins” category, there are ~5 x 10^6 proteins per cell in fast growth (hence higher N in the elemental ratio of CHNOPS of total biomass); while in slow growth, black bars, there are only about ~1 x 10^6 proteins per cell and hence would give a HIGHER C:N.

Which factor is not affected by ocean pH?

a. Solubility of iron and hence its bioavailability for oceanic photoautotrophs

b. Charge on certain compounds, e.g. ammonia vs ammonium, affecting bioavailability of nitrogen for certain types of microbes

c. Adsorption of key nutrients, such as phosphate and nitrate, to solid surfaces

d. Salinity of the ocean water, affecting osmotic balance for certain microbes

d. Salinity

The barcoding gene for prokaryotes is ____, while the gene that is most often
sequenced to phylogenetically characterize eukaryotic microbes is ______.

16S SSU rRNA for prokaryotes, 18S SSU rRNA for eukaryotes

The relative abundance of elements in the Earth’s crust drastically differs from the relative abundance of elements in living cells and organic matter. The image from the book below demonstrates that Fe, Si, Mg, Na, and Ca are enriched in the ______.

a. Atmosphere

b. Biosphere

c. Lithosphere

d. Hydrosphere

c. Lithosphere

What is the most likely reason for why the most common oceanic bacteria do not have quorum-sensing genes?

a. Most oceanic bacteria have flagella, so there is no need for quorum-sensing and communication with other bacteria in the same species.

b. Heterotrophic bacteria are spaced do not often encounter particles, which are rich sources of particulate organic matter.

c. Even though there are many viruses (~10X the abundance of bacterial abundances), the spacing between a bacterium and a virus is quite large.

d. Unlike the situation in biofilms, the spacing between a bacterium and another bacterium from the same species is quite large.

d. Unlike the situation in biofilms, the spacing between a bacterium and another bacterium from the same species is quite large.

The image from the book shows approximate spacing between different types of
marine microbes forming the base of all oceanic food webs. Which example microbe shown
in the image would NOT be captured on a GF/F filter (pore size 0.6 micron, 0.6 um)?
a. alga
b. virus

b. virus

Cyanobacteria are ________.

a. Photolithoautotrophic and perform the FORWARD reaction in the simplified equation shown below.

b. Chemoorganotrophic and perform the REVERSE reaction in the equation.

c. Photolithoautotrophic and perform the REVERSE reaction in the equation.

d. Chemoorganotrophic and perform the FORWARD reaction in the equation.

Simplified equation: CO2 + H2O → CH2O + O2

a. Photolithoautotrophic and perform the FORWARD reaction in the simplified equation shown below.

Prokaryote chromosomes are ______.
a. Linear, in the nucleus, with lengths ranging from 100 to 150 million bp
b. Circular, in the cytoplasm of the cell, with lengths ranging from 1 to 6 million bp
c. Circular, in the cytoplasm of the cell, lengths ranging from 100 to 150 million bp

b. Circular, in the cytoplasm of the cell, with lengths ranging from 1 to 6 million bp

According to the mean abundance of bacteria compared to mean abundance of
viruses in Figure 1.8 below, you can calculate the estimated approximate density of viruses
in the samples shown in the Table. What is the estimated abundance of viruses in the Ice
House Pond in January? (Ignore the Standard Error, SE).
a. 1.08 viruses per mL
b. 1.08 x 10^6 viruses per mL
c. 1.08 x 10^7 viruses per mL
d. 1.08 x 10^10 viruses per mL
e. 2.11 x 10^7 viruses per mL

c. 1.08 x 10^7 viruses per mL

Which one of the below-listed elements is a trace biogenic element (micronutrient)?
a. C (carbon)
b. P (phosphorus)
c. Fe (iron)
d. S (sulfur)
e. N (nitrogen)

c. Fe (iron). This is also the most important micronutrient for microbes, as it is a limiting resource for photosynthetic microbes.

TRUE or FALSE? All photoautotrophic microbes in the oceans are eukaryotic and
hence have DNA in a nucleus.
a. True
b. False

b. False

Which environmental parameter is the proper X-axis label for the figure shown below?
a. Oxygen concentration (%)
b. pH (unitless)
c. Temperature (degrees C)
d. Fe concentration (micromolar)
e. Salinity (ppt)

c. Temperature (degrees C)

Generally, natural bacteria in the environment are ______ bacteria in mammalian guts.
a. smaller than
b. larger than
c. the same size as

a. smaller than

The surface to volume (S/V) ratio of natural bacteria in the oceanic environment is generally
____ the S/V ratio of bacteria in mammalian guts.
a. smaller than
b. larger than
c. the same size as

b. larger than

What is a microbe, by definition?

All organisms that can be observed only with a microscope and are smaller than about 100 um

What are the 7 main reasons to study microbes?

1. Microbes cause diseases of macroscopic organisms, including humans.

2. Microbes help to make our food and other useful products.

3. Microbes degrade and detoxify pollutants (like DDT).

4. Microbes are models for exploring principles in ecology and evolution.

5. Microbes living today are models for early life on Earth and perhaps even life on other planets.

6. Microbes mediate biogeochemical processes that affect global climate.

7. Microbes are everywhere, doing nearly everything.

True or false: Pathogenic microbes are the exception, not the rule.

True. Pathogenic microbes are much less abundant than beneficial ones.

True or false: An adult human has more bacterial cells in their body than they do human cells.

True. However, the biomass of the human cells far outweighs the bacteria.

This man was one of the founders of microbiology and also disproved the idea of spontaneous generation.

Louis Pasteur

Organisms that rely on microbes to digest the polysaccharides in the grasses they eat are called ______.

Ruminants

As a general rule, the SMALLER/LARGER an organism is, the more abundant they are.

Smaller organisms are generally more abundant.

What factors contribute to “The Great Plate Anomaly”

• An agar plate is a foreign habitat to most bacteria and microbes, and they are not adapted to thrive in a petri dish

• There are also sometimes with the direct count method, as inert particles can be confused with microbes due to staining problems

Who was the first scientist to use rRNA sequencing (of the 16s genome) to identify archaea?

Carl Woese

What are the important distinguishing characteristics between prokaryotes and eukaryotes?

• A prokaryotic cell looks empty when viewed by light microscopy since it doesn’t have membrane-bound organelles

• Size (eukaryotes are bigger)

• Prokaryotes are usually simple cocci, Eukaryotes may be rod or bacillus shape, or comma-like cocci

• Eukaryotes are usually autotrophic or heterotrophic, but prokaryotes have more variations from methanogens to nitrogen fixation

True or false: the composition of microbes grown in the laboratory differs from that of microbes in natural environments.

True. These differences give clues about how microbes survive in nature.

Which 3 elements seen in this figure most commonly limit microbial growth in nature?

Carbon, nitrogen, and phosphorus. Some of these elements are very enriched in cells, while others are only present in low amounts.

What is the definition of homeostasis?

A microbe’s capacity to maintain elemental ratios the same even when those ratios change in their growth conditions

What is the Redfield ratio of planktonic nutrients?

106:16:1 (C:N:P)

Vascular plants on land have vastly more carbon per nitrogen or phosphorus than aquatic primary producers. Why?

Land plants have large amounts of cellulose, lignin, and other structural polysaccharides needed for structure on land. That’s why their Redfield ratio is larger.

Bacteria, especially heterotrophic bacteria, tend to be more _____ rich and have lower ____ ratios than other microbes.

They are more Nitrogen rich and have lower C:N ratios.

_______ account for not only a large fraction of total RNA (80%), but also of dry weight (20-40%). Given the high cost of synthesizing this, a cell will only have the amount it needs for protein synthesis.

Ribosomes. Because of the connection with P-rich ribosomes and growth, C:P ratios vary with growth rate.

To facilitate the transport of molecules across membranes, all cells have _____ that span the phospholipid bilayer.

Membrane proteins

Small hydrophobic molecules and gases may pass the lipid bilayers, but ____ or _____ compounds cannot.

hydrophilic, charged

For most compounds, if concentrations are ______ inside the cell than outside, diffusion will not work.

higher

As this figure shows, peptidoglycan is the main component of the cell wall in _____.

bacteria (especially gram-positive bacteria)

Cyanobacteria have a gram NEGATIVE/POSITIVE type cell wall.

Negative, but the peptidoglycan layer is much thicker than typical of gram-negative bacteria.

What is the difference between polar and peritrichous flagella?

Polar is when a bacterium has a flagella on each side (pole) of its body, and peritrichous flagella are all over the body.

________ and _______ are like flagella, except they are shorter and not involved in motility.

Fimbriae and pili (used to attach the bacterium to surfaces or other cells)

The membranes of bacteria and eukaryotes are similar and consist of ester-linked lipids. What kind of lipids do archaea have?

Archaea have ether-linked lipids.

All cells are about ____% water by weight.

70%. This means that all organisms require water for growth, and liquid water is needed for any substantial microbial activity.

Of all the environmental parameters, _____ has one of the most profound effects on microbial activity.

Temperature. The rate of all chemical reactions increases with temperature (generally increases x2 with each 10 C temperature increase)

Svante Arrhenius was one of the first scientists to understand ______

how greenhouse gases impact climate change.

What adaptations do microbes have for UV light?

• Some microbes have “sunscreen” made of pigments like carotenoids that absorb light

• Other microbes adapted their behavior to live at a depth where UV rays can’t reach.

• Microbes also have enzymes like RecA to repair damage done by UV

Piezophiles (deep-sea microbes living at high pressures) are thought to have evolved from what?

Piezophiles probably evolved from low-pressure psychrophiles found in high-latitude environments. Both have similar adaptations, like highly unsaturated lipids and similar protein and DNA alterations.

What is a GF/F filter?

It stands for Glass Filter Fine, and it is used to determine if something is particulate or dissolved. The filter retains molecules of about 0.6 um, and anything that slips through is considered dissolved.

True or False: It is the genes encoded by the microbial genomes, and not the “taxonomy” (i.e., the “phylogeny”) of the microbes, that dictate the success, or failure, of the microbe in certain circumstances.

True. Genes determine success.

True or False: In most natural bacteria, there is usually only 1 chromosome.

True. However, some may have plasmids at certain points in their lives.

True or False: Phylogeny is based on the sequence of the SSU ribosomal RNA gene

18S for prokaryotes

16S for eukaryotes

(Partially) False. It is 16S for prokaryotes and 18s for eukaryotes, but is is based on the SSU ribosomal RNA gene.

In a typical drop of seawater, total viruses are ____-fold more abundant than total bacteria.

A. 1000-fold

B. 100-fold

C. 10-fold

D. 2-fold

C. 10-fold

On average, marine viruses are ____-fold smaller than the average marine bacterium.

A. 1000-fold

B. 100-fold

C. 10-fold

D. 2-fold

SIZE is on the X-axis (size, in microns)

C. 10-fold

True or False: The graph shows that marine cyanobacteria are more phylogenetically diverse than marine bacteria.

False. It only gives information about size and abundance, not diversity.

What are the most common body shapes for aquatic microbes?

Coccus (sphere), Bacillus (rod), and Vibrio (comma).

What do these figures represent?

Accelerating methane growth rates and emissions over recent decades. (A) Observed methane annual growth rates (ppb yr−1) through 2022 or 2023 (B) Estimated emissions and sinks through 2023

Anaerobic environments are still common on earth. They include environments like:

(a) a bog
(b) the rumen (the first compartment of a cow’s stomach)

What is a hyperpiezophile?

An organism that grows under high pressures (>80MPa)

What is a hyperthermophile?

An organism capable of growth in temperatures >80 C.

True or False: the term “protist” encapsulates both autotrophic and heterotropic organims.

True. Examples of autotrophic protists include diatoms and algae, whereas a heterotrophic protist would be zooplankton.

True or False: Fungi is a eukaryotic microbe.

True! They are non-photosynthetic microbes, like yeast.

What three things do all metabolisms need?

Carbon, energy, and electrons

This type of metabolism is seen in extreme environments:

Chemolithoautotroph

Which one of the red molecules is Dissolved Inorganic Content (DIC) and which is Dissolved Organic content (DOC)?

The CO₂ is DIC and the right side is DOC.

In an oligotrophic environment, being small is more advantageous. WHY?

Smaller cells have larger S/V ratios and thus can have a more efficient exchange of nutrients with it surroundings than can a large cell.

What does

Metabolism = Catabolism + Anabolism

mean?

Catabolism = conservation of energy, e.g. making ATP

Anabolism = Biosynthesis of macromolecules (primarily CHNOPS)

Together, this is metabolism.

What is the Redfield Ratio hypothesis?

The atomic ratios between the chemical components of marine plankton (C, N, P) are identical with their relative proportions in the open ocean.

What is the function of the Redfield Ratio hypothesis?

Measuring Redfield ratio in unfiltered an seawater can give you idea of the NET HETEROTROPHY or NET PHOTOTROPHY – And can tell you which elements are limiting at that place at that time.

With an increased growth rate, the proportion of _____ increased.

Ribosomes, and therefore N

What do pili do?

• Adhesion

• Communication

• Transfer information (sex)

True or False: Most open-ocean bacteria have flagella.

False. Only about 5% have flagella in most cases.

A cell’s adhesion starts with pili, but it says because of ______

EPS (extracellular polysaccharides)

True or False: Biofilms are usually composed of one type of microbe.

False. They are not like baklava with layers composed of the same ingredients- biofilms are complex.

Which of the below 3 listed processes are important for forming bacterial colonization of a surface?

-Antibiotic resistance

-Quorum sensing

-Flagellum formation

Quorum sensing.

What are the 3 main steps to biofilm production shown in this figure?

1. Colonization

2. Growth

3. Polymer production

What turns on EPS production?

EPS production gets “turned on” after quorum sensing signaling happens, and everyone in the community expresses the needed genes for extruding this CHO-rich substance

Why is the C:N:P ratio in a biofilm different than the Redfield equation?

C:N:P from a biofilm is composed of biomass AND the EPS, so it will be RICH in C, compared to biomass collected on a filter of planktonic organisms from ocean (which will be more like 106:16:1).

What is the difference between EPS and EPM?

EPM = Extracellular Polymeric Matrix

EPS = Extracellular Polymeric Substance

There is no difference, they are different names for the same thing.

True or False: Biofilms are more likely to develop on aged plastics.

True. Understanding the makeup of the bacterial community colonizing the plastic particles helps predict how quickly the plastics will age

POM is composed of:

• Particulate organic matter

• Living cells and detritus

DOM is composed of:

• dissolved organic material, such as sugars, amino acids, etc.

Text box for GF/F (note the pore sizes and what it can catch)

SPACING between detrital particles, viral particles & microbes such as bacterioplankton and phytoplankton:
Depends on the ______ of each, and ______.

Concentration, diffusion

AMMONIA/AMMONIUM is easily taken up across cell membrane without extra effort (or specialized gene to make the transport protein. AMMONIA/AMMONIUM is not easily taken up by cells (requires a special transport protein in the membrane)

Ammonia is easily taken, ammonium is not.

What are all the correct classifications for the bacteria within these tubes?

What does this figure represent?

Protein content and means across the groups.

According to the Finkel article, what is the median macromolecular composition of exponentially growing microalgae?

• 32.2% protein

• 17.3% lipid (fats)

• 15.0% carbohydrate (sugars)

• 17.3% ash (the inorganic residue that remains after the sample is combusted: P, S, Na, Cl, K, Ca, Mg. In the Bacillariophyta and calcified microalgae, Si and Ca are the ash)

• 5.7% RNA (genetic material)

• 1.1% chlorophyll-a (photosynthetic pigment)

• 1.0% DNA (genetic material)

In a typical rapidly-growing, exponential phase culture of E. coli, the ratio of 16S SSU rRNA molecules to mRNA molecules is approximately:

a. 13:1 (13 rRNA molecules to 1 transcript molecule)

b. 1:13 (1 rRNA molecule to 13 transcript molecules)

c. 1:1 (roughly equal number of SSU rRNA molecules to number of transcript molecules)

d. 6.7:1 (6.7 rRNA molecules to 1 transcript molecule)

e. 1:6.7 (1 rRNA molecule to 6.7 transcript molecules

a. 13:1 (13 rRNA molecules to 1 transcript molecule)

Which type of macromolecule is enriched in N?

Protein.

This image demonstrates that Fe, Si, Mg, Na, and Ca are enriched in the _________.

Lithosphere

What do you call a bacterium that consumes organic compounds for both carbon and energy?

Chemoorganotrophs, also called chemoorganoheterotrophs.

Symbiosis (all)

The entire spectrum of interactions between organisms, ranging from those in which the organisms are indifferent to each other to outright antagonism (parasitic relationships)

The inclusion of parasitism and pathogenicity doesn’t fit with the everyday use of “symbiosis” and may be more confusing than illuminating.

True, that is why an alternate definition was proposed.

The benefit to the host (eukaryote) for ruminant symbiosis.

Organic Carbon

The benefit to symbiont (could be archaea, bacteria, or protozoa) for ruminant symbiosis

Organic carbon

The benefit to corals in their symbiotic relationship with zooxanthellae.

Organic carbon it can eat for energy and making new biomass

The benefit to algae in their symbiosis with coral

Organic carbon, Inorganic nutrients (coral waste like NH4) and safety within coral structure

Ectosymbiosis

This is when the symbiont is on the outside of the host

Endosymbiosis

This is when the microbe is inside the host

The rumen is…

A large stomach-like pouch consisting of several muscular sacs. It is the main site where ingested plant material is digested and converted to compounds assimilated by the ruminant.

This insect has two bacterial symbionts: Tremblaya princepts and Moranella endobia.

The citrus mealybug

Quorum sensing

The mechanism by which microbes communicate with each other and signal to form a biofilm.