I will give you the question on May 12 10a.m (EST), please review the study guide by using the ppt and prepared for answering question in the exam.
GLG(MBI) 402/502
Final Exam Study Guide
This is not meant to be all-inclusive. You will be asked to apply this knowledge similar to
the homework; thus, simply memorizing this sheet does not guaranty a passing grade.
Information for these topics are in the notes and/or readings.
Origins of life
1. The generally accepted beginning of life
a. 3.5-3.8 billion years ago
2. Some hypotheses for the origins of life
Panspermia
Surface origin
Hydrothermal origin on sea floor (generally believed)
3. The early history of life?
Sterile world -> the RNA world -> Protein and RNA and finally DNA-RNA-protein
The role of DNA, RNA and protein in modern biology
4. Major biological evolutionary events and affect on Earth
a. Origin of life
b. Origin of oxygenic phototrophs
Banded iron formations are common around 2.2. Ga and are a result of Fe redox
cycle.
Effect of biology on minerals
Mineral roles on emergence and evolution of life
Organic minerals
Cell biology
1. Three domains of life: bacteria, archaea, and eukaryotes
2. Physical properties: morphology, color and size. Know their general morphology and size
ranges.
3. Per dry weight basis, proteins are most abundant macromolecules in a cell.
4. Gram staining (or Gram’s method) is a method of differentiating bacterial species into two
large groups (Gram-positive and Gram-negative). It is based on the chemical and physical
properties of their cell walls. Primarily, it detects peptidoglycan, which is present in a thick
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layer in Gram positive bacteria. A Gram positive results in a purple/blue color while a Gram
negative results in a pink/red color.
5. Prokaryotic cell structure:
a. Cytoplasmic membrane: pass in nutrients and pass out wastes
b. Cell wall: located outside the membrane and supports the cell
c. Cytoplasm: a complicated mixture of substances and structures
d. Ribosomes: contain RNA and protein and the cell’s protein-synthesizing factories
e. DNA: carries the genetic blueprint for the cell
f. RNA: Converts the blueprint into defined amino acid sequences in protein
6. Pay special attention to cell membrane: lipid bilayer structure and its functions.
7. Nucleotide consists of deoxyribose (in DNA) or ribose (in RNA), a nitrogen base and
phosphate. It is the most basic building block of DNA and RNA. In DNA, the bases are
ATGC and in RNA it’s AUGC.
8. Adenosine-5′-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells
as a coenzyme. ATP consists of the ribonucleoside adenosine to which three phosphate
molecules are bonded in series. ATP serves as the prime energy carrier in living organisms,
being generated during exergonic reactions and being used to drive endergonic reactions.
Energy is released when the two high energy anhydride bonds are broken via hydrolysis.
9. DNA is built from multiple nucleotides connected together via phosphodiester bonds and
has a double helix structure and their nitrogen bases are complementarily paired (with a
direction from the 5’ end to 3’ end). RNA is single chain, but can have secondary structures.
10. Proteins are made of a sequences of amino acids bonded together by peptide bonds. There
are 21 different kinds of amino acids. Proteins can have complicated 3-D structures that will
determine their functions.
Nutrition, metabolism and growth
Catabolic and Anabolic Reactions
1. The sum of all chemical reactions within a living organism is known as metabolism.
2. Catabolism refers to chemical reactions that result in the breakdown of more complex
organic molecules into simpler substances. Catabolic reactions usually release energy.
3. Anabolism refers to chemical reactions in which simpler substances are combined to
form more complex molecules. Anabolic reactions usually require energy.
4. The energy of catabolic reactions is used to drive anabolic reactions.
5. The energy for chemical reactions is stored in ATP.
Enzymes
1.Enzymes are proteins, produced by living cells, which catalyze chemical reactions by
lowering the activation energy.
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Energy classes of microorganisms:
1.
2.
3.
4.
Autotrophs vs heterotrophs: depending on the source of carbon
Also phototrophs, chemotrophs etc.
Macro- and micro-nutrients serve as specific purposes for a cell’s metabolism and growth
A defined medium contains amounts of macro- and micro-nutrients. Undefined medium
gives a complex ingredients and hope that cells can use some of it.
A Summary of Energy Production Mechanisms
1. Sunlight is converted to chemical energy in oxidation-reduction reactions carried on by
phototrophs. Chemotrophs can use chemical energy.
2. In oxidation-reduction reactions, energy is derived from the transfer of electrons.
3. To produce energy, a cell needs an electron donor (organic or inorganic), a system of
electron carriers, and a final electron acceptor (organic or inorganic).
4. Enzymes are used to lower activation energy of a reaction so that that reaction becomes
favorable.
5. Electron tower is used to calculate the amount of energy released when a reductant and
oxidant are coupled in a reaction.
6. Respiration and fermentation are two major pathways of metabolism.
7. During respiration, organic molecules are oxidized. Energy is generated from the electron
transport chain.
8. In aerobic respiration, O2 functions as the final electron acceptor.
9. In anaerobic respiration, the final electron acceptor is usually an inorganic molecule other
than O2. The common ones include Fe+3, NO3–, SO42–, and CO32–.
Microbial growth
The Requirements for Growth
1. The growth of a population is an increase in the number of cells.
2. The requirements for microbial growth are both physical and chemical.
Physical Requirements
3. On the basis of preferred temperature ranges, microbes are classified as psychrophiles (coldloving), mesophiles (moderate-temperature–loving), and thermophiles (heat-loving).
4. The minimum growth temperature is the lowest temperature at which a species will grow, the
optimum growth temperature is the temperature at which it grows best, and the maximum
growth temperature is the highest temperature at which growth is possible.
5. Most bacteria grow best at a pH value between 6.5 and 7.5 but there are acidophiles and
alkaliphiles.
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6. Halophiles can tolerate high salt concentrations.
Chemical Requirements
7. All organisms require a carbon source; chemoheterotrophs use an organic molecule, and
autotrophs typically use carbon dioxide.
8. Nitrogen is needed for protein and nucleic acid synthesis. Nitrogen can be obtained from the
decomposition of proteins or from NH4+ or NO3–; a few bacteria are capable of nitrogen (N2)
fixation.
9. On the basis of oxygen requirements, organisms are classified as obligate aerobes, facultative
anaerobes, obligate anaerobes, aerotolerant anaerobes, and microaerophiles.
10. Other chemicals required for microbial growth include sulfur, phosphorus, trace elements,
and, for some microorganisms, organic growth factors.
Generation Time
1.The time required for a cell to divide or a population to double is known as the generation
time.
Logarithmic Representation of Bacterial Populations
4.Bacterial division occurs according to a logarithmic progression (two cells, four cells, eight
cells, and so on).
Phases of Growth
5. During the lag phase, there is little or no change in the number of cells, but metabolic activity
is high.
6. During the log phase, the bacteria multiply at the fastest rate possible under the conditions
provided.
7. During the stationary phase, there is an equilibrium between cell division and death.
8. During the death phase, the number of deaths exceeds the number of new cells formed.
Direct Measurement of Microbial Growth
9. A standard plate count reflects the number of viable microbes and assumes that each
bacterium grows into a single colony; plate counts are reported as number of colony-forming
units (CFU).
10. A plate count may be done by either the pour plate method or the spread plate method.
11. In a direct microscopic count, the microbes in a measured volume of a bacterial suspension
are counted with the use of a specially designed slide.
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Phylogeny (what microbes)
16S ribosomal RNA (or 16S rRNA) is a component of the 30S small subunit of prokaryotic
ribosomes. It is approximately 1.5kb (or 1500 nucleotides) in length. The genes coding for it are
referred to as 16S rDNA or 16S rRNA gene and are used in reconstructing phylogenies.
This DNA fragment has conservative and variable regions. The conservation region allows
alignment of microbial species so that their evolutionary relationship can be studied. The
variable region allows distinction of one species from another.
This gene is used to classify all prokaryotes, whereas 18S rRNA gene is used to classify all
eukaryotes.
The typical steps in identifying a microbial species involves DNA extraction from pure culture
(or environmental samples), PCR and sequencing. After alignment between your species and
those in the GenBank, evolutionary distances are calculated and their phylogenetic relationships
can be represented in a phylogenetic tree.
Microbial sampling
1. Be aware of different sampling methods depending on your target lithology
2. Contamination is a serious issue, especially when you use drilling fluids to cool off drill
bits.
3. Different ways are used to detect contamination of subsurface rocks by surface microbes
including chemical tracers, micro-spheres (same size as microbes) and microbes
themselves (the ones that you usually do NOT see in the sursurface).
4. The main objective of sample processing is to minimize any disturbances to them.
Anaerobic glove box, sterile laminar hoods, and rock splitters/chisels are often used.
5. Be aware of storage-related problems and their reasons.
Detection of microbes in your samples:
1. CFU vs. direct count (AODC or DAPI)
2. FISH (fluorescence in situ hybridization) is a cytogenetic technique that is used to detect and
localize the presence or absence of specific RNA sequences in a cell. FISH uses fluorescent
probes that bind to only those parts of RNA sequence with which they show a high degree of
sequence complementarity. Fluorescence microscopy can be used to find out where the
fluorescent probe is bound to RNA, thus it allows localization of certain groups of bacteria
and archaea. FISH can help define the spatial-temporal patterns between different groups of
cells (often with different functions). There are general and specific FISH probes.
3. SEM and TEM are direct visualization tools. TEM allows you to see through on thin
sections. SEM allows you to see 3-D morphology.
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Detection of activity
Physiological methods based on the following reaction are often used.
•
Substrate + nitrogen + TEA → cell mass + CO2 + water source
More recently, other stable isotope based methods are used more and more often.
Microbial processes
1. Living systems by definition are not at equilibrium, but kinetic!
2. Identify electron donors and acceptors.
3. The redox processes are zoned according to the order: reduction of O2, NO3-, Fe3+, SO42-,
and CO2.
4. The reason for zonation is competition. The O2 reduction reaction releases the most
amount of energy. Thus, O2 reducing (aerobic) organisms are most competitive, followed
by nitrate reducers, iron reducers sulfate reducers and methanogens.
5. Know systems where this occurs
6. The zonation can be either vertical or horizontal.
7. Specific groups of organisms are active in a given zone.
8. Be aware of complications: not all zones have to be present in a given site. Not all zones
have to be of equal size either!
Biologically controlled mineralization
1. General features of magnetotactic bacteria: diverse, Gram negative, motile, magnetotaxis,
a negative tactic and/or growth response to atmospheric levels of O2 (~21% O2); they are
all anaerobes or microaerophiles or both, respiratory form of metabolism, play important
roles in the cycling of C, S, N and Fe.
2. They are widespread in diverse environments.
3. Magnetotaxis describes an ability to sense a magnetic field and coordinate movement in
response.
4. Magnetosome chains are membranous prokaryotic organelles present in magnetotactic
bacteria. They contain 15 to 20 magnetite crystals that together act like a compass needle
to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search
for their preferred microaerophilic environments. Each magnetite crystal within a
magnetosome is surrounded by a lipid bilayer, and specific soluble and transmembrane
proteins are sorted to the membrane. Recent research has shown that magnetosomes are
invaginations of the inner membrane and not freestanding vesicles.
5. Overall, magnetosome crystals have high chemical purity, narrow size ranges
(magnetically single domain), species-specific crystal morphologies and exhibit specific
arrangements within the cell. These features indicate that the formation of magnetosomes
is under precise biological control and is controlled biomineralization.
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6. There is a variety of minerals that make up the magnetosomes includign magnetite,
gregite, mackinawite, pyrite, and pyrrhotite.
Why Make Magnetosomes?
1. A survival advantage and evolutionary trait: Magnetotaxis appears to increase efficiency
of chemotaxis in vertical chemical gradients (e.g., Fe3O4-producers and O2 gradients) by
reducing a 3-dimensional search problem to a 1-dimensional search problem
2. Physiological reason: energy released from Fe redox reactions inside the cell.
How do they make magnetosomes?
Appears to be a complex process that involves a number of steps…
1) Magnetosome vesicle formation
2) Uptake and transport of Fe into the cell
3) Transport of Fe into the magnetosome vesicle
4) Biomineralization of Fe3O4 in the magnetosome membrane vesicle
All these steps are highly controlled by specific genes and proteins!
Biologically induced mineralization
1. What is BIM and how does it distinguish it from BCM in terms of the mechanism and
mineral products formed?
2. Minerals that form by biologically induced mineralization processes generally nucleate
and grow extracellularly as a result of metabolic activity of the organism and subsequent
chemical reactions involving metabolic byproducts. In many cases, the organisms secrete
one or more metabolic products that react with ions or compounds in the environment
resulting in the subsequent deposition of mineral particles. Thus, BIM is a presumably
unintended and uncontrolled consequence of metabolic activities.
3. The minerals that form are often characterized by poor crystallinity, broad particle-size
distributions, and lack of specific crystal morphologies. In addition, the lack of control
over mineral formation often results in poor mineral specificity and/or the inclusion of
impurities in the mineral lattice. BIM is, in essence, equivalent to inorganic
mineralization under the same environmental conditions and the minerals are therefore
likely to have crystallochemical features that are generally indistinguishable from
minerals produced by inorganic chemical reactions.
4. But certain minerals can still be used as bio-signatures if these minerals and/or textures
are only formed by BIM and are distinct from those inorganically formed. This would be
important to look for biological activity in ancient rock records.
5. Indeed, minerals and microbes have co-evolved through much of the earth history.
6. In the modern world, microbes are intimately associated with solid minerals via biofilm
formation.
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7. A biofilm is an aggregate of microorganisms in which cells adhere to each other on a
solid surface. These adherent cells are frequently embedded within a self-produced
matrix of extracellular polymeric substance (EPS). Biofilm EPS, which is also referred to
as slime (although not everything described as slime is a biofilm), is a polymeric
conglomeration generally composed of extracellular DNA, proteins, and polysaccharides.
The microbial cells growing in a biofilm are physiologically distinct from planktonic
cells of the same organism, which, by contrast, are single-cells that may float or swim in
a liquid medium.
8. Microbes form a biofilm in response to many factors, which may include cellular
recognition of specific or non-specific attachment sites on a surface, nutritional cues, or
in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of
antibiotics. When a cell switches to the biofilm mode of growth, it undergoes a
phenotypic shift in behavior in which large suites of genes are differentially regulated.
9. As a result of microbial attachment to mineral and rock surfaces, rocks and minerals
undergo weathering. There are three mechanisms of weathering:
a. Organic acid production
b. Chelation.
c. Reduction-oxidation reactions.
10. In nature, P is often the limiting nutrient and any minerals that contain P are favorable
attachment sites for microbes.
11. As a result of microbial weathering, rocks and minerals undergo weathering and lead to
soil formation. The silicate mineral weathering sequence in the presence of microbes is
different from the one by chemical and physical weathering.
Microbe-clay minerals and changes in soil properties
1. Smectite – a group of clay minerals with a 2:1 structure (i.e. one octahedral layer sandwiched between two tetrahedral layers) and that display the property of expansion and
contraction of their structure during a wetting and drying cycle
2. Illite – a clay mineral with a similar structure to muscovite and smectite (2:1 structure).
Its composition lies between that of muscovite and that of smectite. Because of its high
net negative charge (0.6–0.9 per half unit cell), its structure is not expandable.
3. Smectite-to-illite reaction – smectite is stable at low temperature and pressure and is a
major constituent of surface soils and sediments. As these materials are buried,
temperature and pressure increase, and smectite becomes unstable and transforms to
illite.
4. Clay minerals such as smectite and illite are likely the most common minerals that we
encounter in our daily lives. They form the soils in which plants grow, and they are the
primary materials used in a range of applications including cat litter and animal feed,
pottery, china, oil absorbants, pharmaceuticals, cosmetics, waste water treatment, and
even antibacterial agents.
5. Microbial reduction of Fe(III) in smectite can happen with and without electron shuttle.
With electron shuttle, reduction efficiency (rate and extent) go up.
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6. The consequences of microbial Fe(III) reduction are: decrease surface area but less
exchangeability, and less swelling. As a result, cations and nutrients would be trapped
inside smectite interlayers and will be less available to plants. Farmers would need to
plow their lands to re-oxidize Fe(II) in smectite.
7. However, reduced smectite is more effective in degrading pesticides and other organic
contaminants.
8. Microbes can promote the smectite-to-illite reaction by reductively dissolving the
smectite structure and re-precipitating illite. This is because Fe(II) is a much larger cation
than Fe(III) and the smectite cannot accommodate the size and stress if the extent of
Fe(III) reduction is too large (>30%).
9. This microbially catalyzed smectite-to-illite reaction is one example of the catalytic effect
that microbes have to mineral reactions. Recognition of these is important for a number
of reasons. In the case of the smectite-to-illite reaction, the role of microbes should be
recognized when this reaction is used as in index to help petroleum exploration.
Life on Mars
1. Basics of Mars: most similar to Earth (among all planetary bodies of the solar system) in
terms of distance to the sun, size, and surface topography etc, but there are enough
differences. Mars has a weak magnetic field, no water on the surface, and therefore no
life on the surface. Mars has a very different atmospheric composition than the earth’s
atmosphere, etc.
2. But evidence has shown that Mars used to be wetter and might have supported life.
Today, life may have existed in the subsurface.
3. Much of our understanding about life on Mars has come from meteorites. Some of the
meteorites are inferred to be from Mars based on a number of evidence (such as
chemistry including isotopes, volatile contents and age to some degree).
4. ALH84001 is a particular meteorite from Mars. How do we know it’s from Mars?
5. Six criteria for mineralogical evidence: 1) narrow size range, 2) definite width to length
ratio, 3) chemical purity, 4) crystallographic perfection, 5) unusual crystal morphology,
and 6) elongation of crystals.
6. Given all things considered, what is the likelihood of finding life on Mars? Consider all
physical and chemical properties of the present and ancient Mars, and requirement of life
as we know it here on Earth.
7. What are some additional things that you would propose to test to prove or disprove there
is life on Mars?
8. There are other minerals that have been detected on Mars such as hematite, clays and
gypsum. These minerals provide stronger evidence for life on Mars because based on our
knowledge on Earth they typically form in aqueous environment.
9. Detection of methane and its heterogeneous distribution is a possible evidence for life on
Mars. Methane is quickly destroyed in the Martian atmosphere in a variety of ways, so
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the discovery of substantial plumes of methane and its continued persistence in the
northern hemisphere of Mars indicate some ongoing process is releasing the gas, either
geologically or microbiologically. Organisms release much of Earth’s methane as they
digest nutrients. However, other purely geological processes, like oxidation of iron
(reaction of mafic silicates and water to produce serpentine and other minerals through a
process called serpentinization), high temperature and pressure alteration, gas hydrate
degrassing, and volcanic degassing, also release methane.
10. However, a group of scientists from Mexico presents recent evidence that “the
discharges, caused by electrification of dust devils and sand storms, ionize gaseous CO2
and water molecules and their byproducts recombine to produce methane”. Read more at
http://www.universetoday.com/97280/could-dust-devils-create-methane-in-marsatmosphere/.
11. More definitive evidence for the biogenic origin of methane would be carbon isotopes
(very negative delta 13C values).
New Material from after the mid-term
Microbes in hydrothermal vents
1. What is hydrothermal vent? A hydrothermal vent is a fissure in a planet’s surface from
which geothermally heated water issues. Hydrothermal vents are commonly found near
volcanically active places, areas where tectonic plates are moving apart, ocean basins,
and hotspots. Hydrothermal vents exist because the earth is both geologically active and
has large amounts of water on its surface and within its crust. Common land types include
hot springs, fumaroles and geysers. Under the sea, hydrothermal vents may form features
called black smokers. Relative to the majority of the deep sea, the areas around
submarine hydrothermal vents are biologically more productive, often hosting complex
communities fueled by the chemicals dissolved in the vent fluids. Chemosynthetic
archaea form the base of the food chain, supporting diverse organisms, including giant
tube worms, clams, limpets and shrimp. Active hydrothermal vents are believed to exist
on Jupiter’s moon Europa, and ancient hydrothermal vents have been speculated to exist
on Mars.
2. There are two different types of hydrothermal vents: black and white smokers. A black
smoker is a type of hydrothermal vent found on the seabed, typically in the abyssal and
hadal zones. They appear as black chimney-like structures that emit a cloud of black
minerals, mostly metal sulfides, as a result of reaction of dissolved H2S and metals from
magma with oxic seawater. White smokers are vents that emit lighter-hued minerals, such
as those containing barium, calcium, and silicon. Carbonates are common in such
smokers and Lost City is a famous example. These vents also tend to have lower and
more alkaline temperature plumes.
3. In hydrothermal vents, H2, H2S, CH4, NH3, S2O3, Fe (II), NO2- are electron donors, and
O2, NO3, Fe (III), CO2 are electron acceptors. Various combinations of these redox
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reactions can produce energy and support different types of chemosynthesis. Specific
nature of electron acceptors and donors depend on specific vent fluid composition and
their reaction with host rocks. For example, when ultramafic rocks (such as basalt)
interaction with seawater, H2 is the main product. Abundant H2 is the main source for
autotrophic methanogenesis.
4. Chemosynthetic microbial communities for the base of the food chain. Larger organisms
such as snails, shrimp, crabs, tube worms, fish, and octopuses form a food chain of
predator and prey relationships above the primary consumers.
5. Importance of studying hydrothermal vent biological communities: hydrothermal origin
of life, the deep hot biosphere, life on Jupiter’s moon Europa, and ancient hydrothermal
vents have been speculated to exist on Mars, as well economic reasons (massive metal
sulfide deposits and novel organisms and enzymes).
Microbial weathering of oceanic crust
1. Microbial weathering of basaltic glass is distinctly different from abiotic alteration
pattern. Abiotic weathering of oceanic crust is controlled by simple diffusive processes
and dissolution is along fractures. Abiotic weathering results in decreased surface area
due to infilling of fractures and fissures by clay mineral precipitation. Biotic weathering
induces pH change in contact area (between microbes and basaltic glass) and increased
surface area. Granular or tubular textures are produced. Because these textures are unique
to microbial activity, they can be used as a biosignature to infer past microbial activity.
2. The details of this process remain unclear. Considering negative δ13C values of
carbonates in glassy rims where these tubular textures are observed (relative to those
from glass interior where no microbial alteration texture is observed), it is likely that
organic matter oxidation (which usually have low δ13C compared with carbonates) by
heterotrophs is a mechanism because once oxidized, the negative δ13C signal from
organic matter will be added to carbonate (i.e., respired light CO2 combines with Ca2+
and Mg2+ to form calcite and dolomite).
3. Indeed, such bio-signatures have been used to infer past biological activity in ancient,
metamorphosed rocks from S. Africa and Australia. These bio-signatures are confirmed
by enrichment of C and other life-essential elements as well as depletion of carbon along
these textures.
4. This discovery has important implications for life on early Earth.
5. However, in 2014 and 2015, there is a debate about biogenicity of the tubular textures (by
Grosch and McLoughlin 2014, rebuttal by Staudigel 2015, and further response by
McLoughlin and Grosch 2015).
Energy sources in basalt aquifers (SLIMES)
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1. Recognize that the Stevens and McKinley (1995) is one of the first to discover the
potential H2-based chemolithoautotrophic ecosystem.
2. Learn that to work on a given system, the first thing to do is to identify all possible
electron donors and acceptors. In this case, organic carbon was scarce but anaerobic
organisms were abundant. In particular, high concentrations of H2 and methane were
detected. The H2 concentration was much higher than would be expected from organic
matter fermentation.
3. The key plot is the DIC (dissolved inorganic carbon) vs. δ13C of DIC. The inverse
relationship proves that DIC (CO2 in this case) is the reactant. Remember biological
activity always takes up the light isotope (12C in this case). All biogenic materials have
light isotopes (or negative δ13C values).
4. Pay attention to their experimental design: lower pH than the in-situ value, and crushed
basalt. Whereas some of these conditions may not be realistic, it is also important to keep
the experiment feasible in the lab. It’s impossible to wait for millions of years to
complete an experiment. When you design your own experiment, try to be as realistic as
possible, but also as feasible as possible.
5. The Anderson et al. experiment is clearly more reasonable by running the experiment
under more relevant field condition, but they did not consider any differences between
different types of basalts. Particle size was not directly comparable either.
6. The follow-up study by S & M is certainly much more realistic considering all possible
experimental artifacts and they provided some assessment for compensation (for
example, longer reaction in the field would compensate for artificially increased surface
area of basalts etc).
7. The question-answer is a classic example of a scientific debate, and you should learn the
lesson that science is objective and must be repeatable. Do not let personal bias play any
role in your argument. The final comment by a well-respected microbiologist Ken
Nealson provides an impartial judgment.
Elemental cycling of C, S, N, P, Fe, Cu, U, Au, and Hg
This is an important lecture and make sure you review it carefully, especially in regards to major
pathways related to the C, S, N, and Fe cycles.
1. The C cycle is the most important among all elemental cycles. When we talk about
autotrophy and heterotrophy, it refers to C. The two largest reservoirs of carbon are fossil
fuels and carbonates. These two reservoirs are gradually built up throughout geological
history through two important processes: photosynthesis, and weathering and carbonate
deposition. These two processes were responsible for removing CO2 from the primitive
atmosphere and fixed them into the organic (fossil fuel) and inorganic (carbonates)
reservoirs. The removal of CO2 from the atmosphere allowed gradual cooling of the earth
to the point that life became possible. In the modern world, photosynthesis and
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2.
3.
4.
5.
respiration are two major C pathways. In the absence of light, chemosynthesis becomes a
dominant pathway to fix CO2 to organic carbon.
The N cycle: the atmosphere is the major N reservoir because N2 is a very stable
molecule and is accumulated to the present-day level through a long geological history.
Nitrate salts in the Earth’s crust are the second largest reservoir and it occurs as KNO3
and NaNO3 in deserts. Nitrogen fixation, nitrification and denitrification are three major
redox processes. Ammonium and nitrate are bio-available forms of nitrogen and major
forms of nitrogen fertilizer. Over-fertilization leads to excess ammonium and nitrate
which will promote algal growth and when they die an anoxic zone (dead zone) can
develop, such as the Gulf of Mexico. This is detrimental to fisheries and ocean
ecosystem.
The S cycle is the more complex among all elemental cycles, because S exists in any
oxidation state ranging from -2 to +6 with lots of organic S compounds. Gypsum in the
earth crust is the largest reservoir and is not actively cycled. The oceans contain lots of
soluble sulfate and accounts for why sulfate-reducing bacteria are often abundant in
marine sediments. Chemolithotrophic sulfide-oxidizing bacteria oxidize sulfide and
sulfur to sulfate, whereas heterotrophic sulfate-reducing bacteria reduce sulfate back to
sulfide.
The Fe cycle is important because it affects water quality (for example, high
concentrations of Fe2+ from Fe oxide reduction and acidity from Fe2+ oxidation),
degradation of organic contaminants because Fe3+ reduction is often coupled with
oxidation of organics (electron donor). The Fe redox cycle often results in mineral
transformation which could mobilize and immobilize a wide range of contaminants
including metals and organics. Acidophilic chemolithotroph Thiobacillus ferrooxidans
are responsible for acid mine drainage due to its active role in pyrite oxidation. Both coal
and metal sulfide deposits can result in acid mine drainage because of presence of
sulfides in both cases. Yellow boy is a common mineral (mineral name jarosite).
However, this bacterium can also recover precious metals (such as Cu and Au) from
metal sulfide deposits by dissolving and leaching dispersed metals from large piles of
low-grade ore deposits.
The Hg cycle is important in certain contaminated sites such as lakes. The Hg toxicity
increases as you go from metallic Hg to H2+ to methylated Hg. However microbial
reduction of Hg2+ to Hg in absence of oxygen drives the reaction towards Hg which can
be volatilized. This reaction detoxifies methyl mercury according the following
sequential reaction. Common metal-reducing and sulfate-reducing bacteria can
accomplish this job.
CH3Hg -> Hg2+ -> Hg
Life in extreme environment – deep continental subsurface
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1. There is an overall decrease of biomass and microbial activity with increased depth. The
limiting conditions are temperature, porosity, nutrient, and water.
2. Precautions to keep in mind when studying deep subsurface microbiology: contaminant
issues, sample storage related phenomena etc.
3. Currently there are only a few dedicated deep continental drilling projects around the
world. Most drilling projects are tagged on oil drilling operations. But some new
opportunities are emerging.
4. In extreme environment, syntrophic (or symbiotic) relationship appears to be a common
strategy where different functional groups of microorganisms (such as Fe reducers and
oxidizers) live together. The waste of one organism becomes food for another.
5. Ultimately geomicrobiologists are trying to match all biogeochemical reactions with
specific microbial groups (functions).
6. One of the ultimate goals of the deep subsurface microbiology is to assess the relative
importance of geographic isolation vs. environmental factors (so called biogeography).
Biogeography has been well-studied for plants and people, but much less so for
microorganisms except for a few special groups such as hyperthermophiles from hot
springs.
7. Subsurface microbes have various applications such as CO2 sequestration, microbially
enhanced oil recovery, and conversion of coal to methane gas.
Life in extreme environment – deserts
1. Definition of desert: desert is a landscape or region that receives an extremely low
amount of precipitation, less than enough to support growth of most plants.
2. Endoliths, Epiliths and hypoliths are different forms of life in desert environment.
Endolithic and hypolithic microorganisms inhabit regions where high ultraviolet
radiation, aridity, and high daily temperature range typify the environment, such as in
extreme desert. In such inhospitable conditions, the endolithic microorganisms migrate
into fractures or in pore spaces where the necessary nutrient, moisture, and light are
sufficient for survival. It is predicted that epiliths are more tolerant to more extreme
conditions than endoliths and hypoliths.
3. Eukaryotes and archaea are not abundant (