Geomicrobioloy Practice Questions

Lecture 2 (Jan. 30)
Co-evolution of life and Earth
• Early Earth
• Origin of life
– Panspermia
– De novo on Earth
– Alternative
• Co-evolution of life and earth
Early Earth
• 4.5 Ga- accretion of Earth
• 4.4 Ga- presence of liquid water
• 1221L of water delivered from cometary collisions
Early Earth
• 4.1 Ga- continents and oceans formed
Origin of Life
• Panspermia
– Preformed life arrived on this planet in the form of a
spore from another world (Weber and Greenberg, 1985)
– Bacillus subtilis enveloped in a mantle of 0.5 mm
thickness or greater of composition of H2O, CH4, NH3,
and CO in equal parts
– The mantle shielded them from UV radiation
– Could survive over a period of 4.5-45 Myr to allow
them to travel from one solar system to another
Origin of Life
• Surface Origin Hypothesis
– The first membrane-enclosed, self-replicating cells
arose out of a primordial soup rich in organic and
inorganic compounds in a “warm little pond”.
– However, surface conditions were too hostile:
•
•
•
•
•
Dramatic temperature fluctuations
Meteorite impacts
Dust clouds
Storms
Highly oxidizing atmosphere
Subsurface Origin Hypothesis
• Hydrothermal vents on the ocean floor
– Abundant energy from disequilibrium between
the reduced species from magma (H2, H2S etc.)
and cool, more oxidized seawater
– Precipitations of pyrite, silicates, carbonates,
and Mg-rich clays
– These minerals can serve as catalysts to
polymerize amino acids, peptides, sugars, and
nitrogenous bases, and RNA
Early History of Life
Co-evolution of life and earth
What Is Mineral Evolution?
A change over time in:
• The diversity of mineral species
• The relative abundances of minerals
• The compositional ranges of minerals
• The grain sizes and shapes of minerals
What was the first
mineral in the cosmos?
Supernovas
Diamond & Graphite
Diamond
Graphite
“Ur”-Mineralogy
Pre-solar grains contain about a dozen
micro- and nano-mineral phases:
•
•
•
•
•
•
•
•
•
•
•
•
Diamond/Lonsdaleite
Graphite (C)
Moissanite (SiC)
Osbornite (TiN)
Nierite (Si3N4)
Rutile (TiO2)
Corundum (Al2O3)
Spinel (MgAl2O4)
Hibbonite (CaAl12O19)
Forsterite (Mg2SiO4)
Nano-particles of TiC, ZrC, MoC, FeC,
Fe-Ni metal within graphite.
GEMS (silicate glass with embedded
metal and sulfide).
Mineral Evolution:
How did we get from a dozen
minerals (with 10 essential
elements) to >5000 minerals
(with 72 essential elements)
on Earth today?
Stage 1: Primary Chondrite Minerals
Minerals formed ~4.56 billion years ago in
the Solar nebula by melting and cooling.
~60 mineral species
Stage 2: Aqueous alteration, metamorphism
and differentiation of planetesimals
Stage 2: Alteration of planetesimals by
heat, water, and impacts
~250 mineral species (4.56-4.55 billion years)
•
•
•
•
•
•
Feldspars
Quartz
Micas
Clays
Zircon
Calcite
Stage 3: Planet Formation
Stage 3: Formation of a “Dry” Planet
~300 mineral species?
Is this the end point of the Moon and Mercury?
Stage 3: Formation of a Wet Planet
(4.5 to 4.0 billion years ago)
~420 mineral species (hydroxides, clays)
Stage 4: Granite Formation
(More than 3.5 billion years ago)
>1000 mineral species (pegmatites)
Partial melting of basalt and/or sediments.
Stage 4: Granite Formation
(More than 3.5 billion years ago)
>1000 mineral species (pegmatites)
Pollucite
Beryl
Tourmaline
Spodumene
Tantalite
Complex pegmatites require multiple cycles
of re-melting and element concentration:
All known examples are younger than 3.0 Ga.
Stage 5: Plate tectonics
(More than 3 billion years ago)
~108 km3 of reworking
Mayon Volcano, Philippines
New modes of volcanism
Stage 5: Plate tectonics
(More than 3 billion years ago)
Massive base metal deposits (sulfides, sulfosalts)
Stage 5: Plate tectonics
(More than 3 billion years ago)
Chalcocite
Luzonite & Enargite
Covellite & Djurleite
Bournonite
Geochronite
Massive base metal deposits (sulfides, sulfosalts)
Stage 5: Plate tectonics
(More than 3 billion years ago)
1,500 mineral species
Coesite SiO2
Glaucophane, Lawsonite, Jadeite
High-pressure metamorphic suites
(blueschists; granulites; UHP phases)
Stages 3-5: Chemical and physical
processes in Earth’s crust and mantle.
New geologic processes, especially
fluid-rock interactions associated
with igneous activity and plate
tectonics, led to a greater diversity
of geochemical environments and
thus new mineral species.
~1500 mineral species
Earth’s chemical and physical
processes resulted in up to 1500
different mineral species.
How did we get to 5000 mineral
species on Earth today?
The answer is life.
Minerals as Protection
After Joseph Smyth et al., 1998
Minerals as Catalysis
After Jay Brandes et al., 1998
Minerals as Reactants
After George Cody et al., 2001
Minerals as Scaffolds
After Gustaf Arrhenius et al. (1990, 1994, 1996, etc.)
Co-evolution of Life and Rocks
The origin of life ~4 billion years ago required
some minimal degree of mineral evolution.
Sulfides
Borates
Clays
But further mineral evolution depends on
life: hence the co-evolution of the
geosphere and biosphere.
Stage 6: Anoxic Archean biosphere
(4.0-2.5 billion years ago)
~1,500 mineral species (BIFs, carbonates)
D. Papineau
F. Corsetti, USC
Stage 7: Paleoproterozoic Oxidation
(2.5-1.85 billion years ago)
>4,500 mineral species, including perhaps
>3,000 new oxides/hydroxides/carbonates
Negaunee BIF, ~1.9 Ga
Rise of oxygenic photosynthesis.
Hypothesis
Approximately 2/3rds of all
known mineral species
cannot form in an anoxic
environment.
Most known minerals are
thus a consequence of
biological activity.
The Rise of Atmospheric Oxygen
?
Kump (2008) Nature 451, 277-278.
The early rise of oxygen in the
ocean
Lyons et al., 2014
Copper Minerals
log fO2 (oxygen fugacity)
0
Azurite & Malachite
-20
-40
Cu2+
Cuprite
Cu1+
Native Copper
-60
-80
Cu Metal
>400 of 650 Cu Minerals Won’t Form
Azurite & Malachite
Libethenite
Aurichalcite
Linarite
Turquoise
Brochthite & Linarite
Dioptase
Uranium minerals
log fO2 (oxygen fugacity)
0
-20
Uranyl (U6+)
Lepersonnite,
Studtite ,& Curite
-40
-60 Uraninite (U4+)
-80
Uraninite
>220 of 254 U Minerals Won’t Form
Autunite
Fourmarierite & Becquerelite
Boltwoodite
Lepersonnite,
Studtite ,& Curite
Kasolite & Torbernite
What was the oxygen
level in the Archean Eon?
log fO2 (oxygen fugacity)
0
Annabergite
-20
Ni3+
-40
-60
-80
Ni2+
Nickel Metal
Awaruite
>100 of 154 Ni Minerals Won’t Form
Annabergite
Hellyerite & Zaratite
Gillardite on Gaspeite
Falcondoite & Willemseite
Honessite
log fO2 (oxygen fugacity)
0
MnO2 (Mn4+)
Manganese
Minerals
-20
Mn2O3
Rhodocrosite
(Mn2+)
(Mn3+)
-40
-60
Mn3O4
(Mn3+ & Mn2+)
MnO (Mn2+)
-80
Hollandite,
Romanachite,
Birnessite
(Mn4+)
Stages 6-10: Co-evolution of the
geosphere and biosphere
Changes in Earth’s atmospheric
composition at ~2.4 to 2.2 billion
years ago represent the single
most significant factor in our
planet’s mineralogical diversity.
>4600 mineral species
Stage 8: The “Intermediate Ocean”
(1.85-0.85 billion years old)
>4600 mineral species (few new species)
Oxidized surface ocean; deep-ocean anoxia.
Sulfate-reducing microbes.
Stage 9: Snowball Earth and Neoproterozoic
Oxidation (850 to 542 million years ago)
>4600 mineral species (few new species)
Skeleton Coast, Namibia
Glacial cycles triggered by albedo feedback.
Stage 10: Phanerozoic Biomineralization
(Less than 542 million years old)
>4,900 mineral species (biominerals, clays)
Stage 10: Phanerozoic Biomineralization
(4,900 mineral species
hazenite
carbonate
silica
Stage 10: Phanerozoic Biomineralization
Abelsonite—NiC31H32N4
Ravatite—C24H48
Dashkovaite—Mg(HCOO)2.2H2O
Evankite—C24H48
Oxammite—(NH4)(C2O4).H2O
> 50 Organic Mineral Species
Biomineralization—Trilobite Eyes
ROOTS: The Rise of the Terrestrial Biosphere
Clays
Rivers
Clouds
Fungi
Microbes
Worms
Rhynie Chert (~410 million years old)
ROOTS: The Rise of the Terrestrial Biosphere
First extensive production of
terrestrial clay minerals
The Story of Earth
CONCLUSIONS
Earth has transformed repeatedly,
evolving over 4.5 billion years, and
it continues to change today.
Life and rocks have co-evolved as
a consequence of many positive
and negative feedbacks.
Lecture 3 (2/4/20)
Cell biology
• Reading:
– Chapter 4, Madigan et al. Brock Biology of
Microorganisms, 12th edition
Cell biology
• Microbial diversity
– Bacteria
– Archaea
– Eukarya
• Cell physical properties (phenotype)
– Morphology (size, shape, flagella, polysaccharide)
– Color
– Density
• Cell chemical properties
• Cell structure
Cell chemical properties and cell structure
• Cell chemical properties
– Composition
– Chemical reactions with different stains
• Reactions with Gram stain
• Cell structure
–
–
–
–
–
–
Cell wall
Cytoplasmic membrane
Cytoplasm
Ribosomes
DNA and RNA
Proteins
Cell Biology
• Microbial diversity – three domains of life:
– Bacteria – pathogens, phototrophy
– Archaea – common in extreme environments
– Eukarya – animals, humans
Cell: the single smallest unit of life
Three Domains of Life
Cell physical properties (phenotype)
– Morphology (size, shape, flagella,
polysaccharide)
– Color
– Density
Cell physical properties
(phenotype)
– Morphology
• size
• shape
• flagella, cilia
– Color
Star shape found from South African Gold mine
Typical shapes
The Cell Internal Structure
Eukarya
Bacteria & Archaea
Heliobacterium
modesticaldum
Saccharomyces cerevisiae
Chemical composition of cells
Structure dictates function
• Cell structure
– Cytoplasm: a complicated mixture of substances and
structures in side the cell
– Cytoplasmic membrane: lets nutrients in and wastes out
– Cell wall: Supports the cell
– DNA: carries the genetic blueprint for the cell
– RNA: Converts the blueprint into defined amino acid
sequences in protein
– Protein: catalyzes reactions and performs cellular
functions
– Ribosomes: contain RNA and protein and the cell’s
protein-synthesizing factories
Structure of Cytoplasmic Membrane
Phopholipid bi-layer
The Major Functions of the Cytoplasmic Membrane
Structure dictates function
• Cell structure
– Cytoplasm: a complicated mixture of substances and
structures in side the cell
– Cytoplasmic membrane: lets nutrients in and wastes out
– Cell wall: Supports the cell
– DNA: carries the genetic blueprint for the cell
– RNA: Converts the blueprint into defined amino acid
sequences in protein
– Protein: catalyzes reactions and performs cellular
functions
– Ribosomes: contain RNA and protein and the cell’s
protein-synthesizing factories
Cell Wall Structure
Gram-negative
Leucothrix mucor
Gram stain
Gram stain
Positive
Negative
Structure dictates function
• Cell structure
– Cytoplasm: a complicated mixture of substances and
structures in side the cell
– Cytoplasmic membrane: lets nutrients in and wastes out
– Cell wall: Supports the cell
– DNA: carries the genetic blueprint for the cell
– RNA: Converts the blueprint into defined amino acid
sequences in protein
– Protein: catalyzes reactions and performs cellular
functions
– Ribosomes: contain RNA and protein and the cell’s
protein-synthesizing factories
Nucleotide
DNA
DNA
https://www.youtube.com/watch?
v=GIzNlISbCxI
https://www.youtube.com/watch?v=o
_-6JXLYS-k
https://www.achievement.org/achieve
r/james-d-watson/
Structure dictates function
• Cell structure
– Cytoplasm: a complicated mixture of substances and
structures in side the cell
– Cytoplasmic membrane: lets nutrients in and wastes out
– Cell wall: Supports the cell
– DNA: carries the genetic blueprint for the cell
– RNA: Converts the blueprint into defined amino acid
sequences in protein
– Protein: catalyzes reactions and performs cellular
functions
– Ribosomes: contain RNA and protein and the cell’s
protein-synthesizing factories
Levels of Protein Structure
THREONINE
VALINE
HISTIDINE LEUCINE
PROLINE GLUTAMATE
GLUTAMATE
Levels of Protein Structure
Enzyme Example: Cleavage of Sucrose
Sucrose (disaccharide substrate)
Glucose and fructose
(monosaccharide products)
Sucrase (enzyme)
http://lhs.lps.org/staff/sputnam/Biology/U4Metabolism/enzyme.gif
Lecture 4 (2/6/20)
Nutrition and Metabolism
• Reading: Chapter 5, 6, Madigan
Nutrition and Metabolism
•
•
•
•
Energy class of microorganisms
Microbial nutrients
Fermentation and respiration
Biosynthesis
Definitions
• Metabolism
– All the chemical processes taking place within a cell
• Anabolism
– The process by which a cell is built up from simple
nutrients also called biosynthesis
• Catabolism
– The process by which chemicals are broken down and
energy released
Energy Classes
• Phototrophs
– use light as an energy source
• Chemotrophs
– use chemicals as an energy source
• Chemoorganotrophs
– use organic compounds
• Chemolithotrophs
– use inorganic compounds
Energy Classes
• Autotrophs: build all of their organic
structures from CO2 with energy obtained
from either light or inorganic chemicals
• Heterotrophs: build their structures from
organic C
Fig. 5-1
Microbial Nutrients
Group
1
2
4
3
5
6
7
8
9
10
11
12
Period
1
2
3
4
5
6
Key:
Essential for all microorganisms
Essential cations and anions for most microorganisms
Trace metals, some essential for some microororganisms
Used for special functions
Unessential, but metabolized
Unessential, not metabolized
13
14
15
16
17
18
Microbial Nutrients
• C
– 50% of dry weight of a typical cell, major
element in all classes of macromolecules
– Get C from CO2, or organic C
• N:
– 12% dry weight, a major element in proteins,
nucleic acids, and several other constituents
– NH3, NO3, and N2 as a source
Microbial Nutrients
• P, S, K, Mg, Ca, Na, Fe
– P: required in the cell for synthesis of nucleic acids and
phospholipids, available in PO4
– S: required by several amino acids, available in SO4 or
HS– K: required by all organisms, enzymes. available in K
ions
– Mg: functions to stabilize ribosomes, cell membranes,
and nucleic acids and required for the activity of many
enzymes.
Microbial Nutrients
• P, S, K, Mg, Ca, Na, Fe
– Ca: helps stabilize the bacterial cell wall
– Na: non-essential, seawater organisms need it
for its habitat
– Fe: Play a major role in cellular respiration,
being a key component of Fe-S proteins
involved in electron transport
– Fe-binding agent called siderophores which
solubilize Fe and transport it into the cell
Table 5-1
Micronutrients and Growth Factors
• Micronutrients
– Cr, Co, Cu, Mn, Mo, Ni, Se, W, V, Zn, Fe
• Growth factors
– Vitamins, amino acids, purines and pyrimidines
• Culture media
– Chemically defined
– Undefined
Table 5-2
Table 5-3
Table 5-4
Fig. 5-5
Isolated colonies
at end of streak
Confluent growth at
beginning of streak
Energetics
•
•
•
•
•
•
A+BC+D+G
Exergonic: releases energy
Endergonic: adsorbs energy
Concept of activation energy
Concept of enzymes
Oxidation-reduction reactions
Concept of Activation Energy
Fig. 5-6
Free energy
Activation
energy—
no enzyme
Substrates (A  B)
∆G0 = Gf0(C  D)
Gf0(A  B)
Activation
energy with
enzyme
Products (C  D)
Progress of the reaction
E0 (V)
Redox couple
-0.60
-0.50
-0.40
Oxidation-reduction reaction
and electron tower
H2 
2e-
+
-0.30
(1)
-0.20
-0.10
0.0
2H+
+0.10
(2)
+0.20
1/2O2 +
2e-

+0.30
O2-
+0.40
+0.50
2H+
+O
2-
+0.60
 H2 O
+0.70
(3)
2H+
+
2e-
 H2
+0.80
+0.90
(1) H2  fumarate2
(2) H2  NO3
E0 = -0.421 V
(3) H2 
1
2

O2
2
succinate
NO2
H2O

+ H2O
∆G0  = –86 kJ
∆G0  = –163 kJ
∆G0  = –237 kJ
Metabolic Pathway
• Fermentation
– Redox reactions occur in the absence of any
added terminal electron acceptors
• Respiration
– Molecular oxygen or other oxidant serves as the
terminal electron acceptor
Fig. 5-15
STAGE I: PREPARATORY
REACTIONS
Glucose
Hexokinase
Isomerase
Glucose-6-
Fructose-6-
Phosphofructokinase
Fructose-1,6Aldolase
STAGE II: MAKING ATP
AND PYRUVATE
Glyceraldehyde-3-
2
Glyceraldehyde-3-P
dehydrogenase
2
1,3-Bisphosphoglycerate
2
2 NAD+
Electrons
2 NADH
To
Stage III
Phosphoglycerokinase
2 3-Phosphoglycerate
2 2-Phosphoglycerate
Enolase
2 Phosphoenolpyruvate
STAGE III: MAKING
FERMENTATION
PRODUCTS
Pyruvate kinase
2 Pyruvate
NADH
To Stage II
NAD+
Lactate
Pyruvate
dehydrogenase decarboxylase
Pyruvate:Formate lyase
Acetate formate
Lactate
Acetaldehyde
Alcohol
dehydrogenase
Formate
hydrogenlyase
H2  CO2
NADH
NAD+
Ethanol
CO2
To Stage II
Respiration
• Electron acceptor
– O2, NO3, Fe3+, SO4, CO3
• Electron donor:
– Organic carbon, H2, Fe2+, H2S, NH3
Biosynthesis
•
•
•
•
Sugars
Amino acids
Nucleotides
Fatty acids
Microbial Growth
•
•
•
•
•
•
Overview of growth
Growth cycle of population
Measurement of growth
Effect of temperature on growth
Microbial growth at low or high pH
O2 as a factor in microbial growth
Microbial Growth
• Overview of growth
– Binary fission
– Population growth: defined as an increase in the
number of microbial cells in a population
– Growth rate: the change in cell number or cell
mass per unit time
– Exponential growth N = N02n
Fig. 6-1
One generation
Cell elongation
Septum
Septum
formation
Completion
of septum;
formation of
walls; cell
separation
Number of cells
(arithmetic scale)
Logarithmic
Arithmetic
102
500
10
100
0
1
2
3
Time (h)
4
5
1
Number of cells
(logarithmic scale)
Fig. 6-8
1000
103
Fig. 6-10
Growth phases
Exponential
Stationary
Death
1.0
10
Log10 viable
organisms/ml
0.75
9
8
Turbidity
(optical density)
0.50
Viable count
0.25
7
6
0.1
Time
Optical density (OD)
Lag
Growth Cycle of Population
• Lag phase
– Time required for the cells to reactivate
• Exponential phase
– Healthiest state, desirable for studying enzymes or
other components
– The rate is influenced by environmental conditions
• Stationary phase
– Generation time of 20 min for 48 hours would produce
biomass of 4000 times the weight of the Earth
– Two effects inhibits growth and stationary phase
• Wastes built up
• Essential nutrients used up
• Death phase
Measurements of Growth
• Total cell count
• Viable count – plate count
• Turbidimetric counts: optical density in a
photometer or spectrophotometer
Fig. 6-14
Direct Count
To calculate number
per milliliter of sample:
12 cells  25 large squares  50  103
Ridges that support coverslip
Coverslip
Number /mm2 (3  102)
Sample added here; care must be
taken not to allow overflow; space
between coverslip and slide is 0.02 mm
1
( 50
mm). Whole grid has 25 large
squares, a total area of 1 mm2 and
a total volume of 0.02 mm3.
Microscopic observation; all cells are
counted in large square (16 small squares):
12 cells (in practice, several large squares
are counted and the numbers averaged.)
Number /mm3 (1.5  104)
Number /cm3 (ml) (1.5  107)
Fig. 6-15
Viable Cell – Plate Count
Spread-plate method
Surface
colonies
Incubation
Sample is pipetted onto
surface of agar plate
(0.1 ml or less)
Sample is spread evenly over
surface of agar using sterile
glass spreader
Typical spread-plate results
Pour-plate method
Surface
colonies
Solidification
and incubation
Sample is pipetted into
sterile plate
Sterile medium is added and
mixed well with inoculum
Subsurface
colonies
Typical pour-plate results
Fig. 6-16
Sample to
be counted
1 ml
1 ml
1 ml
1 ml
1 ml
1 ml
9-ml
broth
1/10
Total
dilution (10–1)
1/100
(10–2)
1/103
(10–3)
1/104
(10–4)
1/105
(10–5)
1/106
(10–6)
Plate 1-ml samples
159
17
2
0
Too many colonies colonies colonies colonies colonies
to count
=
159  103
Plate Dilution
count factor
1.59  105
Cells (colony-forming
units) per milliliter of
original sample
Effect of Temperature on Growth
• Cardinal temeprature
– Minimum temp: freezing of the cytoplasmic
membrane
– Optimum temp: rapid growth
– Maximum temp: inactivation of one or more
key proteins in the cell
– Characteristic of each type of organism, but not
completely fixed. Depending on environmental
conditions
Fig. 6-18
Enzymatic reactions occurring
at maximal possible rate
Growth rate
Optimum
Enzymatic reactions occurring
at increasingly rapid rates
Minimum
Maximum
Temperature
Membrane gelling; transport
processes so slow that growth
cannot occur
Protein denaturation; collapse
of the cytoplasmic membrane;
thermal lysis
Fig. 6-19
Thermophile
Mesophile
Growth rate
Example:
Escherichia
coli
Psychrophile
Hyperthermophile
Example:
Geobacillus
stearothermophilus
Example:
Thermococcus celer
Hyperthermophile
Example:
Pyrolobus fumarii
60°
106°
88°
39°
Example:
Polaromonas
vacuolata
4°
0
10
20
30
40
50
60
Temperature (°C)
70
80
90
100
110
120
Temperature Classes of Organisms
• Psychrophiles
– In oceans, Antarctic
– Optimal: 15oC, Max: 20oC, Min: 0oC or lower
– Molecular adaptations: different structures of
enzymes. They function optimally in the cold,
and are inactivated at even moderate temp.
Microorganisms from Antarctic sea ice
Temperature Classes of Organisms
• Thermophiles
– Soils at mid day 50-70oC
– Optimal temp: > 45oC
– Three conclusions
• Prokaryotic organisms able to grow at higher temp than
eukaryotes
• The most thermophilic of all prokaryotes are certain species of
archaea
• Nonphototrophic organisms able to grow at higher temp than
phototrophic forms
Table 6-1
Temperature Classes of Organisms
• Hyperthermophiles
– Hot Springs, boiling water, Yellowstone
National Park
– Hydrothermal vents in the bottom of the
oceans: > 350oC
– Optimal temp: > 80oC
Growth of
hyperthermophiles
in boiling water
Temperature Classes of Organisms
• Molecular adaptations to thermophily
– Enzymes and other proteins are stable to heat,
and function optimally at high temp.
– Ribosomes, other constituents, cytoplasmic
membrane are heat stable, saturated fatty acids
– Protein-synthesizing machinery itself needs to
be heat stable
Microbial Growth at Low or High pH
• Acidophiles: pH 1000 m or more
> 100 m/day
Disadvantage: contamination
Drilling holes
Detection of Contamination
Chinese Continental Scientific Drilling Project
Subsurface sampling of rocks
• Quality control
– Sterilization of processing tools
– Controls, blanks, replicates
– Multiple tracers to detect sources of
contamination
•
•
•
•
Dyes
Ionic tracers (barium, sulfate, ammonium, Bromide)
Particulate tracers (beads)
Microbial tracers
Sampling and Contamination
• Sampling processing
– Anaerobic chamber – Glove bag
– Sterile environment – Laminar flow hood
– Rock splitters/crusher
Sampling and Contamination
• Sampling processing
– Anaerobic chamber – Glove bag
– Sterile environment – Laminar flow hood
Sampling and Contamination
• Storage related phenomenon (SRP)
– Community level changes
– Changes in microbial compositions
– Factors affecting SRP
Sampling and Contimation
• Storage related phenomenon (SRP)
– Community level changes
• Increased culturable counts
• Increased microbial activity
• Decreased culturable diversity
Sampling and Contamination
• Storage related phenomenon (SRP)
– Factors affecting SRP
•
•
•
•
•
Moisture content
Permeability of sample
Sample perturbation (homogenization)
O2
Temperature: higher, more SRP changes
Sampling and Contamination
• Storage related phenomenon (SRP)
– Changes in microbial compositions
• Some members of the community can no longer be
cultured, while others are culturable only after the
storage
• Hypotheses:
– “After” storage isolates result from the growth that were
previously below the detection limit
– “After” storage organisms result from the resuscitation of
organisms that could not initially be cultured by standard
plating techniques
Detection and activity of microorganisms
• Detection of microbes
–
–
–
–
–
–
–
Direct count
Plate count (CFU/ml)
FISH
SEM
TEM
Laser confocal microscopy
AFM
FISH (fluorescent in situ hybridization)
• Gene probing
– Target gene in a sample: AUUCGGAAU
– Gene probe:
UAAGCCUUA
• The gene probe is radioactive or fluorescent to
allow easy detection
• If the target gene is universal to all bacteria, then I
detect all bacteria
• If the target gene is specific to a species, then I
detect a particular species within a microbial
community
• It allows detection and activity measurement of
microbes
• https://www.youtube.com/watch?v=b81DcJC1jAs
Signature Sequences from 16S or 18S RNA
defining the three domains of life
Not stained
FISH
Universal probe
Eukaryal probe
FISH
Ammonia-oxidizing bacteria
Not stained
Nitrite-oxidizing bacteria
SEM Image Showing Bacteria-Smectite Interactions
Subsurface Bacteria – TEM Pictures
Detection and activity of microorganisms
• Activity measurement – Why measure it ?
• Activity is a function of physical, chemical and
biological parameters as well as nutrient status
• In undisturbed environment, allows one to
determine the microbial contribution to nutrient
cycling
• In disturbed environment, evaluate impact of
disturbance on microbial community
• Important indicator in evaluating the process of
restoration of disturbed sites, such as intrinsic
bioremediation or natural attenuation
Detection and activity of microorganisms
• Activity measurement – How to measure it
?
– Physiological methods
– Nucleic acid-based methods
– Phospholipid fatty acid
Physiological Methods
• Substrate + nitrogen + TEA  cell mass +
CO2 + water source
– Substrate disappearance measured by UV
spectrophotometry, liquid or gas
chromatography
– Nitrification: add 15N labeled ammonium and
measure product using a mass spectrometer
Physiological Methods
• Substrate + nitrogen + TEA  cell mass + CO2 +
water source
– TEA disappearance (Terminal electron acceptor): O2,
NO3
– Cell mass production: turbidity, protein production
– Incorporation of radiolabeled tracers into cellular
macromolecules
• 1.
Incorporation of thymine into DNA: thymine is a base of
DNA.
• 2.
Incorporation of leucine into protein
Lecture 7
(2/18/2020)
Groundwater-Microbe Interactions
• The equilibrium approach
• The kinetic approach
E0 (V)
Redox couple
-0.60
-0.50
-0.40
Oxidation-reduction reaction
and electron tower
H2 
2e-
+
-0.30
(1)
-0.20
-0.10
0.0
2H+
+0.10
(2)
+0.20
1/2O2 +
2e-

+0.30
O2-
+0.40
+0.50
2H+
+O
2-
+0.60
 H2 O
+0.70
(3)
2H+
+
2e-
 H2
+0.80
+0.90
(1) H2  fumarate2
(2) H2  NO3
E0 = -0.421 V
(3) H2 
1
2

O2
2
succinate
NO2
H2O

+ H2O
∆G0  = –86 kJ
∆G0  = –163 kJ
∆G0  = –237 kJ
The Equilibrium Approach
• Hydrogen electrode
– The electrical
potential between
the Pt and the
solution is zero
– The standard free
energy of formation
of H+ ions in
solution is zero
– The standard free
energy of formation
of an electron in
solution is zero
Coupled Electrodes
If Eh > 0, cell A donates electrons to cell B,
If Eh Fe2+ + H+
• Eh = E0 + (2.303RT/nF)log(aFe3+/aFe2+)
• Pe = -log[e-] = (F/2.303RT)Eh
• Eh is only meaningful when a solution is at
chemical equilibrium
Indications of Kinetic Processes
Describing Kinetic Processes in
Groundwater systems
• Identify electron donors
– Organic carbon
– Reduced species
• Identify electron acceptors
– O2, Mn(IV), Fe(III), sulfate, and carbon
dioxide
Microbial Ecology and Competition
• H2 is the most widely used substrate for anaerobic
v: rate of H2 uptake
respiration.
v max [ H 2]B
v
Ks  [ H 2]
dB
 (vY )  (bB)
dt
bB
v
Y
Ks
[ H 2] 
(v max Y / b)  1
vmax: max rate of H2 uptake
Ks: H2 concentration at which
v = 0.5vmax
B: number of grams of H2
consuming microorganisms
Y: yield coefficient (grams of
cells formed per mole of H2
consumed)
b: cell death coefficient
The hydrogen concentration depends solely on the physiological
characteristics of the microorganisms consuming the hydrogen
Methanogen Sulfate reducer Fe/Mn reducer Nitrate reducer
H2 Responses to Various Reduction Processes
Concentration Change of O, N, Fe, S, CH4 and H2
Along a Flowpath of a Aquifer
Block Diagram for Identifying Redox Processes
A Segregated Groundwater Aquifer
Characteristic vertical profile of redox
processes in aquatic sediments
Solute transport is via diffusion
No advection is present to mix different
zones
https://www.youtube.com/watch?v=5TP0CrzPVZ0
Redox Zonation in Groundwater
• Because groundwater is constantly mixing
by advection, concentrations of redox
sensitive parameters are not so reliable
• Combine the following three:
– Consumption of electron acceptors
– Production of reduced products
– H2 concentration
Lecture 8 (2/20/2020)
Biomineralization
A few video clips
https://www.youtube.com/watch?v=
4JUYyMHOHb8
 https://www.youtube.com/watch?v=
B0ot4chQNqA
 https://www.youtube.com/watch?v=
7cEjCLMZ9sQ
 https://phys.org/news/2018-09magnetic-bacteria-uniquesuperpower.html

Biologically controlled
mineralization

Biologically controlled mineralization
• Prokaryotes: Magnetite, dolomite
• Eurokaryotes: Silica, carbonate, and
phosphate skeletons
The Little Engineers That Could:
Construction & Significance of the Bacterial
Magnetosome Chain
I. Introduction
II. Background information on Magnetotactic Bacteria
III. Background information on Magnetosomes
a. Composition
b. Shape
c. Size
IV. Significance of the Magnetosome Chain
V. Why Make Magnetosomes?
VI. Molecular Basis Construction of the Magnetosome Chain
VII. Biomarkers on Earth and Beyond
Courtesy of Dennis A. Bazylinski
School of Life Sciences
University of Nevada, Las Vegas

IMPORTANT FEATURES OF THE
MAGNETOTACTIC BACTERIA
They are diverse with regard to morphology and physiology:
“Magnetotactic Bacteria” has no taxonomic meaning
• All known are Gram-negative members of the Domain Bacteria and belong
phylogenetically to various subgroups of the Proteobacteria and the
Nitrospira phylum
• All known are motile by means of flagella
• All display a negative tactic and/or growth response to atmospheric levels
of O2 (~21% O2); they are all anaerobes or microaerophiles or both
• They all have a respiratory form of metabolism; only one is known to be
capable of fermentation (pyruvate to acetate and H2)
• They have great potential in the biogeochemical cycling of several key
elements in natural environments (N, S, C and Fe etc.)
• They are ubiquitous in aquatic habitats and cosmopolitan in distribution.
Locally confined to or slightly below the oxic-anoxic interface.
That internal compass of Bellini…?
Magnetotactic Bacteria Biomineralize
Magnetosomes
Defined as an intracellular magnetic mineral crystal, either
magnetite (Fe3O4) or greigite (Fe3S4), surrounded by a lipidbilayer membrane (the “magnetosome membrane”)
From: Gorby, Beveridge & Blakemore, J. Bacteriol. 1988
Magnetosomes
Note consistent speciesspecific magnetosome
crystal morphology:
First suggestion of genetic
and crystallochemical control
over magnetosome
biomineralization
Uncultured rod-shaped bacterium from Little Styx River, New Zealand
Scale Bar = 0.5 µm (from R.P. Blakemore)
Minerals Produced by Magnetotactic
Bacteria: In General High Chemical Purity
Mineral (magnetism)
Formula
Magnetite (+)
Fe3O4:
Greigite (+)
Fe3S4
Many-celled
Magnetotactic
Prokaryote (MMP),
Rods
? (-)
Sphalerite-type FeS*
MMP, Rods
Mackinawite (-)
Tetragonal FeS*
MMP, Rods
Pyrite (-)**
FeS2
MMP
Pyrrhotite (+)**
Fe7S8
MMP
Intermediates in greigite formation.
Produced by
Fe2+Fe3+2O4
Cocci, Spirilla, Rods
**Probably errors in mineral identity.
From: Mann, Sparks, Frankel, Bazylinski & Jannasch, Nature 1990; Farina,
Esquivel & Lins de Barros, Nature 1990; Pósfai, Buseck, Bazylinski &
Frankel, Science 1998
Magnetosome Crystal
Morphologies
Magnetosome crystals are
generally of high structural
perfection…
Idealized Crystal Morphologies
from HRTEM Studies
a-d: Fe3O4; a, cubo-octahedron
(equilibrium form); b-c, hexahedral
prisms; d, elongated cubooctahedron
e-f: Fe3S4; a, cubo-octahedron
(equilibrium form); b, rectangular
prismatic crystal
The elongated and tooth-shaped
crystals of magnetite are unique and
have been used as biomarkers or
“magnetofossils” in sediments and meteorites
Magnetosomes Contain Crystals that
are Stable Single-Magnetic-Domains
• Magnetotactic bacteria produce crystals that are the
smallest crystals that can be formed of Fe3O4 or Fe3S4 and
still be permanently magnetic at ambient temperature
• Thus, these organisms, by forming SMDs, have
maximized the magnetic remanence of the individual
magnetosome crystals
Electron Holography in the Electron Microscope
Magnetic induction map of partial chains and
scattered magnetite crystals in a cell of a freshwater
magnetotactic bacterium
So Magnetosomes are Clearly a Masterpiece
of Microbial Engineering…
But Why
Make
Magnetosomes?
The Big Question…
Magnetic Field Effect on
Magnetotactic Bacterial Cells
Bacterium
experiences a torque
tending to align it
along magnetic field
lines like a compass
needle (passive)
Bacterium is not
pulled in any
direction
Dead cells react like
living cells except
they cannot swim
Magnetotaxis thus results from passive (magnetic
alignment) and active (swimming) forces
Magnetotactic Bacteria Need to Find and
Maintain an Optimal Position in Gradients
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
←
[O2]-gradient
culture of MV-1
But is this the complete story? Role of magnetite, possibly.
But why do cells take up and process so much Fe in the first place?
Major Hypothesis
That there is a physiological reason for why
magnetotactic bacteria biomineralize
magnetosomes and take up and process so much
Fe…
Remember that it requires up energy to take up so
much Fe… there must be a reward for the cell in
doing this…
What is the physiological reason and what is the
reward?
Fe(III) reduction? Fe(II) oxidation?
Physiological Links to Fe?: Salt Pond Vibrio Grown with
Soluble Fe(II) in [O2] Gradients
Uninoculated
Medium
Band of
Fe(III) Oxy-hydroxides
Band of Cells
Autotrophic Fe(II) oxidation?
How Do Magnetotactic Bacteria
Construct the
Magnetosome Chain?
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
Keep in mind… Not all steps are temporally ordered within the cell
Magnetotactic bacteria pump lots of Fe! 1-3% Fe on a dry weight
basis
(Compare to Escherichia coli… 0.025% Fe (Madigan et al., 2003))
Genes and Proteins Involved in
Construction of the Magnetosome Chain
Protein Profiles of
Fractions of strain MV-1
SF: Soluble Cell Fraction
MF: Membrane Fraction
(without magnetosomes)
MM: Magnetosome
Membranes
MW: Molecular Weight
Markers
Purified Magnetosomes with Membranes
←
←
←
←
100 nm
Above Treated with 1% SDS
Magnetosome Membranes Contain Unique Proteins
The Magnetosome Membrane Originates
as an Invagination of the Cell Membrane
50 nm
Use of Electron Cryotomography
(Magnetospirillum magneticum strain AMB-1)
From: Komeili et al., Science 2006
Magnetosomes from cells of Magnetospirillum gryphiswaldense
grown with 50 µM Fe+3 citrate and 50 μM MnCl2
Acquire HAADF
50 nm
50
nm
Fe
Mn
Mn
09.50.56 Acquire EDXFe
Acquire HAADF Area 1
09.52.12 Acquire EDX Acquire HAADF Area 2
150
150
O
Cu
Fe
Cu
Fe
O
C Cu
Counts
Counts
100
Fe
100
C
Fe
Cu
Cu
Cu
50
50
Fe
Si
2
Cl
Cl
Ca
Ca
Cu
Si
Mn
4
6
Energy (keV)
Cu
8
10
2
Cl
Cl
Ca
Ca
Fe
Cu
Mn
4
6
Energy (keV)
8
The small Mn peak in EDX (energy dispersive X-ray analysis) spectra indicates
there is at least 2 wt% Mn in these magnetosomes.
10
Magnetosomes from cells of Magnetospirillum gryphiswaldense
grown with 50 µM Fe3+ citrate and 50 μM MnCl2
EELS (electron energy loss spectroscopy) elemental
maps taken from the same area: carbon, iron, oxygen, manganese:
brightness is proportional to the element concentration.
carbon
manganese
iron
oxygen
← Bright field TEM image of
chain of magnetosomes from
cell of M. gryphiswaldense,
same area
Work of PerezGonzalez, Prozorov,
Prozorov, Mallapragada
& Bazylinski
“MAGNETOFOSSILS”?
Important question: Can magnetosome crystals be used as a reliable
biomarker for the indication of the past presence of magnetotactic
bacteria?
“Magnetic separate”
from Irish Sea
sediment (TEM
courtesy of Z. Gibbs)
Note morphology of
crystals of Fe3O4 and
presence of chains
Fe3O4 particles are promiscuous!
Fe3O4 particles (magnetosomes) are in higher organisms
including salmon, trout, sea turtles, bees, birds… cows?
And possibly humans!
Are similar genes for magnetite biomineralization present in these organisms?
Bacterially Induced Mineralization

Passive
• Passive mineralization refers to simple nonspecific
binding of cations and recruitment of solution anions,
resulting in surface nucleation and growth of minerals




Fe, Mn, and other metal oxides, e.g., ferrihydrite
(5Fe2O3•9H2O), hematite (α-Fe2O3), and goethite (αFeOOH);
metal sulfates, phosphates, and carbonates;
phosphorite; Fe and Fe-Al silicates; and metal sulfides.
Active
• Active mineralization occurs by the direct redox
transformation of surface-bound metal ions, or by the
formation of cationic or anionic byproducts of metabolic
activities that form minerals on the bacterial surfaces

Carbonates, oxides, and sulfides
Chemically precipitated
magnetite (BIM)
Describe difference between
BCM and BIM magnetite
Can magnetite be formed by both
BCM and BIM?
 If so, what are the differences in
their shape, composition, and
others??

Microbial Polysaccharides Template
Assembly of Nanocrystal Fibers
Energy
generation


Chan et al., 2004, Science
Stalk formation as a physiological
Mechanism to avoid encrustation
by Fe-oxidizing bacteria

Chan et al., 2010


the fibrillar, ribbon-like stalks,
Chan et al., 2010
Comparison of synthetic filaments
with purported ancient microfossils
rope-like, and emanate from
large, clearly abiological aggregates

Banded Iron Formation
Lecture 9 (2/25/20)
Microbial Weathering and Microbe-Clay
Interactions
Why is this topic important?





Soil formation and plant nutrition
Stability of architectural materials
Geochemistry of groundwater and movement of
contaminants
Long-term stability of geological nuclear
repositories
Effects of mineral weathering on climate on a
geologic time scale
Mineral-Microbe Interactions
Microbial colonization on basalts
Jennifer Roberts
Biofilm in Yellowstone National Park
Development of Biofilm
Pathways to tolerate antimicrobial compounds
Water Flows Through a Channel in a Biofilm
Model of a Biofilm Showing Microbial Microcolonies
and Interstitial Voids
Microbial Colonization on Quartz Surface
How Do Silicate Minerals
Weather? Particularly Feldspars

Weathering Rates depend on the
following:





pH
Temperature
Pressure
Ionic Strength
Organic Ligands
pH Dependent


Slowest rates of dissolution at a neutral
pH
Faster rates increasing towards acidic pH
levels
Temperature and Pressure Effects


Fundamental controls of rates of chemical
reactions
-Rate increases at higher temperatures
Pressure not generally a significant factor
on the earth’s surface
Ionic Strength Effects

Feldspar dissolution rates decrease with
increasing ionic strength

This is possibly by the inhibiting of critical ion
exchange reactions at the feldspar surface
Organic Ligand Effects


Metabolic by-products, extracellular enzymes,
chelates, and both simple and complex organic
acids
Influence dissolution rates by:


Decreasing pH
Forming framework destabilizing surface complexes
***Organic acids enhance the dissolution rates of
silicate minerals both in field observations and lab
experiments
What Role Do Microorganisms
play in weathering?



Accelerate the dissolution of silicates by
production of excess proton and organic
ligands
Oxidation and dissolution
Reduction and dissolution
Research Site in Bemidgi, MN
Mineral chips
Bemidgi Research Site



Hydrocarbon contaminated aquifer in
northern Minnesota
Glacial sand aquifer dominated by quartz
and feldspar
Pool of approx 1 m thick petroleum
floating on the water table


Lots of organic carbons below
Extreme anaerobic environment
Silicate Minerals as a source of nutrients?


Anaerobes-use NO3- , Fe(III) and SO42- for
respiration
Most also require nitrogen and phosphorous for
cell growth and metabolism
These nutrients are often limited in groundwater
systems, especially phosphorous
**microorganisms scavenge for P in poorly soluble
silicate minerals (apatite inclusions)

Feldspar: (Na,K,Ca) (AlSi2O8)
Apatite: Ca5(PO4)3(F,Cl,OH)
Microbes on Basalt @ 3 months
Extensive Eth Pits on Magnetite Surfaces
SEM Images of mineral surface colonization
from In-Situ Microcosms
What could have caused the difference
in surface colonization of these mineral
Surfaces ?
Mineral-Microbe Interactions
Mineral Weathering Sequence

Abiotic:


Olivine > Plaoioclase > Albite > anorthoclase
> microcline > Quartz
Biotic:

Quartz > Microcline > Olivine (??)
Typical structure of a clay mineral
Interlayer cation
-OH
O in tetrahedra
O in octahedra
Possible sites of Fe3+
Tetrahedral
Octahedral
Tetrahedral
Inter Layer
Source: J.W. Stucki
Tetrahedra: O at corners, Si4+(but sometimes also Al3+ and Fe3+) in the center
Octahedral Sheet: O at corners, Al3+, Mg2+, Fe3+, and Fe2+ in the center
Swelling clay video

Clay-Microbe Interaction

Bacteria culturing:


Fe(III) in smectite




Shewanella putrefaciens MR-1
electron acceptor
Na Lactate – electron donor:
Medium preparation:
M1 growth medium
Fe(III) reduction
1. Chemically (Dithionite)
2. Biologically (Shewanella putrefaciens CN32)
Na
Na
e-
e-
Acetate+CO2+H2O
Lactate
Fe(III)
Fe(II)
Si, Al
O
OH
Increase in the extent of microbial Fe(III) reduction as a
function of time in different clay minerals
30
Fe(III) reduction, in %
Nontronite-2
20
Nontronite-1
10
Chlorite
Illite
0
0
5
10
15
Time, days
20
NAu-1 Nontronite-2
NAu-2
Mu-Il Illite
CCa-2
Nontronite-1
25
Chlorite
30
Fe(III) Reduction via Shuttling Compounds
Electron donor
Cell
Electron acceptor
Lactate
Fe(II)- smectite
Acetate+
CO2+H2O
Fe(III)- smectite
Oxidation
Reduction
e- shuttle/titrant
AH2DS
AQDS
Typical structure of a clay mineral
Interlayer cation
-OH
O in tetrahedra
O in octahedra
Possible sites of Fe3+
Tetrahedral
Octahedral
Tetrahedral
Inter Layer
Source: J.W. Stucki
Tetrahedra: O at corners, Si4+(but sometimes also Al3+ and Fe3+) in the center
Octahedral Sheet: O at corners, Al3+, Mg2+, Fe3+, and Fe2+ in the center
Surface Area


Surface area decreases after reduction of
Fe3+ to Fe2+ in smectites
Decrease in SA reduces the structural
integrity of smectites in soils, which alters
the capabilities for plants to take up
nutrients
Surface Area
Surface area changes resulting from bacterial reduction
on montmorillonite (Stucki and Kostka, 2006).
Tillage
Swelling
(Stucki and Kostka, 2006)
Importance of Studying the
Smectite to Illite Reaction

The S-I reaction is related to:




Hydrocarbon maturation and oil production
Geopressuring of shale
Formation of growth faults
Changes in pore water chemistry
The S-I Reaction

Abiotic system in nature




Abiotic system in laboratory




100oC
Millions of years
Pressure ??
300-350oC
100 atmosphere
4-5 months
Biotic system



Room temperature
1 atmosphere
14 days
The Importance of Microorganisms
Fe(II) in Clay Mineral: Effective Reductant of Tc(VII)
Major strategy: 2-step redox reaction
1.47[Fe(III)2.73]clay minerals+CH3CHOHCOO- +2H2O→1.47[Fe(II)2.73]clay minerals +CH3COO-+HCO-3+5H+
Tc(VII) + 3Fe(II) = Tc(IV) +3Fe(III)
soluble
insoluble
Our vision on Tc(VII) remediation using Fe(II) in NAu-2
Fe(II) in nontronite colloids
Tc(VII)
Tc(IV)
Tc(VII)
Tc(IV)
Tc
Tc(VII)
Tc(VII)
Tc(VII)
Tc(IV) Tc(IV)
Tc(VII)
Tc
Tc
Tc
Tc(VII)
Tc
oxic/suboxic
—- —- – –
— – –
Jaisi et al.
2009
LECTURE 10 (2/27/2020)
LIFE ON MARS?
MINERALOGICAL EVIDENCE
 https://www.youtube.com/watch?v=DMMPY
kRrd4o
The Red Planet Mars
True Color Viking Image
Significance: Life on Mars
 General public interest.
 Proof that other planets/moons can
support life.
 Europa (Jupiter).
 Titan (Saturn).
 Future space missions.
 Origin of life.
Why Mars?
 Similarities to Earth:
 Terrestrial planet.
 Similar distance to sun
 Mars: 1.5 au.
 Earth: 1 au.
 Size
 About ½ the diameter of Earth.
 Surface area is about the same as
dry land on Earth.
 Water
 Polar ice caps.
 Similar axial tilt.
 (http://mars.jpl.nasa.gov)
NASA Image PIA03154
Conditions on Mars
 Current conditions cannot
 Past conditions were more
support life as we know it.
friendly to life.
 High CO2 atmosphere.
 More oxygenated
 Temperature extremes
 Weak magnetic field
atmosphere.
 Liquid water.
 Current magnetic field is
remnant of past.
How do we know a piece of
rock came from Mars?
Meteorites as Evidence
 Meteorites can come from asteroids, other planets,
comets, etc.
 Origin identified by chemistry, volatile content, age
to some degree.
 Conclusive evidence for Martian meteorites: volatile
content trapped in meteorites matches atmospheric
concentrations measured by Viking probe.
Meteorite ALH84001
(Thomas-Keprta et al., 2002)
 Found in Antarctica in
Dec. 1984.
 “Highly-shocked, grayishgreen, achondrite, 90%
covered with fusion crust.”
 Identified as Martian
based on oxygen
isotopes.
Martian Meteorite ALH84001
(http://www2.jpl.nasa.gov/snc/alh3.gif)
Meteorite ALH84001: Geology
(Thomas-Keprta et al., 2002)
 Volcanic orthopyroxenite:
 Dominantly orthopyroxene.
 Minor chromite, olivine, pyrite,
apatite, Si-rich glass.
 Secondary carbonate globules
 (~1 %) in cracks.
 Formed at temperatures low




enough for life.
Martian origin.
Little to no alteration on Earth.
Concentrically zoned in Ca, Mn, Fe,
Mg carbonates.
Nanometer-sized magnetite evenly
distributed.
Carbonate globule and the meteorite
Geologic History of ALH84001
(Thomas-Keprta et al., 2000; 2002)
 Rb-Sr crystallization age:
~4.5 Ga.
 Oldest known Martian
meteorite.
 Older than any rocks on Earth!
 Secondary carbonate: 3.90
+ 0.04 Ga (Rb-Sr).
 Age is older than oldest
evidence of life on Earth (~3.8
Ga).
 Ejected from Mars ~16 Ma.
 Captured by Earth’s
gravitational field ~13 Ka.
Fresh-cut surfaces of ALH84001,
from http://www2.jpl.nasa.gov/snc/alh.html
McKay et al. (1996): Life on Mars Debate
Microfossil(?) found in ALH84001
Mineralogical Evidence in Question:
Magnetite
 ~25% of magnetite crystals in carbonate globules
resemble biogenic magnetite crystals produced by
magnetotactic bacteria (MV-1) (Thomas-Keprta et
al., 2000).
 These nm-sized magnetite crystals in carbonate
may be evidence of life (Thomas-Keprta et al.,
2000).
Magnetite crystals in Meteorite ALH84001, from Thomas-Keprta et al.(2000).
Magnetite Assay for Biogenicity (MAB)
(Keprta et al., 2000; 2002)
 Narrow size range (35-120 mm, discussed last week in





class)
Definite width to length ratio.
Chemical purity.
Crystallographic perfection.
Unusual crystal morphology.
Elongation of crystals.
Sizes and morphologies of MV-1
(terrestrial microbe) magnetite and
ALH84001 possibly biogenic
magnetite (Thomas-Keprta et al.,
2000).
Narrow Size Range and Width-to-Length Ratio
 Necessary for
magnetotaxis.
 Too big: doesn’t have
necessary magnetic
moment.
 Too small: can’t hold
stable net magnetization.
Chemical purity
 Magnetite is part of the spinel group of minerals .
 Usually impurities in abiotic magnetite.
 May contain Ti, Cr, Mn, Al, other substitutions.
 Magnetotactic bacteria usually produce pure Fe3O4
(Thomas-Keprta et al., 2000; 2002).
 Result of Fe acquisition and transport systems in the cell.
 Multiple chelation and redox steps exclude other cations.
EDS Spectra for ALH84001
magnetites. Si and Cu are
from acid extraction of
magnetite and TEM support
grid, from Thomas-Keprta
et al. (2000).
Crystallographic Perfection
 Lattice defects are normal in abiotic crystals.
 Common to see twinned grains in most minerals.
 Could alter crystal’s properties.
 No twinning or other lattice defects in biogenic
crystals (Thomas-Keprta et al., 2000).
 Occasional twinning of {111} plane.
 {111} is magnetically “easy” axis; doesn’t affect
magnetism.
Unusual crystal morphology and preferred
elongation direction.
 Hexaoctahedral crystals
(Thomas-Keprta et al.,
2000)
 Not in thermodynamic equilibrium.
 Anisotropic morphology.
 Preferred growth in [111] direction.
 Genetically controlled.
 Growth in other directions
restricted by membrane around
magnetosomes?
Additional MAB Characteristic?
 Magnetic crystals aligned in chains.
 Difficult to preserve because the chains usually fall apart
after the host organism dies (Thomas-Keprta et al.,
2002).
 Imaged using SEM-BSE combination (Friedmann et al.,
2001).
SEM-BSE image of magnetite crystal chain in carbonate globule, ALH84001, from Friedmann
et al. (2001).
Non-Martian Extraterrestrial Magnetite
(Thomas-Keprta et al., 2000)
 Usually larger crystals in meteorites (outside
size range for biogenic magnetite).
 Chemically impure (substitutions).
 Often occur as rims on interplanetary dust
particles, dispersed through them.
 Trace amounts of Cr.
 Irregular morphology.
Chemically precipitated
magnetite (BIM)
HOWEVER…
THE DEBATE RAGES ON…
Using their own words against them…
 Buseck et al. (2001):
 Only a minority (~25%) of ALH84001 magnetite fits the
MAB.
 Friedmann et al. (2001) did no tests to be sure that they
were imaging magnetite!
 Biogenic magnetite is unlikely to survive geological
processes, even here on Earth.
Inorganic Processes and Magnetite
(Golden et al., 2001; 2004)
 Easy to precipitate carbonate globules similar to
those in ALH84001.
 Zoned carbonate precipitation under low T (150° C)
conditions.
 Chemically pure magnetite forms from brief heating to
470 ° C.
 Carbonate globules and magnetite could result from CO2
–rich hydrothermal activity.
 However, Jimenez-Lopez et al. (2008) and ThomasKeprta et al. (2009) found Ca, Mg and Mn in chemically
synthesized magnetites
Precipitated
carbonate globules
and ALH84001
globules are very
similar, from Golden
et al. (2001).
(a) experimentally
produced globules;
and (b) carbonate
globule in Martian
meteorite ALH84001
Further Discussion
 Thomas-Keprta et al. (2007): Experimental carbonate
precipitation doesn’t account for the complexity seen in
ALH84001.
 Fe oxides produced this way incorporate more Mg and Mn
than the magnetites in ALH84001 contain.
 Carbonates in ALH84001 show different zonation.
 Thomas-Keprta et al 2009, the vast majority of the
nanocrystal magnetites present in the carbonate
disks could not have formed by any of the currently
proposed thermal decomposition scenarios
 Conclusion: Carbonates and magnetites in ALH84001
not completely the result of inorganic processes.
Further Discussion
 Amor et al. 2015: Chemical signature of
magnetotactic bacteria
 In biomagnetite, most elements are at least
100 times less concentrated than in abiotic
magnetite
Name: ______________
Basic concept (22 points):
Multiple Choice: Circle the best answer for each question (2 points each)
1. The earliest evidence for life on Earth is:
a. Banded iron formations
b. Stromatolites
c. Oxygen in the atmosphere
d. Micro-fossils in meteorites
2. Which of the following is more widely accepted for the origin of life?
a. Panspermia
b. Surface origin hypothesis
c. Hydrothermal vents
d. None of the above
3. If you amend methanogenic sediment with nitrate, what will happen to H2
concentration?
a. Increase
b. Decrease
c. No change
d. Difficult to know, because it depends on environmental conditions
4. Is a Domain of life:
a. Bacteria
b. Archaea
c. Eukaryota
d. All of the above
5. Synthesizes proteins in the cell:
a. DNA
b. Proteins
c. Ribosomes
d. Cytoplasmic membrane
6. Enzymes:
a. Are proteins
b. Reduce activation energy of chemical reactions
c. A and B
d. None of the above
7. What is the biologically available form of nitrogen?
a. N2
b. NO
c. NH4
d. N2O
8. Mineral evolution refers to a change over time in:
a. The diversity of mineral species
b. The relative abundance of minerals
c. The compositional range of minerals
1
d. The grain sizes and shapes of minerals
e. All of the above
f. Oxidation state of minerals
9. A facultative aerobe is:
a. Grows better in the presence of O2
b. Grows worse in the absence of O2
c. Does not care about O2
d. Requires O2 but at levels lower than atmospheric O2
10. What happens to the surface area of smectite after biological reduction of structural
Fe(III)?
a. Increase
b. Decrease
c. No change
d. Unknown because it depends on environmental conditions.
11. An organism that grows optimally at a temperature of 15OC:
a. Hyperthermophile
b. Thermophile
c. Psychrophile
d. Mesophile
12. (8 points) Briefly describe how geological and microbial processes interact and give
an example of such interaction (hint: it’s a mutual interaction, e.g., bi-directional;
think about geological environment, limiting conditions and impact of life on the
geological process/environment).
13. (6 points) Organisms are classified by their carbon and energy source. Describe the
carbon (organic or inorganic carbon) and energy sources (needs) for
chemolithoautothrophs, photoautotrophs, and chemoheterotrophs.
14. (4 points) Why do microbes weather minerals?
2
15. (4 points) Give two mechanisms of how microbes weather minerals?
depth
16. (12 points) Sketch concentration profiles that would indicate the following microbial
metabolisms (include the relative changes in concentrations of O2, NO3-, Fe2+, SO42-,
CH4 and indicate where with depth these organisms would thrive): Aerobic
heterotrophy, iron reduction, sulfate reduction, nitrate reduction, aerobic
methanotrophy (methane oxidation), and methanogenesis.
Note: now that it’s electronic, you can use whatever you feel comfortable to do
this. You can use drawing tools in word, powerpoint, even draw the profiles by
hand on a piece of paper. Then you can take a picture and send it to me via
email.
Concentration
17. (7 points) Can a mineral be formed by both BCM and BIM? If so, how would you
determine its biogenic origin?
3
18. Refer to the following electron tower to answer this question:
a. (4 points) If you use structural
Fe(III) in smectite as the sole
electron acceptor and methanol,
acetate or lactate as 3 possible
electron donors and carbon sources
in a neutral pH growth medium.
Which one should be most
efficient (consider rate and extent)
in reducing the Fe(III) and why?
b. (3 points) If the oxidation product
of lactate, pyruvate, were able to
serve as an electron shuttle, would
your answer to part a) be still true?
c. (6 points) What are some consequences of microbial reduction of Fe(III) in smectite
on soil properties? How would a farmer mitigate these negative impacts?
19. (7 points) If there is life on Mars, do you necessarily expect to find magnetite
crystals in Martian meteorites that have the same characteristics as those produced
by magnetotactic bacteria on Earth? Why and why not? Be specific.
4
20. (5 points) Geomicrobiologists have cultured a great diversity of microorganisms in
various geological environments but they know that an even greater diversity exists,
especially in extreme environments, despite the fact that they have never seen these
organisms or grown them in the laboratory. How do they know greater diversity
exists in nature? What types of methods do they use to detect the diversity?
21. (12 points) A friend of yours in Spain sent you a picture (see SEM picture below)
and asked for your advice. She was studying rocks (volcanic tuff) from the K/T
(Cretaceous/Tertiary) boundary, and all of sudden she saw lots of microbe-like
objects in her rock (the rod-shaped objects near the center of the image). How
would you help her determine if these objects are really microbes? This task could
be very significant if microbes exist in such old rocks (the K/T boundary is about 66
million years ago when dinosaurs went extinct!). Remember: you are a
geomicrobiologist by training, so you look for both geological and
microbiological evidence. Come up as many reasons as you can. In other words,
give me your approach of how you would prove or disprove whether or not these
are indeed microbes.
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