Microbes and Earth Materials
• Microbes are any life form too small to be seen
with the naked eye
• Classification of life forms:
– Eukaryotic = Plants, animals, fungus, algae, and
even protozoa
– Prokaryotic = archaea and bacteria
• Living cells can:
–
–
–
–
Self-feed
Replicate (grow)
Differentiate (change in form/function)
Communicate
Tree of life
diatom
forams
• Archaea and Bacteria can vary in size
– Some are as large as 600 x 80 mm
– Most are on the order of a 0.5-2 mm
– Some are thought to be as small as 100 nm or
smaller (nanobacteria)
• Your hair is around 35 mm thick (35,000 nm)
• Archaea and bacteria come in many shapes
– Cocci
– Bacilli (rods)
– Many others – corkscrews, helices, spirals, stars,
squares, and more…
• Spores – analogous to seeds
Prokaryote Structure
Cell wall
Nuclear material
membrane
Membrane is critical part of how food and waste are transported
- Selectively permeable
Phospholipid layer
Transport proteins
Cell Nuclear Material
• Genetic information in the nucleoid – single DNA
molecule in a gel-like form, twisted and folded to fit
inside the cell.
• RNA around that – they do the work – both by carrying
messages and catalyzing reactions
• Why is DNA and RNA important in thinking about
microbes as an Earth material??
– Identify organisms in environments
– Use genetic information for info about what they eat and how
– Understand evolutionary relationships
Movement
• Flagella – spin
corkscrew motion
• Vesicles – gas
filled for buoyancy
Cell Metabolism
• Based on redox reactions
– Substrate (food) – electron is lost from this
(which is oxidized by this process)
– that electron goes through enzymes to harness
the energy for the production of ATP
– Electron eventually ends up going to another
molecule (which is reduced by this)
Nutrition value
• Eukaryotes (like us)
eat organics and
breathe oxygen
• Prokaryotes can use
other food sources
and acceptors
Redox gradients and life
• Microbes harness
the energy present
from
DISEQUILIBRIUM
• Manipulate flow of
electrons
C2HO
Other nutrients needed for life
• Besides chemicals for metabolic energy,
microbes need other things for growth.
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–
–
–
–
–
–
Carbon
Oxygen
Sulfur
Phosphorus
Nitrogen
Iron
Trace metals (including Mo, Cu, Ni, Cd, etc.)
• What limits growth??
Nutrient excess can result
in ‘blooms’
Diversity
• There are likely millions of different microbial
species
• Scientists have identified and characterized
~5,000 of these
• Typical soils contain hundreds- thousands of
different species
• Very extreme environments contain as little as
a few different microbes
Environmental limits on life
• Liquid H2O – life as we know it requires liquid
water
• Redox gradient – conditions which limit this?
• Range of conditions for prokaryotes much more
than that of eukaryotes – inactive stasis
• Spores can take a lot of abuse and last very long
times
• Tougher living = less diversity
• Closer to the limits of life – Fewer microbes able to
function
Microbial evolution
• Oldest fossil evidence - ~3.5 g.a (Stromatolites)
• Evidence for microbial activity argued for
deposits > 3.7 g.a.
• Couple fossil evidence with genomic
information (analysis of function from genetic
info)
• Put against backdrop of early earth conditions
– Significant atmospheric O2 after 2.0 g.a.
• Look at most ‘primitive’ microbes in selected
environments (similar to early earth)
Tree of life
Identifying microbes
• Morphological and functional – what they look
like and what they eat/breathe
– Based primarily on culturing – grow microbes on
specific media – trying to get ‘pure’ culture
• Genetic – Determine sequence of the DNA or
RNA – only need a part of this for good
identification
• Probes – Based on genetic info, design molecule
to stick to the DNA/RNA and be visible in a
microscope
Microbes & Minerals
• Direct precipitation/dissolution
– Metabolism results in the precipitation of minerals – excrete
something that reacts with other ions to form minerals
– Utilize solids as e-donors/acceptors, resulting in dissolution
• Indirect precipitation
– Changes in local environments – e.g. pH
– Microbes may induce mineralization by forming shells/testes
– Microbes may serve as templates for minerals to easily form
on them
Sulfate reducing bacteria
• Eat organics – things like acetate and
glucose
• ‘Breathe’ sulfate, exhale H2S
• H2S really likes metals – form sulfide
minerals:
– Pyrite (FeS2), Sphalerite (ZnS), Galena (PbS),
etc.
White biofilm picture
Iron Oxidizers
• Eat Fe2+, Breathe O2
• Fe3+ product likes O, OH
– forms oxyhydroxides
(FeOOH)
– Goethite,
Schwertmmanite,
‘Amorphous’ FeOOH
SEM of fluffy
sampling picture
Iron Reducers
• Eat Organics, ‘breathe’ Fe3+, yielding Fe2+
• Get Fe3+ from FeOOH minerals
• How to eat/breathe a solid millions of times your
size…
– Solubilize the material
– Iron reducers use organics called siderophores to
solubilize Fe3+ and bring it inside the cell
– Also use special organics as shuttles, which actually carry
the electron between the microbe and the solid.
Magnetotactic Bacteria
• Form magnetic minerals from as a result of Fe3+
reduction (commonly magnetite, Fe3+2Fe2+O4, and
greigite, Fe3+Fe2+S4) which are deposited inside
the cell and used as a compass or sensor to guide
the microbes’ position in an environment
Microbes & Direct Mineralization
• Through affecting metals, sulfur, and oxygen - a
number of minerals may be precipitated as a
result of microbial metabolisms
• Microbes may also affect minerals through
dissolution – which yields increased weathering
Sulfur oxidizing microorganisms
• Sulfur exists in
different forms of
varying redox state
• Microbes can use
many of them as
substrate, using
O2, NO3-, Fe3+ as
electron acceptors
C2HO
H2S oxidation
• Use H2S as e- donor
• H2S is very reactive towards proteins and
enzymes – rips them up – why it is toxic to
humans
• Microbes that eat this are more resistant to this,
but will still die if exposed to too much H2S
• Some of them oxidize the H2S to elemental
sulfur (S8) and store it in intracellular vacuoles
Copyright 1997 Microbial Diversity, Rolf Schauder
S8
Beggiatoa spp.
colony
Elemental Sulfur Oxidation
• Elemental Sulfur very hydrophobic
• Low pH environments – abiotic dissolution
very slow
• Several species of microbe can utilize S8 as a
substrate
Pyrite Oxidation
AMD neutralization
• Metals are soluble in low pH
solutions – can get 100’s of grams
of metal into a liter of very acidic
solution
• HOWEVER – eventually that
solution will get neutralized
(reaction with other rocks, CO2 in
the atmosphere, etc.) and the metals
are not so soluble  but oxidized S
(sulfate, SO42-) is very soluble
• A different kind of mineral is
formed!
Where is all the
2+
Fe
coming from?
• S in FeS2 goes to SO42-  14 electrons
• Can be oxidized by Fe3+  yielding Fe2+
• Microbes then eat Fe2+ (breathing O2)
Fe3+
Fe3+
Sx
FeS2
Fe2+
Fe2+
SO42-
• This is the principle reason
behind the problem of Acid
Mine Drainage
A drift Snottites
A Slump
Microbes & Petroleum
• Petroleum is a good substrate, but microbes
cannot live inside oil (need water to live)
• Inhabit the interface
SRB activity is important in
oil deposits – H2S degrades oil,
Makes it more expensive to clean
For cleaning up spilled organics,
microbial activity is stimulated
Microbes & Methane
• Microbes can both produce and destroy CH4
• Methanogens  Use CO2 as an electron
acceptor, reduces it to CH4 – commonly these
organisms use H2 as the e- donor
• Methanotrophs  Use CH4 as an e- donor,
coupled to O2 as the e- acceptor
Natural Attenuation
• Catch all term in dealing with organic
contaminants in the environment tantamount
to letting microbes consume the reduced
organics as food, coupled to oxidation of O2,
Fe3+, NO3-, SO42-, CO2
Mineral Templating
• Minerals are atoms arranged in a specific orientation
• Microbial surfaces have many different sites where
atoms may be ‘held’
• This can result in precipitation of different forms of
chemically identical minerals (polymorphs) or
completely different minerals than what would form
without the microbe
O
Si
Si
Si
O
Fe3+
OH-
filaments in
TEM
Redox gradients
C2HO
Profiles and microbial habitats
O2
3
2
depth
O2
Minerals
Expected?
H2S
Fe2+
4
H2S
1
Org. C
Concentration
Org. C
• Lake Champlain
– Phosphorus limited?
– Algal blooms
– What controls P??
• Cycling of iron minerals (FeS2 and FeOOH)
affects P concentrations dramatically
• SRB activity higher in summer
PO43-
PO43-
PO43PO43-
PO43-
Org C + SO42FeOOH
3-
PO4
H2S
PO43-
FeS2
PO43-