Download Lecture 6 Environmental microbiology and Aqueous Geochemistry

Lecture 6
Environmental microbiology and
Aqueous Geochemistry of Natural
Waters
Please read these Manahan chapters:
Ch 6 (aquatic microbial biochemistry)
Ch 22 (environmental biochemistry)
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(Aquatic) Microbial Biochemistry
Almost all geochemical processes that occur within the
exogenic cycle are influenced by biological activity
Some examples include:
production/
consumption of organic
matter
oxidation-reduction
dissolution/ precipitation
of inorganic materials.
Many polluted/contaminated environments are also rife with
microbial life and associated chemical transformations.
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All organisms can be classified as either
producers - those that utilize light or other
energy sources to create complex organic
molecules (autotrophs)
or
reducers - those that re-extract that energy by
breaking down those organic molecules
(heterotrophs)
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Microorganisms can also be classified based on
where they derive their energy and carbon: Respiration
Energy
sources
Chemical
Photochemical (light)
producers
reducers
Carbon
sources
Organic matter
Chemoheterotrophs
All fungi and protozoans,
most bacteria. Chemoheterotrophs use organic sources
for both energy and carbon.
Photoheterotrophs
A few specialized bacteria that
use photoenergy, but are
dependent on organic matter for
a carbon source
Inorganic carbon
(CO2, HCO3-)
Chemoautotrophs
Use CO2, for biomass and
oxidize substances such as
H2 (Pseudomonas), NH4+,
(Nitrosomonas), S (Thiobacillus) for energy
Photoautotrophs
Algae, cyanobacteria ("bluegreen algae"), photosynthetic
bacteria that use light energy
to convert CO2 (HCO3-) to
biomass by photosynthesis
harvest solar
energy, but
can’t
synthesize
organic
matter from
inorganic
carbon - rare.
Figure 6.2. (Manahan) Classification of microorganisms among chemoheterotrophs,
chemoautotrophs, photo- heterotrophs, and photoautotrophs.
Carbon fixation (synthesize organic matter from
inorganic carbon) w/o energy from sun light: use
chemical energy not solar energy.
Photosynthesis
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Photoautotrophs and Photosynthesis
Algae are one important class of microorganism that conduct photosynthesis.
☼
Algae are producers and Photoautotrophs
☼
Photosynthesis can be crudely abbreviated as
[A]. nCO2 + nH2O ↔ [CH2O]n + nO2
where [CH2O]n is generic carbohydrate.
photosynthetic production of organic matter actually requires
other nutrients, particularly N and P.
Our text gives a somewhat more accurate equation for
photosynthesis by aquatic organisms: the Fogg formula
[B]. 5.7CO2 + 3.4H2O +NH3 ↔ C5.7H9.8O2.3N + 6.25O2
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[C]. We use a still better depiction: the Redfield reaction
106CO2 +16NO3- + HPO42- + 122H2O +18H+
↕
C106H263O110N16P + 138O2
or (CH2O)106(NH3)16(H3PO4) + 138O2
Green algae
The Redfield ratio C:O:N:P=106:110:16:1 is an important relationship to
remember. The Redfield Ratio is a mean value for aquatic autotrophs that
holds to within a percent for marine phytoplankton and maybe a few
percent for most freshwater organisms.
In all three versions of the photosynthesis reaction,
Respiration is the reverse reaction.
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notice important stoichiometric relationships N and P "move" in these ratios in much of the hydrosphere
∆O2 (+)/∆CO2 (-) = 138/106 = 1.3
∆N (+)/∆P (+) = 16/1 = 16
∆CO2 (+)/∆N (+) = 106/16 = 6.6
∆CO2 (+)/∆P (+) = 106/1 =106
∆O2(+)/∆N(-) = 138/16 = 8.6 & ∆O2(+)/∆P(-) = 138/1 = 138
also... Photosynthesis consumes hydrogen ions. Respiration
liberates hydrogen ions
∆N (+)/∆H+ (+) = 16/18 = 0.9 (about equal)
∆CO2 (+)/∆H+ (+) = 106/18 = 5.9
Notice the signs of all of these changes.
e.g., as O2 diminishes, CO2, NO3- and PO43-all increase. This is
occurs at excess respiration over photosynthesis.
The opposite is true during photosynthesis
("free" N, P and C are consumed and O2 is liberated)
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(Aquatic) Microbial Biochemistry
Your book divides microorganisms into 2 categories
Eukaryotes: (having well-defined cell nuclei enclosed in a
membrane). These include Plants, Fungi, Animals, etc.
Only some eukaryotes are microorganisms
Prokaryotes: (lacking in nuclei and having genetic material more
dispersed through out the cell). These include "True bacteria" and
possibly precursor organisms to cellular organelles such as
mitochondria or chloroplasts.
All prokaryotes are microorganisms.
cyanobacteria (previously known as bluegreen algae) are an ancient bacteria group
that are photosynthetic prokaryotes.
www.ucmp.berkeley.edu/bacteria/cyanointro.html
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There are two taxonomic types of Prokaryote in this
classification scheme:
Bacteria and Archaea (or Archaebacteria).
Archaea were first discovered in the 1970s.
Archaea exist in some of the most extreme environments on
Earth (high temperature, low temperature, high pressure, etc..), as
well as more “normal” settings.
Together with some bacterial groups, they are likely candidates
organisms for extra-terrestrial environments.
Archaea include very ancient types of
organisms that are "tuned" to survive in special
environments; some are chemosynthetic; i.e.,
producers that use chemical energy sources to
synthesize biomolecules (e.g., Methanogens,
Halophiles, Sulfolobus, and their relatives).
Methanococcus janaschii www.ucmp.berkeley.edu/archaea/archaeamm.html
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Microorganisms are widely dispersed in the
environment.
Many exploit specific ecological niches at chemical or
physical interfaces where food sources tend to
accumulate.
For example:
• The air-sea interface
• Biofilms coating rocks or water
A microbial mat
www.personal.psu.edu/faculty/j/e/jeL6/biofilms/
• The sediment-water interface
• oxidized-reduced interface in soils, sediments, etc.
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No organisms have a greater effect on more environments
than microorganisms
Another key aspect of bacteria & archaea are their small size:
0.5 µm to several µm.
This size and their broad ranges of shapes gives bacteria
surface area to volume ratios that are 100 - 1000 times
larger than eukaryotic cells.
This means that a relatively small bacterial biomass can have
a very large impact on natural waters, compared to a similar
mass of Eukaryotic cells.
Lifestyles of the small and not so famous
bacteria are small and widely dispersed in the environment.
Bacteria have relatively simple life cycles, which may last only
hours to years.
Nevertheless, bacteria can effect very rapid chemical
transformations in aquatic environments.
Fecal coliform bacteria from a
polluted stream.
a typical view of a marine microbial
community stained with SYBR Gold 2X
http://www.virusecology.org/
Marine bacteria, St. Petersburg, FL, USA
http://gallery.usgs.gov/photos/06_14_2010_jn1Qht6GGb_06_14_2010_0
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Bacterial population dynamics
After "getting used to" a new environment (the lag phase),
growth progresses in exponential fashion (the log phase).
Exponential growth continues until some resource (space,
food, etc..) is used up or some other byproduct of metabolism
accumulates to toxic concentration (stationary phase).
The death phase begins some time after this.
From Manahan, “Environmental Chemistry”
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Temperature, substrate concentration, and variables like pH
also control bacterial growth and activity rates.
The effects of substrate concentration, temperature
and pH on bacterial metabolism are shown below.
Many bacteria are adapted
to live and flourish in semi
restricted ranges of pH and
temperature.
Bacterial metabolism rates
are measured by enzymatic
activity, the enzyme being
used in some way to
catalyze a reaction that
occurs during growth.
Under favorable conditions
bacterial growth can be
extremely rapid.
From Manahan, “Environmental Chemistry”
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Classification of microorganism types
2 approaches to the “tree of life” classification of organisms:
the traditional “5 kingdoms” approach using
physiological differences
16S rRNA using genetic differences
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“5 kingdoms” approach
Uses size, structure and behavior
16S rRNA
uses genetic differences
“Stick” length reflects extent of
difference in genetic make-up
“Microorganisms” emphasized in the lecture are
highlighted in red.
Figure from Nealson, Ann. Rev Earth Planet. Sci.
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Physical differences amongst
eukaryotes, e.g., animals,
are much greater than
amongst the procaryotes,
leading to the large animal
branch and the small
procharea branches in the
classical phylogeny
Figure from Nealson, Ann. Rev Earth Planet. Sci.
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Metabolic differences:
big rRNA differences between bacteria
(compared to for instance all animals),
largely reflects the wide range of
bacterial (and archaeal) metabolisms vs.
the limited variation in animals.
The current view of Life’s Major Domains
www.ucmp.berkeley.edu/exhibits/historyoflife.php
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Bacterial metabolism
Heterotrophic metabolism
is based on the oxidation of organic chemicals, such as
sugars, proteins, etc.., to yield ATP and simpler organic
compounds.
These chemicals are in turn used by bacterial cells for
biosynthethesis or for transformative and assimilatory
reactions.
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Bacterial metabolism – 2 related activities
Bacterial anabolism:
the physiological and biochemical activities for
acquisition, synthesis, and organization of the chemical
constituents of a bacterial cell.
Bacterial catabolism:
the biochemical activities for the net breakdown of
complex substances to simpler substances by living
cells.
Substances with a high energy level are converted to
substances of low energy content, and the organism
utilizes a portion of the released energy for cellular
processes.
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Bacterial metabolism
anabolism
Raw
materials
Complex
bio
molecules
http://www.bact.wisc.edu/
ATP
cycle
catabolism
Usable energy
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Bacteria and Archaea
As mentioned earlier, these prokaryotes include both
heterotrophs and autotrophs.
Together, these microscopic organisms are responsible for
many of the important transformations of organic and
inorganic matter in the environment, such as oxidation and
reduction processes in aquatic environments.
Recall from last time
Aerobic Respiration
Recall, respiring organisms utilize O2 H2O to oxidize organic matter.
Anaerobic Respiration
Once O2 is used up, various bacteria continue to oxidize available organic
matter to derive energy for their metabolism, leading to the redox-ladder.
They play a vital role in poising pE and thus governing the
geochemistry of many metals in the hydrosphere.
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“Redox Ladder” transformations of Fe by Chemoautotrophs
in polluted Environments: Examples from acid mine drainage
Ground or surface waters issuing from metal ore mines are often acidic because of
the oxidation of pyrite associated with the ore body.
4FeS2(s) + 14O2(g) + 4H2O(l) → 4Fe2+(aq) + 8SO42-(aq) + 8H+(aq)
Abiotic pyrite oxidation to produce ferric ions and hydrogen ions is slow.
30,000X magnification
But Thiobacillus ferrooxidans (left)
catalyzes the oxidation of FeS2,
producing ferric ions and hydrogen ions.
It is responsible for iron and inorganic
sulfur oxidation of in mine tailings and
coal deposits where these compounds
are abundant.
Subsequent Fe2+ oxidation by
organisms like Gallionella produces Fe3+
in these environments (next 2 slides)
http://www.mines.edu/fs_home/jhoran/ch126/index.htm
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Gallionella is a microbe that catalyzes Fe oxidation to get energy.
4Fe2+ (aq) + O2 (g) + 4H+ (aq) → 4Fe3+(aq) + 2H2O(l)
http://www.buckman.com/eng/micro101/2266.htm
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This organism probably produces Fe-hydroxide strands as a means of
eliminating waste Fe(III)
4Fe3+(aq) + 12 H2O(l) →
4Fe(OH)3(s) + 12H+(aq)
http://www.buckman.com/eng/micro101/2266.htm
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Fe(OH)3 precipitates cause a
rusty color in acid mine drainage
waters. Low pH makes these
waters quite corrosive in the
environment, an attribute that
remediation needs to eliminate.
http://www.science.uwaterloo.ca/research/ggr/MineWasteGeochemi
stry/AcidMineDrainage.html
see also a related site for a great description of
Cr(VI) remediation:
http://www.science.uwaterloo.ca/research/ggr/PermeableReactiveBa
rriers/Cr-TCE_Treatment/Cr-TCE_Treatment.html
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“Artificial wetland” as
passive treatment of
acid mine drainage.
Abundant plant organic
matter provides reducing
capacity required to drive
waters anoxic, allowing
microbial sulfate reduction
to kick-in. What are the
beneficial consequences
of this?
http://www.mines.edu/fs_home/jhoran/ch126/amd.htm
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Microbes and Material Transformation
in Exogenic Cycles and Ecosystems
Microbes play numerous important
roles in chemical transformations in
Earth’s surface reservoirs.
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Microbes are responsible for:
a. “fixation” of the
nutrient element
N to biologically
usable forms …
b. regeneration of
nutrient elements
from decaying
organic matter
(cycling nutrients
through an
ecosystem
multiple times)
c. releasing
inorganic
nutrients from
minerals.
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Microbes and organic matter cycling
Microbes play an
essential role in the
cycling of organic
matter in various subreservoirs of a healthy
ecosystem via the
reaction types we
have just discussed
(and many others)
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Microbes and Elemental Cycling
The nitrogen cycle stands out as being particular
dependent upon microbial activity because of the wide
number of oxidation states and forms of Nitrogen, whose
transformations are microbialy-mediated.
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Microbes and Elemental Cycling
Nitrogen is very important in metabolic pathways and is an
abundant element in Earth's exogenic environment (e.g., it is
the most abundant element in the atmosphere).
But... the most common form of nitrogen (N2) is not utilizable
by most organisms. For instance, we breath N2 in and out
thousands of time each day without changing it.
It is largely through the action of microorganism that "fix" N2
molecules to either oxidized or reduced forms, that N is made
usable to the rest of the biosphere for biomolecule synthesis.
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Microbes and Elemental Cycling
Most biomolecules are based on Nitrogen Nitrogen in the
-3 oxidation state (e.g., amines and amino acids).
N +5 in NO3- is the form of N
that is easiest for plants to
absorb from the
environment.
Oxidized forms
such as this can
be absorbed by
organisms but
must then be
enzymatically
reduced to N -3 be
used in OM
synthesis.
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Biological nitrogen fixation
The primary Nitrogen fixation mechanism is by reduction to
ammonia via the enzyme nitrogenase, which contains
Fe – S - Mo cluster complexes as electron transfer centers.
Redox!
MoFe protein-Fe
protein complex
from involved in
nitrogen
conversion to
ammonia.
http://www.chem.cmu.edu/groups/achim/research/magneto.html
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Biological nitrogen fixation
Energy Intensive:
It takes a great deal of energy to break the N≡N triple bond in N2.
Energy Source:
Microbial nitrogen reduction (“fixation”) by nitrogenase uses
energy from soil organic matter or from sunlight stored in ATP.
When microbes have a symbiotic relationship with a the host
plant the plant often provides the energy source as fixed OM.
Locally Reducing Conditions:
Nitrogenase is very sensitive to oxygen, therefore the organism
or its host adopts strategies to exclude oxygen from the sites of
nitrogenase activity.
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Biological nitrogen fixation
N2 is converted into plant-utilizable oxidation states by a few
genera of microorganisms, providing an important source of
this nutrient to natural and agricultural ecosystems.
Nitrogen fixing bacteria take two main forms:
•free-Iiving in soil
•symbiosis with plants.
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Nitrogen-fixing
bacteria form
symbiotic
associations with
the roots of legumes
(e.g., clover and
lupine) and trees
(e.g., alder and
locust).
Visible nodules are
created where
bacteria infect a
growing root hair.
Nodules formed where Rhizobium bacteria infected soybean roots.
http://soils.usda.gov/sqi/concepts/soil_biology/bacteria.html
The plant supplies simple carbon compounds to the bacteria, and the
bacteria convert N2 into a form the plant host can use. When leaves or
roots from the host plant decompose, soil nitrogen increases in the
surrounding area.
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Phosphorous cycling is less dependent on microbial
transformations that convert oxidation state, but microorganisms
in soil and water do control transformations between organic and
inorganic forms.
hydrosphere
Anthrosphere
biosphere
geosphere
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Fungal Microorganism and Phosphorous Cycling
Arbuscular mycorrhizas are an important type of fungus found
on the vast majority of wild and crop plants, with an important
role in mineral nutrient uptake (especially Phosphorous) and
sometimes in protecting against drought or pathogenic attack.
The fungus obtains sugars from the plant, and the plant obtains
mineral nutrients that the fungus absorbs from the soil.
arbuscules
Root hairs
Vesicles
http://helios.bto.ed.ac.uk/bto/microbes/mycorrh.htm
Part of a clover root infected by an
AM fungus. The site of penetration
is shown at top right, where the
fungus produced a pre-penetration
swelling, (then it grew between the
root cells and formed finely
branched arbuscules (thought to be
sites of nutrient exchange) and
swollen vesicles (thought to be used
for storage).
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