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Lecture 6Environmental microbiology and

Aqueous Geochemistry of Natural Waters

Please read these Manahan chapters:

Ch 5 (aquatic microbial biochemistry)

Ch 21 (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 energy by

breaking down those organic molecules

(heterotrophs)

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Energy

sources

Carbon

sources

Chemical Photochemical (light)

Organic matter Chemoheterotrophs

All fungi and protozoans,

most bacteria. Chemoheter-

otrophs 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 (Thio-

bacillus) for energy

Photoautotrophs

Algae, cyanobacteria ("blue-

green algae"), photosynthetic

bacteria that use light energy

to convert CO2 (HCO3-) to

biomass by photosynthesis

Microorganisms can also be classified based on

where they derive their energy and carbon:

Figure 6.2. (Manahan) Classification of microorganisms among chemoheterotrophs,

chemoautotrophs, photo- heterotrophs, and photoautotrophs.

Photosynthesis

Respiration

Carbon fixation (synthesize organic matter from inorganic carbon) w/o energy from sun light: use chemical energy not solar energy.

harvest solar energy, but can’t synthesize organic matter from inorganic carbon - rare.

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Photoautotrophs and PhotosynthesisAlgae are one important class of producer, Photoautotroph, aquaticmicroorganism that conduct photosynthesis.

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

Wikimedia Commons

GG4/625 wk 3 L6, S'18

[C]. We use a still better depiction: the Redfield equation

106CO2 +16NO3- + HPO4

2- + 122H2O +18H+

↕

C106H263O110N16P + 138O2

or (CH2O)106(NH3)16(H3PO4) + 138O2

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.

Green algae

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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 PO4

3-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)

GG4/625 wk 3 L6, S'18

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.

(Aquatic) Microbial Biochemistry

cyanobacteria (previously known as blue-green algae) are an ancient bacteria group that are photosynthetic prokaryotes.

www.ucmp.berkeley.edu/bacteria/cyanointro.html

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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.

Methanococcus janaschii www.ucmp.berkeley.edu/archaea/archaeamm.html

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).

There are two taxonomic types of Prokaryote in this

classification scheme:

Bacteria and Archaea (or Archaebacteria).

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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

• The sediment-water interface

• oxidized-reduced interface in soils, sediments, etc.

A microbial mat

www.personal.psu.edu/faculty/j/e/jeL6/biofilms/

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Another key aspect of bacteria & archaea are their small size:

0.5 µµµµm to several µµµµm.

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.

� No organisms have a greater effect on more environments

than microorganisms

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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.

a typical view of a marine microbial

community stained with SYBR Gold 2X

http://www.virusecology.org/

Marine bacteria, St. Petersburg, FL, USAhttp://gallery.usgs.gov/photos/06_14_2010_jn1Qht6GGb_06_14_2010_0

Fecal coliform bacteria from a

polluted stream.

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GG4/625 wk 3 L6, S'18From Manahan, “Environmental Chemistry”

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.

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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.

Temperature, substrate concentration, and variables like pH also control bacterial growth and activity rates.

From Manahan, “Environmental Chemistry”

The effects of substrate concentration, temperature

and pH on bacterial metabolism are shown below.

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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 (Linnaean Phylogeny)

16S rRNA using genetic differences (molecular phylogeny)

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“Microorganisms” emphasized in the lecture are

highlighted in red.

Figure from Nealson, Ann. Rev Earth Planet. Sci.

“5 kingdoms” approach 16S rRNAuses genetic differences

“Stick” length reflects extent of

difference in genetic make-up

Uses size, structure and behavior

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GG4/625 wk 3 L6, S'18Figure from Nealson, Ann. Rev Earth Planet. Sci.

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

GG4/625 wk 3 L6, S'18

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 Domainswww.ucmp.berkeley.edu/exhibits/historyoflife.php

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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.

Bacterial metabolism

GG4/625 wk 3 L6, S'18

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

Raw

materials

Complex

bio

molecules

anabolism

catabolism

http://www.bact.wisc.edu/

Usable energy

ATP cycle

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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.

http://www.mines.edu/fs_home/jhoran/ch126/index.htm

30,000X magnificationBut 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)

GG4/625 wk 3 L6, S'18

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

GG4/625 wk 3 L6, S'18

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/MineWasteGeochemistry/AcidMineDrainage.html

see also a related site for a great description of

Cr(VI) remediation:

http://www.science.uwaterloo.ca/research/ggr/PermeableReactiveBarriers/Cr-TCE_Treatment/Cr-TCE_Treatment.html

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http://www.mines.edu/fs_home/jhoran/ch126/amd.htm

“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?

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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. releasinginorganic 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 sub-reservoirs 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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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.

Microbes and Elemental Cycling

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N +5 in NO3- is the form of N

that is easiest for plants to

absorb from the

environment.

Microbes and Elemental Cycling

Most biomolecules are based on Nitrogen Nitrogen in the

-3 oxidation state (e.g., amines and amino acids).

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.

http://www.chem.cmu.edu/groups/achim/research/magneto.html

MoFe protein-Fe

protein complex

from involved in

nitrogen

conversion to

ammonia.

Redox!

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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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Nodules formed where Rhizobium bacteria infected soybean roots.

http://soils.usda.gov/sqi/concepts/soil_biology/bacteria.html

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.

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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hydrosphere

geosphere

Anthrosphere

biosphere

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.

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Fungal Microorganism and Phosphorous Cycling

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).http://helios.bto.ed.ac.uk/bto/microbes/mycorrh.htm

Root hairs

Vesicles

arbuscules

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.