1 Microbial conversion of inorganic substances (Bio-Geo-Chemical Cycles) Anaerobic respirations of...
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Transcript of 1 Microbial conversion of inorganic substances (Bio-Geo-Chemical Cycles) Anaerobic respirations of...
1
Microbial conversion of inorganic substances (Bio-Geo-Chemical Cycles)
Anaerobic respirations of inorganic electron acceptors
Aerobic oxidation of the endproducts of anaerobic
respirations
Cycles (C, N, S, Fe)
Industrially and environmentally relevant reactions
2
How Can Life without Oxygen Work?
O2 = principal electron acceptor of aerobic life.
Without O2 a different electron acceptor needs to be found.
Bacteria are the only life forms capable of using electron
acceptors other than O2 (anaerobic respiration).
The use of alternative electron acceptors dramatically
changes the chemistry of the environment – usually to the
worse.
3
What are the Typical Electron Accepting Reactions?
O2 + 4e- H2O (aerobic respiration)
SO42- + 8e- H2S (sulfate reducing bacteria)
Fe3+ + 1e- Fe2+ (iron reducing bacteria)
S + 2e- H2S (sulfur reducing bacteria)
NO3- + 5e- N2 (denitrifying bacteria)
NO3- + 8e- NH3 (nitrate ammonification)
CO2 + 8e- CH4 (methane producing bacteria)
4
What Happens with the Electron Acceptors after Accepting Electrons?
By accepting electrons, the acceptors they turn into
reduced species.
Reduced species are reducing agents that dramatically
change the chemistry of the environment
If in contact with O2 , reduced species can become electron
donors for specialised lithotrophic bacteria
The continued cycle of electron acceptors to reduced
species and back to electron acceptors is a typical part of
biogeochemical cycling.
The S, N, Fe cycle are typical examples.
5
Classification of Microbial Metabolic Types
Energy source Photo Chemo
Electrondonor
Organo Litho
C-source Hetero Auto
Examples:
Algae: Photo-Litho-Autotroph,
Bacteria, Fish: Chemo-organo-heterotroph
Thiobacillus: Chemo-litho-autotroph
Photosynthetic bacteria: Photo-Organo-heterotroph
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Life without O2: Alternative Electron Acceptors 1
Electron Acceptors Measure for Energy Released with H2 as Electron Donor (log K)
O2 H2O 21 NO3
- N2 21
NO3- NH4- 15
Fe3+ Fe2+ 8
SO42- H2S 5
So H2S 3
CO2 CH4 2
CO2 Acetate ?
HumOx HumRed ? adapted from Stumm & Morgan
Observation: There is a sequence of use of electron acceptors which is according to the energetic usefulness (redox potential) O2 , nitrate, humic acids, ferric iron, sulfate, CO2
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Electron Acceptors are Reduced and can become e- Donors
Electron Donors Electron Acceptors
organic O2 H2O
H2S So NO3- N2
So SO42- NO3- NH4
+
Fe2+ Fe3+ Fe3+ Fe2+
NO2- NO3- SO42- H2S
H2 H+ So H2S
CO CO2 CO2 Acetate
NH4 NO2- CO2 CH4
HumR HumOx HumOx HumR
8
Interconnection Between Different Electron Donors and Acceptors
Electron Donors
H2 H+
CH4 CO2
H2S So
So SO42-
Fe2+ Fe3+
NO2- NO3-
Electron Acceptors
CO2 CH4
So H2S
SO42- H2S
Fe3+ Fe2+
NO3- NH4
NO3- N2
O2 H2O
9
Competition for Electron Donor by Different Acceptor Systems
General observations with anaerobic respirations:
Threshold level for minimum degradable substrate concentrations decreases with the redox potential of the electron acceptor
CO2 CH4
SO4 2- H2S
NO3- NH4+
H2
Time
Using H2 as a model substrate(accounting for about 30 % of energy flow in anoxic environments):
Organisms with more “powerful” electron acceptor out-compete others by keeping the H2 concentration below “detection limit” of competitors.
This explains the apparent preference for using best electron acceptors (most positive redox potential) first.
10
Sulfate Reduction (SRB)
Sulfate is a suitable and abundant alternative electron acceptor
Typical reactions:4 H2 + SO4
2- + H+ HS- + 4 H2O
CH3-COO- + SO42- HS- + 2 HCO3-
Organisms: Sulfate Reducing Bacteria (SRB), strictly anaerobes, Desulfovibrio, Desulfobacter, etc.
Electron donors: small molecules (breakdown products from fermentations, or geologically formed, e.g. H2, acetate, organic acids, alcohols)
Reduce also elemental sulfur, sulfite and thiosulfate to H2S
Ubiquitous
11
Bacterial Sulfate Reduction When Does it Occur ?
In the presence of organic substances , after depletion of oxygen nitrate
and ferric iron sulfate reduction is next
Initially in sediments, Rates from 0.01 to 10 mM/day
Typically in sediments but also on surfaces (ships) underneath biofilms
Within flocs or intestines of marine animals
Sulfide reacts chemically as a reducing agent (e.g. with O2 or Fe3+)
elemental sulfur formation
Formation of FeS and FeS2 black color of sediment
In typical reduced sediments (e.g. mangroves, estuaries SR may be
higher than O2 use)
Thiosulfate disproportionation (SO32-) into sulfate and sulfide
12
Dissimilatory Sulfate Reduction by SRB
Organisms: Sulfate Reducing Bacteria (SRB), strictly anaerobe
Desulfovibrio, Desulfobacter, etc.
Use of small compounds (H2, acetate, other organic acids alcohols but
not polymers, proteins, carbohydrates, fats)
Cooperation with fermentative bacteria needed to degrade detritus
End product sulfide (H2S HS- + H+) is toxic, reactive, explosive
Typical reactions:
4 H2 + SO42- + H+ HS- + 4 H2O
CH3-COO- + SO42- HS- + 2 HCO3-
Reduce also elemental sulfur, sulfite and thiosulfate to H2S
13
SRB Significance in Marine Environments
Ecologically:
playing a major role in sulfur cycle and sediment activities
sulfide = O2 scavenger “negative oxygen concentration”
responsible for sulfur deposits (H2S + O2 S + H2O)
P-release from sediments
Economically:
End product H2S: poisonous, explosive, corrosive, malodorous
Corrosion of submersed steel structures (e.g. platforms, bridges)
Corrosion of oil pipelines (inside and outside)
Lethal gas emissions on offshore platforms
Petroleum degradation (burning sour gas: H2S + O2 SO2)
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S-ox:
Volcanic Sulfur SpringsE.g. New ZealandYelllowstone National Park
15
SRB Morphology
Typical shape of sulfate reducing bacteria (SRB) of the type Desulfovibrio.
16
SRB Role in Corrosion of Steel
Electrons on the steel surface produce stabilising H2 layerbacteria use H2 as the electron donor for sulfate reductionthis removes electrons and leaves the iron positively chargedThe positive charge favours the release of Fe2+ into solutionOngoing process causes corroding electron flow and weight lossBacteria feed on electricityCathodic protection
H2
e-
H+
SO42-
HS-
Fe2+
FeS
Steel Corrosion current
SRB
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SRB Damage to Pipeline
Microbially influenced corrosion of marine oil pipeline showing typical pitting corrosion.
18
“SRB in Petroleum Industry” Research at Murdoch
Q: Where do SRB in oil pipelines come from?A: Mostly as a biofilm attached inside the pipes. Method SRB monitoring during pig runs.
Q: Are SRB supported by corrosion ?A: SRB can grow on corroding iron. Cathodic protection enhances their growth.
Q: Are treatments effective against SRB?A: SRB can degrade organic biocides.
19
Dissimilatory Nitrate Reducing Bacteria
Dentrification (nitrate to N2) typically involves the aerobic bacteria
Organic electron donor + NO3- N2
Bacteria use complex substrates
Further details in lecture on N-cycle
In sediments nitrate ammonification can play important role
Organic electron donor + NO3- NH3
Nitrate ammonification is due to anaerobic bacteria (e.g. SRB)
20
Dissimilatory Iron Reducing Bacteria
Organisms: Various anaerobic bacteria, no specific group
e.g. Geobacter
e- donors: mainly small compounds
Typical reaction:
H2 + 2 Fe3+ 2 Fe2+ + 2 H+
Reaction results in lowering of redox potential
Reduce also Manganese, elemental sulfur and other metals (e.g. uranium)
End product is magnetite (Fe3O4) and other compounds (black precipitates)
Significance of iron reduction is still being underestimated
Recent research: electricity production using ferric iron reducing bacteria
21
CO2 or HCO3- Reduction(Methane Producing Bacteria)
CO2 is even more abundant than sulfate but difficult to use
By Methane Producing Bacteria (Archeae)
Strictly anaerobic requiring a redox potential of less than -350mV
Highly oxygen sensitive:
4 H2 + HCO3- + H+ CH4 + 3 H2O
Very limited substrate spectrum (H2, acetate, methanol)
Syntrophic associations are formed with fermenting bacteria
Because of poor solubility (bubble formation) some methane from
sediments escapes into atmosphere (greenhouse gas) True
removal of BOD from water.
22
Aerobic Re-oxidation Processes 1 - Sulfide and Fe2+
Contact of reduced (black sediments) with O2 :
bacterial oxidation of sulfide and Fe2+ occurs.
Beggiatoa: 2 H2S + O2 2 S0 + H2O (white algae)
Thiobacillus: H2S + 2 O2 H2SO4 (sulfuric acid)
very low local pH values of <1.
Further microbial pipeline corrosion.
Also insoluble species are re-oxidized e.g. pyrite (FeS2)
bio-leaching of minerals).
Elemental sulfur is often produced as intermediate
(white precipitate (“white smoker”, “white algae”)
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NH4+ oxidation is energetically difficult and slow and
requires oxygen as electron acceptor.
Organisms: Nitrosomonas, Nitrobacter, two step process.
NH4 uptake also possible by assimilation of phytoplankton.
Aerobic Re-oxidation Processes 2 - Ammonia
24
Fate of Sulfide in the Presence of Oxygen
Contact of reduced sulfide (H2S or FeS) with air spontaneous oxidation (H2S) to insoluble S
Microbial Oxidation:
(a) Beggiatoa: 2 H2S + O2 2 So + H2O (“white algae”)
(b) Thiobacillus: H2S + 2 O2 H2SO4 (sulfuric acid)
very low local pH values of <1. Further microbial pipeline corrosion.
Also insoluble species are re-oxidized e.g. pyrite (FeS2) (bio-leaching of minerals).
Elemental sulfur is often produced as intermediate (white precipitate (“white smoker”, “white algae”)
Together, sulfate reduction and sulfide oxidation can close the sulfur cycle.
25
O2
HS-
Microbial S conversion
Highest chemical and biological activity at the interface (presence of electron donors and acceptors)
NO3-
NH4+
H2 , CH4
high Eh
Low Eh
Fe3+
Fe 2+
Concentration
Depth
Sulfate
Sulfide
Brown
Black
Depth Profile of Aerobic Anaerobic Interface
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Scheme of Ocean Hydrothermal Ventfrom Ocean Ridges
www.jamstec.go.jp/jamstec-e/ bio/subext/thergane.html
Extreme Life Conditions:Anaerobic, hydrogen drivenStrong temperature gradientsHigh pressureOrigin of life is thought to have been thermophilic, with H2 and So from volcanic
sources as e-donor and acceptor.
27
Sulfur Cycle at Hydrothermal Vents
SO42-
H2S
Biological oxidation
H2S + O2 S, SO4
2-
Geochemical Reduction
Similar principle in sewer pipes
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“Black Smokers” releasing reduced sufur and iron (e.g. FeS) as potential electron donors for bacteria.
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White “snowblower” producing suspended sulfur bacteria in snow flake type aggregates during a volcanic eruption
Woods Hole Oceanographic Institute East Pacific Rise.
•S oxidising Bacteria as primary producers
30
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
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Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
Dark food-chainIndependent of Sunlight ?
32
Deep-sea mussel Bathymodiolus thermophilus using symbiotic sulfur bacteria.
Photo by Richard A. LutzPhoto by Richard A. Lutz
33
Galatheid crabs lining a fissure at a hot vent on the East Pacific Rise feeding on sulfur bacteria.Courtesy Woods Hole Oceanographic Institution
34
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
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Anaerobic Oxidation of Sulfide
There are principally two conditions allowing sulfur cycle in the absence of oxygen:
1. Presence of light and phototrophic bacteria:Very colorful, play a role in microbial matsCan use light that is not suitable for algaeGreen sulfur bacteria (S outside, Chlorobium)Purple sulfur bacteria (S inside, Chromatium)
2. Presence of other “powerful e-acceptors (e.g. nitrate, Fe3+) are available
Thiomargareta a recent discovery
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Thiomargareta namibiensis
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Thiomargareta namibiensis
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CH4 is a highly energetic e-donor (fuel) in aerobic areas
With electron acceptors O2, Nitrate, Fe3+ methane canbe re-oxidized by methylotrophic bacteria
Recently evidence has been found of CH4 oxidation linked to sulfate reduction.
Those electron acceptors are usually made available by bioturbation,thus CH4 usually does not reach the water column
Where benthic macrofauna has been killed methane productionforms large CH4 bubbles that can escape the water column (does not occur in the open ocean)
Under pressure, methane forms hydrates on the ocean floor around continental shelfes. These hydrates can be used as electron donors for aerobic bacteria food chain.
Aerobic Re-oxidation Processes 2 - Methane
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Gas Hydrate Molecules (dusk.geo.orst.edu/ oceans/lec14.html)
40
Methane hydrate mount under flashlight
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Methane hydrate outcrop from continental shelfMethane hydrate outcrop from continental shelf.. approximately 250 miles east of Charleston, S.Capproximately 250 miles east of Charleston, S.C
courtesy Carolin Ruppelcourtesy Carolin Ruppel
42
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate
Methane hydrate outcrop
Tube worms
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Methane hydrate sample
44
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate
Tubeworm collected from gas hydrate seepage areas
45
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
Spider crab looking for food between the tubeworms growing on a methane hydrate outcrop
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Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate
Mussels with bacterial slime living on methane hydrate
47
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate”
48
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate“Iceworm” living on gas hydrate by
ustilising methylotophic
bacteria
NOAA: The Deep East Expedition – Blake Ridge
Photos from NOAA Alvin dive Sept. 23-28,2001National Oceanic and Atmospheric
Administration
49
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate
Methane hydratewith ice worms
50
Tubeworms (Riftia) living in association with sulfur oxidising bacteria
Micheal Degruy
“Chemosynthetic mussel from methane hydrate
51
Gas Hydrate at the Surface
Under Atmospheric Conditions: gas hydrate separates into flammable CH4 and water
(here cooling hands)
52
Example Locations of Gas Hydrate
53
54
Methane Hydrate (Summary)
Methane hydrate, a curiosity or a significant global phenomenon?
Needed for formation: low temperature and high pressure
Why are hydrates mainly on the continental shelfes ?
Deep oceans lack organic material High biologic productivity (CH4) Rapid sedimentation rates (bury the organic
matter)
55
Aspects of microbial sulfide oxidation
Sulfide oxidation Needed for formation: low temperature and
high pressure Why are hydrates mainly on the continental
shelfes ? Deep oceans lack organic material High biologic productivity (CH4) Rapid sedimentation rates (bury the organic
matter)
56
Summary
• Anaerobic reduction processes and aerobic oxidation processes are increasingly found to go hand in hand.
O2
Sulfate
E-donor
H2S
57
Summary
• Anaerobic reduction processes and aerobic oxidation processes are increasingly found to go hand in hand.
O2
Fe3+
E-donor
Fe2+
58
Summary
• Anaerobic reduction processes and aerobic oxidation processes are increasingly found to go hand in hand.
O2
CO2
H2
CH4
59
Summary
• Anaerobic reduction processes and aerobic oxidation processes are increasingly found to go hand in hand.
O2
NO3-
Organics
NH3
60
Iron reducing bacteria flowing electrons to ferric iron
• Organisms: Geobacter and other anaerobic bacteria, no specific group
•E- donors: mainly small organic compounds
• Typical reaction:
H2 + 2 Fe3+ --> 2 Fe2+ + 2 H+
• Reaction results in lowering of redox potential.
• Reduce also Manganese, elemental sulfur and other metals (e.g... uranium).
• Endproduct is magnetite (Fe3O4) and other compounds (black precipitates)
• Significance of iron reduction is still being underestimated.
•Recent research: electricity production using ferric iron reducing bacteria
61
Magnetite formation as the endproduct of iron reduction
62
Ideas:•solubilise iron (complexing, acid dissolving, etc.)•physically attach to ferric iron•excrete electron shuttling species (mediators)
use e-carriers present in environment
humic acids (quinone, analogue to NADH)
How do IRB transfer electrons to insoluble iron ?
?
63
Ideas:
Geobacter transfers electrons to oxidised humic acid which diffuses to the iron to pass on the electrons (quinone, analogue to NADAH).
Humic acids as natural mediators ?
Red Humics
Ox Humics OH
OH
O
ORed. Ox.
64
By transferring electrons to chlorinated hydrocarbonsReductive dechlorination Bioremediation potential
“Chlorine respiration”?
Other fancy tricks of Geobacter ?
Cl
Cl
e-
65
Own work:
Interspecies electron transfer from Geobacter to other strains
How? Cytochromes?
Wires?
Other fancy tricks of Geobacter ?
Acetate
Geobacter
Wolinella
Nitrate
e-
e-
66
If Geobacter can transfer electrons to almost anything, why not to a carbon anode.
Electricity generation by Geobacter
Outback batteries
Driving force: Organic wastes
Key: Sugar degrading Geobacter type (Rhodoferax)
Geobacter Headlines (Geobacter.com) :Bioelectricity
67
68
69
Simple approach to bio-electricity
70
Geobacters capability of reducing other metal species includes uranium.
By reducing U(VI) to U(IV) which is less soluble limitation of contaminationhas been applied in situ (2003) Tod Anderson
Geobacter Headlines 2:Cleanup of Uranium
71
Geobacters presence of deep ocean vents (black smokers) has been shown.
Temperature tolerance to 121 (autoclave)
Interesting Genome.
Suggestions of iron reducing Archeae to be one of the oldest lifeforms rather then sulfur reducers.
Very old magnetite formations are seen to support this view.
Geobacter Headlines 3:Hottest Bug Strain 121
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Strain 121
73
Lecture Summary
1. Sulfate reduction P- release from sediments,Sulfur deposits,
Corrosion of submerged steel, Lethal gas emissions
2. NO3- reduction to N2
black precipitate, magnetite (Fe3O4), is produced when Fe3+ is reduced to Fe2+
3. CO2 reduction to CH4
Methane - highly energetic e-donor (fuel) in aerobic areas
4. Prolific life at the anaerobic/aerobic interface High activity at chemocline, Black smokers,
Life on CH4
74
Lecture Summary
1. Sulfate reduction P- release from sediments,Sulfur deposits,
Corrosion of submerged steel, Lethal gas emissions
2. Fe3+ reduction to Fe2+ black precipitate, magnetite (Fe3O4), is
produced when Fe3+ is reduced to Fe2+
3. CO2 reduction to CH4
Methane - highly energetic e-donor (fuel) in aerobic areas
4. Prolific life at the anaerobic/aerobic interface High activity at chemocline, Black smokers,
Life on CH4
75
End of lecture, below only for personal interest
76
Methane hydrate
• Methane hydrate, a curiosity or a significant global phenomenon?
• Needed for formation: low temperature and high pressure
• Why are hydrates mainly on the continental shelfes ?
• Deep oceans lack • high biologic productivity (CH4) • rapid sedimentation rates (bury the organic matter)
77
Methane gas hydrate formation
Gas hydrate stability zone on deep-water continental margins.
A water depth of 1200 meters is
assumed.
78
Sea floor slopes on continental margins are stable if the slope is less than 5°. However, many continental margins with shallow slopes have scars from underwater landslides. A potential trigger for shallow slope landslides is sudden gas release from the sediments. This can occur if the methane hydrate layer in the sediment becomes unstable. The hydrate layer can melt if the temperature rises or there is a drop in the confining pressure (below). Melting suddenly releases the methane trapped in the hydrate along with any natural gas trapped below the hydrate layer. Twenty thousand years ago an ice age resulted in the formation of large ice cap that covered much of northern Europe and Canada, and resulted in a 120m drop in sea level. The drop in sea-level reduced the pressure at the sea floor (due to the fact that there was less overlying water). Consequently the methane hydrate layer melted, causing many underwater landslides on the North American continental margin – the scares of which are still visible today and perhaps submarine slide scars recently mapped off Wollongong.
79
Gas hydrates and bubbles in the bermuda triangle
^ A drop in sea-level reduces the pressure at the sea floor and causes the melting of methane hydrate. The sudden release of gas results in landslides and slumps. It can also result in a plume of gas rapidly rising to the ocean surface. Gas in the water reduces the density of water leading to the loss of buoyancy of ocean going craft. Is this what causes the mysterious sinking of ships in the Bermuda Triangle? When sea level dropped during the last ice age, the destabilisation of hydrate and the release of methane may have been sufficient to heat the atmosphere via greenhouse effects and turn back the ice age.
At atmospheric pressure the concentration of methane in hydrate is over 600 times greater than in the free gas form. Methane hydrate is also significantly denser than liquid natural gas. Methane hydrate may provide a cost effective way of transporting and storing methane.