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

6

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

7

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)

14

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

17

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”)

23

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

26

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

28

“Black Smokers” releasing reduced sufur and iron (e.g. FeS) as potential electron donors for bacteria.

29

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

31


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


35

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

36

Thiomargareta namibiensis

37

Thiomargareta namibiensis

38

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

39

Gas Hydrate Molecules (dusk.geo.orst.edu/ oceans/lec14.html)

40

Methane hydrate mount under flashlight

41

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


Micheal Degruy

“Chemosynthetic mussel from methane hydrate

Methane hydrate outcrop

Tube worms

43

Methane hydrate sample

44


Micheal Degruy


Tubeworm collected from gas hydrate seepage areas

45


Micheal Degruy

Spider crab looking for food between the tubeworms growing on a methane hydrate outcrop

46


Micheal Degruy


Mussels with bacterial slime living on methane hydrate

47


Micheal Degruy

“Chemosynthetic mussel from methane hydrate”

48


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


Micheal Degruy


Methane hydratewith ice worms

50


Micheal Degruy


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

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


O2

Fe3+

E-donor

Fe2+

58

Summary


O2

CO2

H2

CH4

59

Summary


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

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

72

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.

1 microbial conversion of inorganic substances (bio-geo-chemical cycles) anaerobic respirations of...

Documents

h s o h

s s o s o

acceptors electron donors

bacteria s

o slide

h ch

s o h2s

typical electron