SMIB022

Biogeochemical Cycles

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MICROORGANISMS AND RECYCLING

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The carbon cycle
• Carbon – backbone of living cells
• constitutes 40 – 50% of dry weight
• most carbon in fossil fuel, coal, oil and gas
• remainder atmospheric and living and dead organisms
• 3 groups involved:
producers
consumers
decomposers

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 The Carbon Cycle
• Carbon is cycled through all of Earth’s major carbon reservoirs

• Amount of C in reservoirs needs to be kept in balance with the

amount that is cycling

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 The Carbon Cycle
• CO2 in the atmosphere is the most rapidly transferred carbon
reservoir

• CO2 is fixed by photosynthetic land plants and marine

microbes

• CO2 is returned to the atmosphere by respiration as well as

anthropogenic activities
– Microbial decomposition is the largest source of CO2
released to the atmosphere
– Nearly 20% increase in atmospheric CO2 levels
primarily from the burning of fossil fuels by humans

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 The Carbon Cycle
• Carbon and oxygen cycles are linked

• Phototrophic organisms are the foundation of the carbon

cycle
– Oxygenic phototrophic organisms can be divided into
two groups: plants and microorganisms
• Plants dominant organisms of terrestrial
environments
• Microorganisms dominate aquatic environments

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 The Carbon Cycle
Oxidations
Reductions
No redox
charge

Cyanobacteria

Nitrosomonas
Thiobacillus

Methylomonas

Methanococcus
Acetobacterium

Syntrophomonas

Purple and green bacteria

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Oxygenic and anoxygenic photosynthesis

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Differences between anoxygenic and oxygenic phototrophs
Anoxygenic phototrophs Oxygenic phototrophs

Reducing power Mostly H2S H2O

Photosynthetic apparatus Bacteriochlorophyll Chlorophyll

Produce oxygen No Yes

Number of photosystems One Two

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Chemolithotrophy
use inorganic compounds (electron donors) as energy source
use CO2 as sole carbon source

Nitrifying bacteria
Ammonia is oxidized to nitrite (nitrosifyers)
Nitrosomonas and Nitrosococcus (prefix “Nitroso”)
Nitrite is oxidized to nitrate (nitrifyers)
Nitrobacter (prefix “Nitro”)

Sulfur-oxidizing bacteria
H2S, S0 and S2O32- oxidized to sulphate
Thiobacillus and Acidothiobacillus

Hydrogen-oxidizing bacteria
H2 oxidized to water
Paracoccus and Ralstonia 12
Methanogenesis
Produced by methanogens (Archaeabacteria)
Obligate anaerobes
Use CO2 as electron acceptor and H2 as electron donor

4H2 + CO2 → CH4 + 2H2O

Other substrates: methanol, formate and acetate

Industrial application:
methane production from sewage waste
methane used for electricity and household purposes

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Waste to electricity generation

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Methanogenesis
Poor solubility of oxygen – a lot of C in anoxic environments
•Anoxic freshwater sediments and anoxic wastewater treatment

Methanogenesis central to carbon cycling in anoxic environments

Most methanogens reduce CO2 to CH4 with H2 as an electron

donor - some can reduce other substrates to CH4 (e.g., acetate)

Methanogens team up with partners (syntrophs) that supply them

with necessary substrates

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 Aerobic
Anaerobic

Methanogenesis 17
Syntrophy
Association in which the growth of one organism either depends on or is
improved by the substrate provided by another organism

Two different microbes cooperate to degrade a substance that neither can

degrade by their own

Syntroph produces and transfer H2 linked to H2 consumption by another

bacterium (denitrifying bacteria, ferric iron–reducing bacteria, sulfate-reducing
bacteria, acetogens, or methanogens)

Example:
Syntrophomonas produces H2 from ethanol

Methanococcus utilizes H2
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The concept of syntrophy

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Syntrophy

Most syntrophic reactions are

secondary fermentations
Organisms ferment the
fermentation products of other
anaerobes

Interspecies H2 transfer at the

heart of syntrophic reactions

Positive ΔG0’ of first reaction is

highly unfavourable – a pure
culture the syntroph will not grow
on the substrate
Syntroph requires H2-
consuming partner organism

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Methanotrophy
Methylotrophs – obligate aerobes which use organic compounds
that lack carbon-carbon bonds

Methanotrophs are methylotrophs that use methane as an electron

donor and carbon source

CH4 +O2 Methane monooxygenase methanol (CH3OH)

Monooxygenase catalyses the incorporation of oxygen atoms from O2 into carbon
compounds

Found near methanogens producing methane

Example: Methylomonas 21
The role of methanogens and methanotrophs in the carbon cycle and the 22
interaction between
Acetogenesis
CO2 abundant in anoxic habitats - major product of
chemoorganotrophs’ energy metabolisms

Acetogens another group of obligate anaerobes which use CO 2 in

energy metabolism

Use CO2 as electron acceptor and hydrogen as electron donor to

produce acetate

Example: Acetobacterium

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Acetogenesis
Acetogens reduce CO2 to acetate by the acetyl-CoA pathway
Acetogens can also ferment glucose directly to acetate

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 Aerobic respiration
Wood: 40 – 50% cellulose
20 – 30% lignin
10 – 30% hemicellulose
capacity of organisms – Fig 28.16
Reactions:
Cellulose cellulase many
cellobiose
Cellobiose ß-glucosidase 2
glucose
Glucose + 6O2 enzymes 6CO2 + 6H2O

Organisms:
Cellulose – Trichoderma, Aspergillus,
Clostridium
Cellobiose – bacteria, molds and
yeasts
Glucose – most organisms

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Greenhouse effect (global warming)
• The warming of the earth atmosphere due to the trapping
of solar radiation due to the increase in gasses

• Greenhouse gases: Carbon dioxide (CO2)

Methane (CH4)

Nitrous oxide (N2O)

Ozone (O3)

Water vapour

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Causes of the greenhouse effect
• Greenhouse gasses increase due to human activity
• Fertilizers in agriculture
• Deforestation
• Burning of organic matter
• Increased use of fossil fuels

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Consequences of the greenhouse effect
• Melting of polar ice caps
• Increase in sea water levels
• Droughts and floods more prevalent
• Increase in tropical storms
• Increase in the number of hot days
• Reduced crop production due to heat and pests

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Consequences of the greenhouse effect
• Microbes could have various positive and negative feedback
responses to temperature
• Diverse microbial communities interact with each other, other
organisms and the environment in complex ways

• Tropical diseases such as malaria spread to other parts

• Emergence of new pathogens – microbes adapting to growth in

human body

• Higher temperatures and environmental stress may alter defence

against pathogens - skin and gut microbiomes may become less
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protective
Chemolithotrophy
use inorganic compounds (electron donors) as energy source
use CO2 as sole carbon source

Nitrifying bacteria
Ammonia is oxidized to nitrite (nitrosifyers)
Nitrosomonas and Nitrosococcus (prefix “Nitroso”)
Nitrite is oxidized to nitrate (nitrifyers)
Nitrobacter (prefix “Nitro”)

Sulfur-oxidizing bacteria
H2S, S0 and S2O32- oxidized to sulphate
Thiobacillus and Acidothiobacillus

Hydrogen-oxidizing bacteria
H2 oxidized to water
Paracoccus and Ralstonia 32
The Nitrogen cycle
•80% of earth’s atmosphere consists of N
•used for proteins and nucleic acids
•Nitrogen gas (N2) is the most stable form and major reservoir for N
on Earth
•Nitrogen gas converted to ammonium by microbes
•Plants and other organisms utilise ammonium as N source
•Proteins, etc. degraded to usable nitrogen by microbes
•Ammonium converted to nitrates by nitrification

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 Oxidations
Reductions
Ni
c ter tro No redox charge
a s
tr ob Comammox om
Ni on
Nitrospira as

Azotobacter (free living)

Rhizobium (symbiotic)

Clostridium
Ba e u
Ps
cil do
lu mo
s

Brocadia
asn

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Nitrogen cycle
 Nitrogen fixation
N2 + 6H+ +6e+ + 12ATP nitrogenase
2NH3 + 12ADP + 12Pi

NH3 + H2O NH4 + OH

Nitrogenase anaerobic

Acetylene test for nitrogenase activity in microbes

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Free-living nitrogen fixing bacteria
•Live in rhizosphere
•Mechanisms to shield nitrogenase from oxygen as follows:
Azotobacter respires rapidly
Azotobacter produce capsules
Anaerobic i.e. Clostridium
Cyanobacteria has heterocysts
Habitat: forests, crop production and grasslands

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 capsule

Capsules by Azotobacter (a) at low

oxygen and (b) at high oxygen
concentration

Heterocyst – site for nitrogen fixation

Heterocysts produced by 37
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300px-CyanobacteriaMicroscope.jpeg
cyanobacteria
Symbiotic nitrogen-fixing bacteria
•Mutualistic partnership between plant roots and bacterium
•Benefits: - plant: ammonia
- bacteria: nutritional requirements
oxygen free environment
(leghemoglobin)

•Examples: Rhizobium – roots of legumes (peas, soybeans)

Azospirillum - grasses, wheat and corn

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 Nodule formation
1. Recognition of bacterium to
specific plant
2. Oligosaccharides excreted by
bacteria (nod factors)
3. Invasion of bacteria in root hair
4. Bacteria move to main root via
infection thread
5. Formation of bacteroids
6. Form mature root nodule

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Symbiotic nitrogen fixation by Rhizobium
Nodule formation
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Advantages of nitrogen fixing symbiotic relationship between plant and microbe

Nodulated legumes can grow well on unfertilised bare soils that are nitrogen deficient,
while other plants grow only poorly on them

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Leghemoglobin
• Nitrogenase sensitive to oxygen
• Oxygen binding protein occurring in nodule
• Leghemoglobin produced via the interactions between root and
microbe
• Acts as oxygen buffer
• Cycling between oxidized Fe3+ and reduced Fe2+ forms of iron

leghemoglobin

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Crossection through nodule
 Oxidations
Reductions
Ni
c ter tro No redox charge
a s
tr ob Comammox om
Ni on
Nitrospira as

Azotobacter (free living)

Rhizobium (symbiotic)

Clostridium
Ba e u
Ps
cil do
lu mo
s

Brocadia
asn

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Nitrogen cycle
Ammonification
Conversion of organic nitrogen to ammonia
proteinases peptidases
•Proteins peptides amino acids
•Organisms: fungi, Clostridium, Pseudomonas and Bacillus
NH2 O
alanine
CH3 CH COOH + ½O2 CH3 C COOH + NH3
alanine deaminase pyruvic acid

NH2
urease
O=C + H2O 2NH3 + CO2

NH2
Urea

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Dissimilative nitrate reduction to ammonia (DNRA)
NO2 or NO3 are reduced to NH3

Anaerobic process

Occurs in reductant-rich anoxic environments

highly organic marine sediments and the
human gastrointestinal tract

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Nitrification
Conversion of ammonia to nitrate
Occurs in well-drained oxic soils
Obligate aerobes involved
•Two steps:
Step 1: ammonia to nitrite (ammonia oxidizers)
2NH3 + 3O2 → 2HNO2 + 2H2O ionization H+ + NO2-
Organisms: Nitrosomonas, Nitrosovibrio, Nitrosococcus
Step 2: nitrite to nitrate (nitrite oxidizers)
NO2- + ½O2 → NO3-
Organism: Nitrobacter
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Comammox (COMplete AMMonia OXidiser)
Conversion of ammonia to nitrate in a single step
Organism: Nitrospira

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Anammox (anoxic ammonia oxidation)
The oxidation of ammonia with NO2 as the electron acceptor to

produce N2

NO2- + NH3 → 2N2

Anaerobic process – sewage and marine sediments

Organism: Brocadia
Anammox occurs in membrane enclosed compartment -
anammoxome

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Denitrification
Nitrates reduced to atmospheric nitrogen
Happens in waterlogged soils (anaerobic conditions)
Extensive denitrification is detrimental – removes fixed N from soil
In wastewater treatment – removes fixed N to minimise algal growth
when treated sewage water is released into lakes and streams
Nitrate used as electron acceptor
2NO3 → 2NO2 → 2NO → N 2O → N2
Nitrate Nitrite Nitric oxide Nitrous oxide Nitrogen gas
Organisms: Agrobacterium, Alcaligenes, Bacillus, Thiobacillus
and Pseudomonas
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The Sulphur cycle
•Sulphur reservoirs include fossil fuels, rocks, sulphur deposits and
minerals
•The ocean most significant reservoir of sulphate
•Three different oxidation states: So (elemental sulphur)
S2- (inorganic sulphides)
SO42- (sulphates)
•Sulphates incorporated into sulphur containing amino acids
•Sulphur dioxide (SO2), enters the S cycle from human activities,
primarily the burning of fossil fuels

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 Oxidations
Reductions
Thiobacillus No redox charge
Microbes and the sulfur cycle

Desulfovibrio

as
on
r om
Desulfovibrio fu
ul
es
D
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Purple and green bacteria
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Oxidation of sulfur to sulfate
2S + 2H2O + 3O2 → 2H2SO4 → 2H+ + SO42-
•Organism: Thiobacillus
•Aerobic chemolithotrophic process
•Help in the control of potato scab

Protein decompoition
Sulfur containing amino acids degraded
CH2SH CH 3
│ desulfarase │
HC—NH2 + H2O C═O + NH 3 + H2S
│ │
COOH COOH
Cysteine Pyruvic acid
Sulfate reduced to hydrogen sulfide
8H + CaSO4 → H2S + Ca(OH)2 + 2H2O
Organism: Desulfovibrio
Anaerobic process

Oxidation of hydrogen sulfide

CO2 +H2S enzymes; light (CH2O) + H2O + 2S
Organisms: green and purple phototrophic bacteria
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DMS and DMSO
Organic S compounds
DMS – dimethyl sulfide
DMSO – dimethyl sulfoxide
DMS – electron donor: phototrophs
chemolitotrophs
chemoorganotrophs
DMS converted to DMSO
DMSO – electron acceptor for anaerobic respiration

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The Phosphorus cycle

•Inorganic phosphate (PO43- ) organic phosphate

•Organic phosphate includes DNA, RNA, ATP, phospholipids
•No gas form = no global redistribution
•No oxidized or reduced state
•Phosphate wash to oceans
•How does it return to land?
Faeces from seabirds (small amounts)
Geological uplift of ocean floors (process slow)
•Phosphate is mined from geological uplifts (America and Africa)
•Phosphate limiting factor in lakes and streams
•Addition or pollution results in eutrophication 55
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(Microorganisms)

The phosphorus cycle

The iron cycle
• Two oxidation states:
Ferrous (Fe2+, soluble) and Ferric (Fe3+, insoluble) iron
• Ferric iron reduced by microbes during anaerobic fermentation
Example:
H2 + 2Fe3+ → 2Fe2+ + 2H+
Organism: Geobacter
• Ferrous iron oxidized by some chemolithotrophs aerobically
Example:
Fe2+ + ¼O2 + H+ → Fe3+ + ½H2O
Acidithiobacillus
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 Oxidations
Reductions
No redox charge

Geobacter
Acidithiobacillus
Anoxic
Oxic

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Microbes involvement in the iron cycle
The iron cycle
• Fe3+ can be used by some Bacteria and Archaea as an electron
acceptor in anaerobic respiration
• Ferric iron reduction is common in waterlogged soils, bogs, and
anoxic lake sediments
• In aerobic acidic pH environments, acidophilic chemolithotrophs
can oxidize Fe2+
• Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans

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Oxidation of ferrous iron. Matt = chemolithotrophic bacteria.
Red-brown precipitate consists of Fe(OH)3 and other ferric
minerals. 60
The iron cycle
• One of the most common forms of iron in nature is pyrite (FeS 2)
• Its oxidation by bacteria can result in acidic conditions in coal-
mining operations

• Bacterially produced Fe2+ leaches away and is carried by anoxic

groundwater into surrounding streams
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Acid mine drainage
• An environmental problem in coal-mining regions
• Occurs when acidic mine waters are mixed with natural waters in
rivers and lakes
• Bacterial oxidation of sulfide minerals is a major contributor
• FeS2 oxidation leads to the formation of H 2SO4 and Fe2+;
• pH values can be lower than 1
• Mixing of acidic mine waters into rivers and lakes degrades
water quality
• Acid and the dissolved metals are toxic to aquatic organisms
• A strongly acidophilic species of Ferroplasma
• Aerobic iron-oxidizing Archaea grows at pH 0, temperatures
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BIOLEACHING
•Def. The extraction of metals from their ores through the use of
living organisms

•Used when chemical means is not economical

Acidophilic bacteria
•Insoluble mineral sulfides soluble mineral sulphates
(oxidation)

•Microbes: Acidithiobacillus ferrooxidans

Leptospirillum ferrooxidans

•Minerals: Copper (chalcocite – Cu2S/covellite – CuS)

Iron (pyrite – FeS2)

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Bioleaching of copper sulfide to produce metallic copper