4 - Microbes and Other Nutrient Cycles Flashcards
Nutrient cycle examples
- Carbon
- Nitrogen
- Sulfur
- Mercury
Mercury cycle
- Not biological nutrient but shows what happens when humans redistribute chemical elements
- Present in wastewater dumped into oceans and from burning fossil fuels
- Mercury as Hg2+ readily absorbs to matter and metabolised by microbes to form methyl mercury
Methylmercury
- Extremely toxic
- Readily absorbed through skin (neurotoxin)
- Bio accumulates in living tissues
Minamata disease
- Neurological disease
- Occured in local people that ate the fish and became ill
- More than 2000 people died
- Due to methylmercury consumption in fish
Nitrogen
- Essential for life
- In proteins, nucleic acids, other cell components
- Substantial component of bacterial cells dry weight
In nature, what is N most available as
- Ammonia: Can be used for N by almost all prokaryotes
- Nitrate: Can be used by many
- Nitrogen gas: can only be used by N fixing prokaryotes
- Some prokaryotes can use organic nitrate (e.g. amino acids)
NItrogen cycle
- Nitrogen gas (N2) is the most stable form of N (a major N reservoir on Earth)
- Very few prokaryotes can use N2 as an N source, must fix atmospheric nitrogen
- So most N cycling is N that is already fixed
- N species may serve as electron donor or acceptor, or both
5 Key processes in the N cycle
- Nitrification
- Denitrification
- Nitrogen Fixation
- Ammonification
- Anammox
Nitrogen fixation
- Process where ammonia is formed from N2
- Catalysed by enzyme complex nitrogenase
- Anaerobic process (enzymes inactivated by O2)
- Some N2 fixers are obligate aerobes as N fixing requires lots of energy
Two enzymes that make up enzyme complex nitrogenase
- Dinitrogenase
- Dinitrogenase reductase
How to obligate aerobes protect nitrogenase enzymes from O2 in nitrogen fixation
- Rapidly removing O2 by respiration
- Producing extracellular slime layers (slows diffusion of O2)
- In some cyanobacteria, enzyme located within
specialised heterocyst (lacks photosytem II: does not generate O2 from photosynthesis)
What organisms can fix nitrogen
- Diverse range
- May be free living (aerobes or anaerobes) or symbiotic (fix N in association with plants)
Nitrification
- Process where fixed nitrogen (NH3) is oxidised to nitrate (NO3)
- Carried out by nitrifying prokaryotes (nitrification produces NO3 whereas denitrification consumes NO3)
- Two steps, both usually aerobic with O2 as TEA
- Major process in oxic, well drained soils at neutral pH
Two steps of nitrification
- NH3 oxidised to NO2 (nitrite): many species of bacteria
- NO2 is oxidised to NO3 (only by bacteria)
Comammox
Nitrospira species that can do both steps of nitrification
Denitrification
- Process where fixed nitrogen is removed from the environment
- Reduction of NO3 to N volatile gases (main means by which N2 and N2O are formed biologically)
- Anaerobic process (NO3 used as TEA for anaerobic respiration)
- Diverse range of organisms capable of denitrification
- Occurs in anoxic soils, sediments and anoxic zones in lakes and oceans
Benefits of denitrification
- NItrogen loss aids wastewater treatment (reduces available nitrogen and eutrophication)
Downside of denitrification
- Nitrogen lost from agricultural soil (if anaerobic)
- NO3 formed by nitrification leaches into anaerobic soil, gets denitrified by anaerobes
Ammonification
- Process where NH3 is released from decomposition of organic molecules (amino acids, nucleotides)
- NH3 is also formed by DRNA
Fate of NH3 in ammonification
- At neutral pH: NH3 exists as ammonium (NH4+), which is rapidly consumed by plants and microbes
- However, NH3 is volatile, some can be lost to atmosphere
- Represents 15% of all N released to atmosphere, bulk is N2 or N2O
DRNA
- Dissimilative Reduction of Nitrate to Ammonia
- Process dominates NO3 and NO2 reduction in anoxic environments that are rich in organic materials
Anammox
- Process where ammonia oxidised to N2 anaerobically (uses NO2 as electron acceptor)
- Major process in sewage, anoxic marine basins, sediments
- Takes place inside anammoxosome
- Anammoxosome membrane composed of unique ladderane lipids
Why is anammox insignificant in oxic soils
As under oxic conditions NH3 is oxidised to NO2 (nitrification)
Major organism that conducts anammox
Candidatus Brocadia anammoxidans
Candidatus Brocadia anammoxidans
- Marine chemoautotroph, strict anaerobe
- Lacks peptidoglycan, doubling time 7-14 days
- Contain cellular compartments called anammoxosomes (Membrane-bound structure)
Candidatus
Characterised but not grown in pure culture yet
Anammoxosome membrane composed of unique ladderane lipids
- Relatively rigid
- Keeps intermediates and enzymes of anammox contained
- Differs from cytoplasmic membrane
- Keeps hyrazine away from cytoplasm (formed as intermediate and highly toxic)
Human activity and the N cycle
- Humans have dramatically increased available nitrogen (anthropogenic nitrogen)
- Make industrially-fixed N for fertiliser
- Most Nh3 is applied to agricultural land (some taken up by plants, some ends up as run off, large amount lost as gases
Nox gases
- NO and N2O
- Both greenhouse gases
- ~280 times the warming potential of co2
- Also released by burning fossil fuels
Sulphur cycle
- Differs from C and N because not fixed from air (already fixed in range of compounds)
- Microbial transformation of S more complicated than N
- Three oxidation states of S are significant in nature
Three oxidation states of S that are significant in nature
- (-2 ox state): Sulfhydryl, rocks reservoirs
- (0 ox state): Elemental sulphur
- (+6 ox state): Sulfate, ocean and rocks reservoir
Key processes in sulphur cycle
- Sulfide/sulfur oxidation
- Sulfate reduction
[3. Sulfur reduction]
[4. Sulfur disproportionation] - Organic sulfur compound oxidation or reduction
[6. Desulfurylation]
Sulfide/sulfur oxidation
- Process where sulfide is oxidised to sulfur then sulfate
- Limited to areas where sulfide emerges from anoxic areas and meets air
- Anaerobic oxidation can occur if light is available (by phototrophic purple and green sulfur bacteria)
- Elemental sulfur is stable (readily oxidised by chemolithotrophs, oxidation produced protons, Results in acidification of environment)
Benefits of an acidic environment due to oxidation of elemental sulfur
Sometimes added to alkaline soils as a cheap and easy way to lower soil pH
Why is sulfide/sulfur oxidation limited to areas where sulfide emerges from anoxic areas and meets air
- With O2 and at neutral pH, sulfides oxidise spontaneously and rapidly AND
- Most organisms capable of sulfide oxidation are aerobes
Sulfate reduction
- Process by which sulfate is reduced to produce sulfide
- Dissimilatory sulfate reduction
- Sulfate is most oxidised form of S (ideal acceptor for electrons and serves as TEA during anaerobic respiration
What is sulfate reduction done by
- Sulfate reducing bacteria
- Highly diverse group of obligate anaerobes
- Both organotrophs and lithotrophs (electron source)
- Distributed widely in nature in anoxic, sulfate-rich sediments
Examples of sulfate reducing bacteria
Desulfovibrio and Desulfobacter
Limitations of sulfate reduction in nature
- Availability of sulfate and H2
- Carbon
- Generally only occurs when lots of organic matter is present
Rate of sulfate reduction increasing significantly with influx of organic matter
- Detrimental because sulfide (waste) is toxic to many plants and animals
- Reacts readily with metals
- Often detoxified in nature by combining with ferrous iron (Fe2+) (forms insoluble black minerals)
Organic sulfur compounds
- Highly volatile and foul smelling
- Most abundant compound is dimethyl sulfide (DMS)
- Produced in marine environments
Production of DMS in marine environments
- Degradation product of DMSP (osmoregulatory solute in marine algae)
- Algae die, release DMSP and bacteria metabolise it to DMS
- Released into the atmosphere
- Converted to several sulfur compounds which serve as nuclei for water droplet formation and have role in cloud formation
Albedo
The amount of light reflected away from the surface of Earth
Human impacts of S cycle
Burning fossil fuels adds sulfur compounds into atmosphere which eventually comes back to earth as acid rain
Interactions between nutrient cycles
- Cycles are interconnected (coupled)
- E.g. chemolithotrophs
Chemolithotrophs
- Use NH4+ and NO2 for electrons, and CO2 as sole carbon source
- Carbon and nitrogen both assimilated
- May be returned to atmosphere later following denitrification
- Large amounts of inorganic molecules oxidised to provide enough energy
- Processing large amounts significantly influences nutrient cycle
