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MICR3310 > 4 - Microbes and Other Nutrient Cycles > Flashcards

4 - Microbes and Other Nutrient Cycles Flashcards

1
Q

Nutrient cycle examples

A
  • Carbon
  • Nitrogen
  • Sulfur
  • Mercury
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2
Q

Mercury cycle

A
  • 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
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3
Q

Methylmercury

A
  • Extremely toxic
  • Readily absorbed through skin (neurotoxin)
  • Bio accumulates in living tissues
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4
Q

Minamata disease

A
  • Neurological disease
  • Occured in local people that ate the fish and became ill
  • More than 2000 people died
  • Due to methylmercury consumption in fish
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5
Q

Nitrogen

A
  • Essential for life
  • In proteins, nucleic acids, other cell components
  • Substantial component of bacterial cells dry weight
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6
Q

In nature, what is N most available as

A
  • 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)
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7
Q

NItrogen cycle

A
  • 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
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8
Q

5 Key processes in the N cycle

A
  1. Nitrification
  2. Denitrification
  3. Nitrogen Fixation
  4. Ammonification
  5. Anammox
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9
Q

Nitrogen fixation

A
  • 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
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10
Q

Two enzymes that make up enzyme complex nitrogenase

A
  • Dinitrogenase
  • Dinitrogenase reductase
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11
Q

How to obligate aerobes protect nitrogenase enzymes from O2 in nitrogen fixation

A
  • 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)
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12
Q

What organisms can fix nitrogen

A
  • Diverse range
  • May be free living (aerobes or anaerobes) or symbiotic (fix N in association with plants)
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13
Q

Nitrification

A
  • 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
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14
Q

Two steps of nitrification

A
  1. NH3 oxidised to NO2 (nitrite): many species of bacteria
  2. NO2 is oxidised to NO3 (only by bacteria)
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15
Q

Comammox

A

Nitrospira species that can do both steps of nitrification

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16
Q

Denitrification

A
  • 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
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17
Q

Benefits of denitrification

A
  • NItrogen loss aids wastewater treatment (reduces available nitrogen and eutrophication)
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18
Q

Downside of denitrification

A
  • Nitrogen lost from agricultural soil (if anaerobic)
  • NO3 formed by nitrification leaches into anaerobic soil, gets denitrified by anaerobes
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19
Q

Ammonification

A
  • Process where NH3 is released from decomposition of organic molecules (amino acids, nucleotides)
  • NH3 is also formed by DRNA
20
Q

Fate of NH3 in ammonification

A
  • 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
21
Q

DRNA

A
  • Dissimilative Reduction of Nitrate to Ammonia
  • Process dominates NO3 and NO2 reduction in anoxic environments that are rich in organic materials
22
Q

Anammox

A
  • 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
23
Q

Why is anammox insignificant in oxic soils

A

As under oxic conditions NH3 is oxidised to NO2 (nitrification)

24
Q

Major organism that conducts anammox

A

Candidatus Brocadia anammoxidans

25
Q

Candidatus Brocadia anammoxidans

A
  • Marine chemoautotroph, strict anaerobe
  • Lacks peptidoglycan, doubling time 7-14 days
  • Contain cellular compartments called anammoxosomes (Membrane-bound structure)
26
Q

Candidatus

A

Characterised but not grown in pure culture yet

27
Q

Anammoxosome membrane composed of unique ladderane lipids

A
  • Relatively rigid
  • Keeps intermediates and enzymes of anammox contained
  • Differs from cytoplasmic membrane
  • Keeps hyrazine away from cytoplasm (formed as intermediate and highly toxic)
28
Q

Human activity and the N cycle

A
  • 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
29
Q

Nox gases

A
  • NO and N2O
  • Both greenhouse gases
  • ~280 times the warming potential of co2
  • Also released by burning fossil fuels
30
Q

Sulphur cycle

A
  • 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
31
Q

Three oxidation states of S that are significant in nature

A
  • (-2 ox state): Sulfhydryl, rocks reservoirs
  • (0 ox state): Elemental sulphur
  • (+6 ox state): Sulfate, ocean and rocks reservoir
32
Q

Key processes in sulphur cycle

A
  1. Sulfide/sulfur oxidation
  2. Sulfate reduction
    [3. Sulfur reduction]
    [4. Sulfur disproportionation]
  3. Organic sulfur compound oxidation or reduction
    [6. Desulfurylation]
33
Q

Sulfide/sulfur oxidation

A
  • 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)
34
Q

Benefits of an acidic environment due to oxidation of elemental sulfur

A

Sometimes added to alkaline soils as a cheap and easy way to lower soil pH

35
Q

Why is sulfide/sulfur oxidation limited to areas where sulfide emerges from anoxic areas and meets air

A
  • With O2 and at neutral pH, sulfides oxidise spontaneously and rapidly AND
  • Most organisms capable of sulfide oxidation are aerobes
36
Q

Sulfate reduction

A
  • 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
37
Q

What is sulfate reduction done by

A
  • Sulfate reducing bacteria
  • Highly diverse group of obligate anaerobes
  • Both organotrophs and lithotrophs (electron source)
  • Distributed widely in nature in anoxic, sulfate-rich sediments
38
Q

Examples of sulfate reducing bacteria

A

Desulfovibrio and Desulfobacter

39
Q

Limitations of sulfate reduction in nature

A
  • Availability of sulfate and H2
  • Carbon
  • Generally only occurs when lots of organic matter is present
40
Q

Rate of sulfate reduction increasing significantly with influx of organic matter

A
  • 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)
40
Q

Organic sulfur compounds

A
  • Highly volatile and foul smelling
  • Most abundant compound is dimethyl sulfide (DMS)
  • Produced in marine environments
41
Q

Production of DMS in marine environments

A
  • 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
42
Q

Albedo

A

The amount of light reflected away from the surface of Earth

43
Q

Human impacts of S cycle

A

Burning fossil fuels adds sulfur compounds into atmosphere which eventually comes back to earth as acid rain

44
Q

Interactions between nutrient cycles

A
  • Cycles are interconnected (coupled)
  • E.g. chemolithotrophs
45
Q

Chemolithotrophs

A
  • 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

MICR3310 (28 decks)

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