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Biogeochem and Ocean Atmos > Biogeochem - Remineralisation of biomass > Flashcards

Biogeochem - Remineralisation of biomass Flashcards

1
Q

Difference between organic and inorganic molecules, particles etc.

A

Organic molecules/particles have carbon present
- eg hydrocarbons, proteins etc

inorganic molecules have carbon absent
- metals, minerals etc

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2
Q

characteristics of marine sediments

A
  • low in organic matter content
  • bulk of their matter is shells, clay particles and other clastic materials
  • sediment organic matter contents decrease with water depth and distance from the coast
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3
Q

What percentage of sediment goes into sedimentation in the open ocean?

A

10%

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4
Q

In the process of organic matter reaching the sediment, what does Gross Deposition mean?

A

the sediment that reaches the seafloor

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5
Q

under what conditions does the recycling of nutrients occur?

A

during upwellings

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6
Q

How does the distance between the photic zone and the sediment impact the organic matter concentration in the sediment?

A

The closer the sediment is to the photic zone layer, the more organic matter reaches in the sediment

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7
Q

how do prokaryotes break down organic matter?

A

most of the organic matter in the ecosystem is in a polymeric state.

Prokaryotes can only take up monomeric molecules (or sometimes oligomers), as they are osmotrophic.

Extracellular enzymes (known as exo or ectoenzymes) are released by the cell which degrade the organic matter so they can take it up

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8
Q

Steps in microbial degradation of organic matter

A
  1. Extracellular hydrolysis of polymeric compounds
  2. uptake of dissolved molecules (monomers)
  3. metabolic conversion (for energy or growth)
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9
Q

What is maintenance energy requirement

A

it is the energy needed to repair and maintain cells.

only once the maintenance energy is spent and energy is still available can cell use this to grow and multiply

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10
Q

What types of reactions are used for maintenance or growth

A

REDOX reactions

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11
Q

REDOX states

A

OIL RIG

oxidation occurs, loss of electron, becomes oxidised, redox state becomes more positive

reduction occurs, receives electron, becomes reduced, redox state becomes more negative

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12
Q

How do cells control single reactions (redox) that occur at the same time

A

They occur in different parts of the cell (one in the cytoplasm, one in the membrane)

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13
Q

What happens if no oxygen is available?

A
  • anaerobic respiration
  • fermentation
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14
Q

What determines the amount of energy available from each (an)aerobic respiration?

A

It depends on the redox potential of the electron acceptor

Oxygen has the highest energy (aerobic respiration)

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15
Q

What happens during the oxidation of organic compounds in a cell

A

electrons will be transferred to NAD+ which will be reduced to NADH. NADH is the electron carrier within cells transporting electrons from where the carbon is oxidised to where the respiration occurs (in the membrane).

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16
Q

Do anaerobes or aerobic organisms gain more energy from respiration

A

Aerobs do as the redox potential difference between oxygen and NAD+/NADH is much greater than the redox potential difference between Nitrate or Iron oxohydroxide.

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17
Q

Where do you typically find prokaryotes that depend on the presence of oxygen?

A

In the water column as oxygen is depleted quickly in sediments

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18
Q

What are the three groups of microorganisms that are strictly anaerobic?

(they can be inactive or killed in the presence of oxygen)

A

sulphate reducers (using sulphate for respiration)

methanogens (producing methane)

fermenters (not respiring at all)

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19
Q

Why do differing redox potentials lead to a vertical zonation of the respiration process?

A

The energy obtained from a respiration process is directly proportional to the redox potential difference between the redox pairs (NAD+/NADH) and the electron acceptor pair.

This means that organisms in different layers of the sediment can outcompete each other depending on what electron acceptor is available

Organisms that can extract more energy from organic matter out compete those which extract less energy

Respiration processes with the highest energy yield occur at the top. Methanogenesis becomes dominant in bottom layers when almost all electron acceptors are gone

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20
Q

What does the term “terminal oxidation” mean/is used for?

A

it is used for processes that convert organic compounds to CO2, the ultimate oxidised form of carbon

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21
Q

How do fermenters differ to aerobes or denitrifiers?

A

They extrete ‘fermentation products’ with similar redox states like their substrates

(eg lactic acid, acetic acid, butyric acid)

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22
Q

what does glucose get fermented into?

A

glucose to 3 lactic acid molecules or 3 aceitic acid molecules

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23
Q

Why do sulphate reducers and methanogens depend on fermenters to do the first steps of degradation?

A

This is because sulphate reducers and methanogens cannot degrade complex organic material, unlike fermenters.

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24
Q

Why are secondary fermenters (synotrophs) needed in the methanogenic zone of sediments?

A

This is because methanogenic organisms can only use acetate (compounds with one carbon or hydrogen atom).

Many fermentation products have 4 or 5 carbon atoms meaning methanogens cant use them.

Synotrophs can split these fermentation products into smaller molecules which can then be used by methanogens

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25
Q

What is the product of lactic acid fermentation?

A

Yoghurt, salami, cabbage

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26
Q

what is the product of alcoholic fermentation?

A

beer, wine, cider…

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27
Q

what is the product of propionic acid fermentation?

A

cheese

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28
Q

what is the product of citric acid fermentation?

A

lemon juice or citric acid for food processing

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29
Q

what is the product of acetone formation?

A

a solvent which is used for industrial applications

30
Q

What is one of the most important bacteria in food poisoning (from fermentation)

A

Clostridium botulinum

31
Q

State the process of the anaerobic food web

A
  • Fermenters break down complex molecules (ie polysaccharides and proteins) into simpler compounds by excreting fermentation products
  • sulphate reducers can use all fermentation products and oxidise them to CO2
  • secondary fermenters (synotrophs) prevent larger fermentation products from accumulating by breaking them down into smaller compounds
  • methanogens use can only use the 1 carbon compounds and acetate, which the synotrophs have broken down so they’re available)
32
Q

In coastal sediments, where is the major place for organic matter degradation?

A

in sulphate-reducing layers

33
Q

In sulphate-reducing layers in coastal sediments, what is the organic matter degraded to?

A

CO2

34
Q

in costal sediments, in the methanogenic layer, what is the organic matter degraded to?

A

CO2 and CH4 (methane)

35
Q

What is the deposition and preservation of organic matter supported by?

A
  1. High primary production
  2. Short sedimentation time
  3. Type of organic matter
  4. Physicochemical conditions
36
Q

When is degradation slower?

A

When the material is strongly:
- cross linked (ie when keratin or chitin is present)
- the sequence of monomers is random (heteropolysaccarides)
- if the compounds become more reduced (oxygen, nitrogen, sulphur content decreasing)
–> alkanes or aromtic compounds are less degradable than sugars

37
Q

Give an example of a molecule that is easy to degrade and hard to degrade?

A

Easy:
- starch

Hard:
- cutan
- algaenan

38
Q

Do terrestial plants or marine phytoplankton have more preservation value?

A

Terrestrial plants contain more (structural) polymers as they are not floating in water, and have waxes with high preservation potential

terrestrial plants have a higher preservation potential

39
Q

What does recalcitrant organic matter mean?

A

organic matter that is resistant to degradation/decomposition

40
Q

give an example of a recalcitrant organic matter

A

Lignin

41
Q

Why is lignin a recalcitrant molecule?

A

Due to its extremely random 3-D molecular structure, enzymatic attack is almost impossible

it can only be degraded in oxic conditions by some fungi

42
Q

What is the process of lignin degradation?

A

involves the enzymatic formation of oxygen radicals and hence requires elemental oxygen

the radicals lead to a breakage of the bonds which will lead to the release of smaller volatile molecules that can be used by the fungus

43
Q

What is a sapropel?

A

They are sediment layers that are strongly enriched in highly recalcitrant organic matter

44
Q

When did the Eastern Mediterranean sapropels form?

A

Formed during anoxic events in the Eastern Mediterranean Basin.

These events occur approx every 20ka and are linked to the Milankovich cycles

45
Q

What conditions did sapropels form under in the Mediterranean?

A

They form in periods of elevated precipitation in the Mediterranean region.

46
Q

How/why did Sapropels form in Eastern Med?

A
  • The environmental conditions over the Med and N Africa were very different. When stronger monsoons occurred, the freshwater input increased in the Eastern Med basin.
    Scientists are arguing if the monsoon or the melting of the glaciers had the biggest impact on these conditions…
  • As the temperatures were cooler, less evaporation was occurring which led to saltier water at depth and less saltier water at the surface
  • This caused stratification as the bottom waters were stagnant, meaning no mixing was occurring. This led to anoxic conditions.
  • When conditions become anoxic, organic matter accumulates as certain compounds can only be degraded in oxic conditions.
  • In the sapropel layers, green sulphur bacteria were found in the sediment. This bacteria photosynthesises using H2S. When H2S is present, it indicated anoxic conditions. It also indicated the anoxic conditions were very close to the surface if the photosynthesis bacteria were found.
47
Q

What factor influences the disappearance of sapropels?

A

When oxic conditions have been re-established

48
Q

What are the current conditions in the Mediterranean?

A
  • Anti-estuarine circulation pattern due to more less freshwater input and more evaporation
  • This causes waters to be more saline, and sink, taking the nutrients and oxygen with it. The oxygenated, saline surface layers go into the deeper layers
  • Causes stratification and a negative water balance. Water to replenish the sinking surface water comes from the Atlantic ocean. This is very nutrient poor.
  • Water in the eastern med gets more saline, carried the nutrients and oxygen away into deeper waters and then flows out into the Atlantic ocean as deep water. This is replenished by nutrient poor salt water from the atlantic
  • The formation of Levantine Intermediate Water (LIW) influences this interaction because the Med is made up of 2 basins
49
Q

What does euxinic mean / what conditions do euxinic waters form under?

A
  • anoxic deep/bottom waters
  • permanent halocline
  • oxidated surface layers
  • sulphide and iron present
50
Q

Examples of current modern day anoxic basins

A

Basins:
Gotland Deep (baltic sea)
Caspian sea
Cariaco Basin (off Venezuela)

Fjords:
Framvaren (Norway)
Mariager Fjord (Denmark)
Saanich Inlet (Canada)

51
Q

What does Ocean Anoxic Events (OAE) refer to?

A

When large areas of the ocean were anoxic… caused lots of organic matter preservation which led to the formation of black shales

52
Q

Give an example of a sediment what was formed due to Ocean Anoxic Events (OAEs)

A

Slate!

53
Q

What would happen if there were no ocean currents

A

The differing layers in the ocean would not mix and overtime that would lead to anoxic deep waters

54
Q

what is the ideal environment for organic matter preservation?

A

High primary production (carbon fixation)

Shallow water depth (short sedimentation)

anoxic bottom waters

55
Q

Why don’t sapropels form in salt marshes and mangroves

A

There is too much clastic material such as silt and sand for sapropels to form

56
Q

How much primary production gets buried in the oceans?

A

0.1% of primary production

57
Q

Where is 90% of the 0.1% buried organic material in sediments found?

A

Present in shelf and in coastal margins sediments

58
Q

list the approximate proportions of sedimentary organic carbon accumulation in marine environments

A

Deltas - 44%
Shelf and upper slope - 42%
Shallow water carbonate - 4%
High productivity slope - 4%
High productivity pelagic - 3%
Anoxic basin - <1%

59
Q

Under what conditions do soils turn completely anoxic?

A

when soils are completely waterlogged

60
Q

example of terrestrial anoxic conditions

A

Bogs
Marshes
Carrs

61
Q

What is a Carr

A

A waterlogged woodland type terrain with willow and other shrubs present

62
Q

What do soils with no organic content and soils with high organic content indicate?

A

it indicates the soils have low biodiversity and low levels of biologically activity

63
Q

what conditions can organic matter be preserved in soils?

A
  • anoxic conditions (ie bogs, marshes, carrs)
  • acidic conditions (bogs, peat formation)
  • dry soils (Mediterranean climates –> lack of water)
64
Q

The process of organic matter preservation in arid soils (and timeline too)

A

The air and soil humidity for organisms is too low for microorganisms and soil-dwelling microfauna. Organic matter is preserved as no organisms are degrading it

if Wildfires occur, the dead organic matter (ie leaf litter) is remineralised and the biomass is converted into inorganic compounds (ammonia, CO2, phosphate, iron)

This makes the nutrients available, making it a perfect fertiliser for plants and organisms.

But, the organic matter is only preserved in arid soils until the next wildfire occurs

65
Q

At what temperatures is the amount of organic matter in the soil the highest?

A

at low temperatures and at higher temperatures

66
Q

Why do cold temperatures correlate to more organic matter preservation?

A

Microorganisms in the soil are chemical reactors. If the temperature is low, the reactions/processes taking place will occur slower so more organic matter is preserved

67
Q

Why do hot temperatures correlate to more organic matter preservation?

A

In warm conditions, the temperature is impacting the activity of the organisms due to the lack of water. No water = organisms that degrade are inactive so organic matter is preserved

68
Q

Why do cultivated soils have less organic matter than a normal soil?

A

The turnover of soils inbetween planting means that both surface and deeper soils are exposed to oxygen. If oxygen is present, organic matter is degraded

69
Q

What is the decay of organic matter dependent on / increased by?

A

pH, oxygen availability and temperature

anoxic conditions (oxygen diffusion and waterlogged soils)

acidic conditions (low pH will inhibit where soil microorganisms can survive)

dry conditions (water and temperature)

70
Q

Characteristics of Mull humus

A
  • dark brown to black
  • well aerated
  • pH 5.5-6.5
  • typically found in deciduous forests with soils that aren’t too wet (anoxic), too dry and not too acidic
  • organic matter is well mixed with the mineral phase due to animal activity
  • organic matter degradation is relatively efficient and only lignin-derived organic matter remains (but can be degraded over months to years)
71
Q

Characteristics of Mor humus

A
  • black
  • nutrient poor (due to leaching from rainwater)
  • pH 3.5-4.5
  • forms several cm thick layer of hard to degrade plant materials (leaves of conifers with wax-like compounds)
  • low pH = no organisms present

Biogeochem and Ocean Atmos (14 decks)

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