Biogeochem - Chapter 8 & 9: Oxygen cycling and Metabolic Diversity Flashcards
list the 2 major reactions in the oxygen cycle
oxygenic photosynthesis
aerobic respiration (organo- or lithotroph)
what can consume oxygen
- biological activities
- spontaneous chemical reactions (wildfires)
how is oxygen a good indicator of sediment microbial community activities?
Higher activity means the oxygen is consumed faster, meaning it won’t penetrate/diffuse into the sediment as deep
does oxygen penetrate deeper in nutrient rich or oligotrophic bodies of water
in oligotrophic bodies of water
What impact does no oxygen depletion have on other nutrients?
If oxygen is not depleted (indicator of no biological activity), nitrate is not used. Because there is no oxidation of organic matter, no CO2 is produced and therefore bicarbonate can be produced.
What is bioturbation?
The displacement and mixing of sediment particles by benthic fauna
(common by larger organisms looking for prey in the sediment, eg manatees)
What is bioirrigation?
the process of benthic organisms flushing their burrows with overlying oxygen rich water
Name a benthic ogrnaisms that bioirrigates.
State what characteristics / nutrient profiles appear in this process
lugworm
You can get the same zonation (aerobic to methanogenic) in the wall of the burrows.
an oxic layer forms around the burrow
where does bioirrigation most commonly occur?
It occurs in particularly nutrient-rich sediments
does lots of organisms bioirrigating impacts the sediment oxygen uptake?
14,000 lugworms (tubifex tubifex) per square meter would be required to impacts the oxygen uptake in sediments
how do ripples impact the solute exchange process across the sediment-water interface?
- flow of waves over a sediment mound/ripple causes pressure on the wave-ward side, pushing water into the sediment. This increases the O2 conc in the sediment
- on the leeward side of the mound, the increase in pressure ‘pulls’ the anoxic pore water out of the sediment. The water reaches the surface, characterised by the darker sediment colour caused by higher concentrations of iron sulphide (FeS)
- if balanced, the oxygen content in the sediment increases significantly
- the anoxic water is now rich in phosphate and iron which aren’t available in oxic conditions
- this impacts the nutrient balance in the water and on the mudflat
What biogeochemically important reactions are driven only by prokaryotes?
nitrogen fixation
sulphate reduction
methanogenesis
cellulose degradation
What is the most crucial energy requirement?
maintenance energy
What organisms use light as their energy source (+ examples)
Phototrophs
- photosynthesis
eg cyanobacteria, algae, plants, anoxygenic phototrophs
What organisms use chemical reactions as their energy source (+ examples)
Chemotrophs
- respiration and fermentation
eg bacteria, archaea, protists, fungi, animals
What different storage compounds to chemotrophs use?
(long term and short term)
short term: ATP
Long term: Lipids, Starch, polyhydroxalkanoates
What organisms use organic material as their electron donors (food)
+ examples
organotrophs
bacteria, archaea, protists, fungi, animals
What organisms use inorganic material as their electron donors (food)
+ examples)
Lithotrophs
eg bacteria, archaea, algae, cyanobacteria
what organisms use an organic material carbon source for growth?
+ examples
Heterotrophs
bacteria, archaea, fungi, animals
what organisms use inorganic material as a carbon source for growth?
+ examples
Autotrophs
bacteria, archae, algae, cyanobacteria
How much energy is required for autotrophic processes
Per molecule of CO2, at least 18 ATP have to be spent.
Why are autotrophic processes the most important in ecosystems?
They convert inorganic carbon CO2 into organic material and biomass. this forms the basis of life for heterotrophic organisms
What are the 3 main metabolic types of microorganisms?
Photolithoautotrophs
Chemoorganoheterotrophs
Chemolithoautotrophs
What do photolithoautotrophs do?
Use light as energy source
Use water or H2S as an electron donor (inorganic electron donor)
Carbon source is CO2
examples
- Cyanobacterium
- Planktonic green algae
- Higher plants
What do chemoorganoheterotrophs do?
- Depend on the oxidation of electron donors as an energy source
- Electron donor is organic maters
- Carbon source is organic material (ie humans)
examples
- aerob or fermenting
- sulphate reducers
- strictly aerobic (humans)
What do chemolithoautotrophs do?
- Energy source is from oxidation of electron donors
- Use the ammonium (NH3), Fe2+, H2S, H2 as electron donors
- Carbon source is from CO2
examples
- thiobacillus novellus (e- donor: H2S)
- Nitrosomonas europaea (e- donor: NH3)
- Acidithiobacillus ferrooxidans (e- donor: Fe2+)
Why are lithotrophs important?
They close biogeochemical cycles
Whats the difference between lithotrophs and organotrophs?
Lithotrophs
- energy source is from inorganic compounds (ie ammonia, minerals or hydrogen gas)
eg hydrogen-sulphide oxidising bacteria
Organotrophs
- energy source is from organic compounds (ie sugars, proteins or fats)
eg most animals, fungi and bacteria
Explain the interation between the lithotrophic organisms and chemolithoautotrophs
- In anoxic layers, fermentation is the first process that occurs
- fermenters convert the organic matter into fermentation products
- sulphate reducers use the fermentation products and oxidise them into CO2
- The electrons are transferred to sulphate (SO42-) which are then converted to H2S
- H2S gets reoxidised (as its toxic)
difference between chemolithotrophs and chemoorganotrophs
chemolithotrophs use inorganic compounds (hydrogen gas, ammonia or ferrous iron) for energy and carbon dioxide for carbon
while chemoorganotrophs use organic compounds (ie sugars, protein and lipids) for both energy and carbon.
What environment does nitrogen assimilation occur in?
anoxic environments
When does nitrogen fixation occur?
if there is no ammonium present (occurs in an oxic environment)
what happens if ammonium is available
Organisms will directly assimilate (take it in) NH4+
What is the enzyme responsible for nitrogen fixation?
nitrogenase
what conditions does nitrogenase operate in?
only under anoxic conditions
What are heterocysts and what do they do?
They are thick-walled cells in cyanobacteria what protect the nitrogenase from being exposed to oxic conditions
Examples of symbiotic nitrogen fixing bacteria
Rhizobium (in Leguminosae)
- eg clover
Frankia (in trees)
- buckthorn and alder
Examples of nitrogen fixing cyanobacteria
- Anabaena
- Azolla
- Gunnera
How was fertiliser created?
Haber and Bosh applied high pressures and temperatures to drive the ammonium reaction to create fertiliser
3H2 + N2 –> 2NH3
What is nitrate reduction
the uptake of nitrate and its reduction to ammonium
What are the 2 steps in nitrate reduction?
Step 1:
reduction of nitrate to nitrite (redox state of -V to -III)
Step 2:
reduction of the nitrite, 2 possibilities:
- nitrite gets reduced to N2, (denitrification)
- nitrite is reduced to NH4+, (nitrate ammonification)
is nitrate consumed in anoxic environments?
Yes. However, if O2 is present, nitrate wont be touched
What is a by product of the reduction of Nitrite?
N2O - Laughing gas
–> it is an efficient greenhouse gas
What is a main source of laughing gas in the atmosphere?
comes from the microflora of earthworm guts
What is nitrification and what organisms does it involve?
The aerobic oxidation of ammonium to nitrate (via nitrite)
involves 2 different chemolithotrophic organisms
What does the degradation of biomass lead to (in terms of the quantity of a substance released)
Larger amounts of ammonium are released which are toxins for fish but ‘fertiliser’ for phytoplankton…
What is the first step in nitrification?
The oxidation of ammonium to nitrite
What bacteria does the first step in nitrification
Nitroso- bacteria
eg Nitrosomonas europaea
What bacteria does the second step in nitrification?
Nitro-bacteria
eg Nitrobacter winogradskyi
What is the most abundant nitrogen-containing compound formed during the degradation of organic matter?
Urea
At sewage treatment plants, why do the bacteria oxidise the urea (ammonium)
because it is toxic to fish
How does the process of nitrification and denitrification work at sewage treatment plants?
Activated sludge (sewage that has been aerated). This is where nitrification happens and ammonium can be converted to nitrite and into nitrate.
Denitrification converts the nitrate into nitrogen (a form that is biologically inert). By removing the excess nitrogen, it can prevent eutrophication
under what conditions does denitrification occur?
Anoxic conditions
How do anoxic conditions (to allow denitrification) occur
The aeration would be switched off in fixed intervals to make the sludge anoxic, enabling denitrification to occur.
what is ANAMMOX?
Anaerobic ammonium oxidation
what does annamox involve?
a one stage process using nitrite as an electron acceptor
disadvantage of Anammox bacteria
they grow very slowly which makes them too slow to use them in wastewater treatment plants
Why has anammox been discovered in stratified water bodies and sediments?
As it requires nitrite or nitrate, it usually occurs in chemoclines (the transition from oxic-anoxic environments) where either nitrite or nitrate are present.
The production of nitrite or nitrate from ammonium requires elemental oxygen, but has to occur in anoxic environments so it is found near the oxic zone.
What dominates in coastal sediments and what dominates in deep-sea sediments, denitrification or anammox? and why?
In coastal sediments, the higher input of organic matter supports denitrification, outcompeting the anammox bacteria
In deep-sea sediments, the lower input of organic matter leaves more nitrate/nitrite left over which can be used by anammox bacteria. Denitrification needs organic matter and as theres less in deep-sea sediments, anammox bacteria dominate.
why is there a constant supply of biomass into the water column?
Algae has a lifespan of 1 week resulting in a constant input of biomass
what does the burial/sedimentation of nitrogen refer to?
the burial of nitrogen thats bound in complex organic matter (eg chitin, plant residues and kerogen)
