Lecture 24: Nitrogen Cycle

Question 1

Why do we study the nitrogen cycle?

Answer 1

1. Nitrogen is essential to all life
2. Large impacts on the environment
3. Large nitrogen reserves are inert
   (‘hidden’), small ones are actively
   recycled (air; 80% N2)

Question 2

What are the different forms of nitrogen

Answer 2

1. Based on oxidation states

2. Forms are transformed by microbes

Question 3

What are the steps of the nitrogen cycle?

Answer 3

1. di-nitrogen (N2) in the atmosphere
2. N-fixation via microbes to organic N in soil
3. This can the be mineralised by microbes
   to ammonia (NH3)
4. Ammonia can undergo nitrification
   from NH3 to NO2- (nitrite) to NO3-
   (nitrate)
5. Nitrate can be reduced via
   denitrification to NO2-, to NO, to
   N2O, back to N2 in the atmosphere
6. “Anammox” (anaerobic ammonia
   oxidation) also occurs, where NO2- and
   NH3 is converted directly back to N2

Question 4

what is the relevance of nitrogen to plants and agriculture?

Answer 4

1. Both ammonia (NH3) and nitrate
   (NO3-) can be up-taken by plants
2. Big challenge in agriculture
3. For good crop yields, fertilizers provide
   additional NH3 and NO3-
4. NO3- (nitrate) can leak into oceans/rivers
   via “leaching”, which is bad for aquatic
   ecosystems
5. N2O (nitrous oxide) is a powerful green
   house gas (300x more than CO2, so
   if isn’t restored to N2 can be harmful
   a. can be prod from denitrification and
   nitrification

Question 5

What is leaching?

Answer 5

1. Nitrate (NO3-) is very mobile in soil so
   can leak into nearby rivers/oceans via a
   process called “leaching”
2. Bad for aquatic ecosystems

Question 6

What is nitrogen fixation?

Answer 6

1. Done in two ways:
   a. Biological
   b. Anthropogenic (industrial)
2. Only process where atmospheric N2 is
   incorporated into biological matter
3. Two different types of organisms able to
   carry out this process:
   a. Free living
   b. Symbiotic

Question 7

What are symbiotic nitrogen fixators?

Answer 7

1. Rhizobium - root nodules of plants

2. Cyanobacteria - lichen

Question 8

What are free living nitrogen fixators?

Answer 8

1. Cyanobacteria

2. Azotobacter

Question 9

What is the key enzyme in nitrogen fixation? BIOLOGICALLY

Answer 9

1. Nitrogenase (nif): catalyses conversion of
   N2 into NH3
   a. N2 + 3H2 -> 2NH3 -> AAs -> proteins
2. V. energy-costly: triple bond of N2 hard
   to break
3. Tightly regulated
4. Oxygen sensitive

Question 10

How is nitrogen fixed industrially?

Answer 10

1. “Haber-Bosch process”
   a. how N fertilisers are made
2. Req. temps of 300-500C & pressures of
   150-250 bars
3. ~50% of worlds human population would
   not exist without this process

Question 11

What happens after nitrogen is fixed and is now bio available for other organisms?

Answer 11

"Mineralisation" 
   a. Organic N to NH3 (ammonia)
   b. Makes it available for plants and 
       microbes
   c. a lot less specialized; done by many 
       plants and microbes

Question 12

What is nitrification?

Answer 12

Ammonia to NO2- (nitrite) to NO3- (nitrate)

1. Important for fertiliser loss because NO3- 
    isn't stable in soil so can be lost
2. Two steps:
   a. NH3 -> NO2-
      i. carried out by AMO (ammonia 
         oxidisers)
      ii. e.g., Nitrosomonas 
   b. NO2- -> NO3-
      i. carried out by nitrite oxidisers
      ii. e.g., Nitrobacter

3. Can lead to leaching; causing 
    eutrophication/environmental 
    pollution
4. Produces NO and N2O which are 
    climate active gases
5. Enzymes involved require:
   a. O2 as an e- acceptor
   b. CO2 as carbon source
   c. NH3 & NO2- as e- donors

Question 13

What are ammonia oxidising bacteria?

Answer 13

1. First discovered by Grace Frankland and
   isolated by Sergei Winogradsky
2. Low cell densities and growth rates -
   difficult to study
3. Typical soil AOB (nitrosospira and
   nitrosomonas) belong to beta-
   proteobacteria, typical marine AOB
   (nitrosococcus) to gamma-proteobacteria

Question 14

What are AOA and what was their significance?

Answer 14

1. AOA = Ammonia oxidising archaea
2. Soil fosmid 54d9 contained 16S and 23S
   ribosomal subunits, enabling
   identification of the fosmid as an
   archaeon
3. amoA and amoB encode for subunits
   of “ammonia monooxygenase” - a key
   enzyme in the global nitrogen cycle
4. Some ammonia oxidiser can also use
   urea and cyanate as substrates
5. Significance? A WHOLE DIFFEERNT
   DOMAIN OF LIFE!
6. AOA can nitrify in conditions where AOB
   struggle (acidic soils, open ocean) -
   THEIR NICHE
   a. N. devanaterra

Question 15

What is comammox?

Answer 15

1. Stands for “complete ammonia oxidation
   into nitrate”
2. Single organism that can do both
   ammonia and nitrite oxidation
3. Nitrospira sp. - nitrite oxidiser which
   acquired ammonia oxidation genes via
   horizontal gene transfer

Question 16

What is anammox?

Answer 16

1. stands for "anaerobic ammonium 
   oxidation"
2. especially significant to N turnover in 
    ocean and is large single source of 
    dinitrogen gas on earth
3. Chemolithoautotrophic bacteria use 
    NH4+ as e- donor and NO2- as acceptor
4. Uses "ladderane" membrane lipids that 
    form acellular "anammoxosome" 
    organelle
   a. site of membrane-bound enzyme 
       combining nitrite and ammonia to N2. 
        Hydrazine is an intermediate
5. New low-cost method for N-removal in wastewater treatment 
6. at least 3 genera of bacteria:
   a. Brocadia
   b. Kuenenia 
   c. Scalindua
7. Process patented:
NH4+ + NO2- -> N2 + 2H2O

Question 17

What is denitrification?

Answer 17

1. Diverse; carried out by all three domains of life
2. sequential formation of N2
3. anaerobic
4. Nitrogen is the electron acceptors -
   essentially like our oxygen in respiration
   a. lots of organisms can switch between
   the two for energy
5. Performed primarily by heterotrophic bacteria. E.g.,
   a. Paracoccus denitrificans
   b. various pseudomonads
6. Some autrophic found:
   a. Thiobacillus denitrificans
7. nirS and nirK encode nitrite reductase
   (key marker gene for population
   studies)
   a. never present together

Question 18

What is the role of denitrification in agriculture and waste water treatment

Answer 18

1. agriculture: remove nitrogen from field (BAD THING)

2. Wastewater treatment: removes nitrogen from system. Prevents eutrophication of receiving waters

Question 19

What is the importance of the nitrogen cycle to climate change?

Answer 19

1. N2O and NO crucial to troposphere
   a. N2O powerful greenhouse gas in
   lower atmosphere
   b. NO reacts in lower atmosphere and
   produces NO2 (nitrogen dioxide)
2. Prod. is result of different processes:
   a. Denitrification
   b. Nitrification

Question 20

How can we ensure the nitrogen cycle doesnt impede on climate change?

Answer 20

1. Sustainable intensification of food 
   production
2. Improving soil N use efficiency
   a. slow release fertilisers
   b. Commercial nitrification inhibitors (e.g., 
       DCD, nitrapyrin)
   c. Demand driven fertilisation