Exam 1: Nitrogen cycle
The nitrogen cycle is the flow of organic and inorganic nitrogen within an ecosystem where there is an interchange between nitrogenous compounds and atmospheric nitrogen.
Living organisms need nitrogen to make amino acids, proteins and nucleic acids. Plants and animals are unable to use nitrogen gas as it is chemically inert (very stable with N2 gas molecules each having three covalent bonds). Instead plants take in nitrates (NO3- ions) in solution through their roots. The organic nitrogen compounds produced by plants (such as nucleic acids e.g. DNA and RNA as well as amino acids and proteins) are transferred through the food chain when primary consumers eat plants (e.g. herbivores). The primary consumers themselves are eaten by secondary consumers and the organic nitrogen is assimilated by the secondary consumer into its own organic nitrogen molecules such as DNA and proteins. When plants and animals both die the mineral and organic nitrogen locked in their bodies, together with the excretory products of animals such as urea, must be decomposed in order to release the minerals back into the soil. Bacteria are the key organisms involved in the process. The main processes involved are as follows:
1. Nitrogen fixation
Atmospheric nitrogen can be converted directly into nitrogen compounds by nitrogen fixing bacteria. Free-living nitrogen fixing bacteria (that are found free-living in the soil rather than on the root nodules of legumes) include Azotobacter. These account for most of the nitrogen fixation. Inside the Azotobacter bacteria are nitrogenase enzymes that fix the atmospheric nitrogen gas (N2) into ammonia or ammonium ions (NH3/NH4+) which are released into the soil where they dissolve in the soil water.
There are also symbiotic nitrogen fixing bacteria, Rhizobium, found in the root nodules of legume plants (peas, beans and clover). The Rhizobium bacteria penetrate the root hairs of the plant cells and form colonies within a root nodule. Here they fix atmospheric nitrogen gas (N2) into ammonia (NH3) which is absorbed into the vascular tissue of the root and transported away to the rest of the legume plant. The legume plant produces sugar (e. glucose) by photosynthesis, which the Rhizobium bacteria absorb and then respire to release energy. The bacteria also get a protective environment in which to replicate. This is termed a mutualistic relationship.
The enzyme in the Rhizobium that fixes N2 gas into NH3 is called nitrogenase. This enzyme is susceptible to high levels of oxygen (i.e. high O2 levels may inactivate nitrogenase). For this reason, the legume plant synthesises the protein haemoglobin which, when in the root nodule, can bind O2 preventing levels getting too high and therefore allowing nitrogenase to work efficiently. The presence of haemoglobin gives the root nodule a pink colour (see picture below).
The free-living Azotobacter do not have any haemoglobin, instead thy have a very high rate of metabolism (aerobic respiration) meaning oxygen is used up quickly, thus preventing oxygen from accumulating inside the bacterium and so ensuring nitrogenase can work effectively.
2. Putrefaction
Bacteria and fungi can decompose dead plants, dead animals, faeces and urine turning these organic nitrogen-compounds into ammonium ions (NH4+) which are released into the soil and dissolve in the soil water. This process is also called "ammonification".
3. Nitrification
The ammonia (NH3) or ammonium ions (NH4+) formed in putrefaction is converted by a process called nitrification first to nitrite ions (NO32-) and then to nitrate ions (NO3-). Various bacteria are involved. For example, ammonia/ammonium ions are converted to nitrite ions first by Nitrosomonas and the nitrite ions are converted to nitrate ions by Nitrobacter. These bacteria require aerobic conditions (the O2 gas from the atmosphere must be able to circulate in between the soil particles).
4. De-nitrification
Nitrogen is lost from ecosystems by denitrification. This is a particular problem in waterlogged soils with anaerobic conditions (lacking O2) where anaerobic bacteria, such as Pseudomonas, can reduce nitrates (NO3- ions) in the soil back to nitrogen gas (N2).
The nitrogen cycle is the flow of organic and inorganic nitrogen within an ecosystem where there is an interchange between nitrogenous compounds and atmospheric nitrogen.
Living organisms need nitrogen to make amino acids, proteins and nucleic acids. Plants and animals are unable to use nitrogen gas as it is chemically inert (very stable with N2 gas molecules each having three covalent bonds). Instead plants take in nitrates (NO3- ions) in solution through their roots. The organic nitrogen compounds produced by plants (such as nucleic acids e.g. DNA and RNA as well as amino acids and proteins) are transferred through the food chain when primary consumers eat plants (e.g. herbivores). The primary consumers themselves are eaten by secondary consumers and the organic nitrogen is assimilated by the secondary consumer into its own organic nitrogen molecules such as DNA and proteins. When plants and animals both die the mineral and organic nitrogen locked in their bodies, together with the excretory products of animals such as urea, must be decomposed in order to release the minerals back into the soil. Bacteria are the key organisms involved in the process. The main processes involved are as follows:
1. Nitrogen fixation
Atmospheric nitrogen can be converted directly into nitrogen compounds by nitrogen fixing bacteria. Free-living nitrogen fixing bacteria (that are found free-living in the soil rather than on the root nodules of legumes) include Azotobacter. These account for most of the nitrogen fixation. Inside the Azotobacter bacteria are nitrogenase enzymes that fix the atmospheric nitrogen gas (N2) into ammonia or ammonium ions (NH3/NH4+) which are released into the soil where they dissolve in the soil water.
There are also symbiotic nitrogen fixing bacteria, Rhizobium, found in the root nodules of legume plants (peas, beans and clover). The Rhizobium bacteria penetrate the root hairs of the plant cells and form colonies within a root nodule. Here they fix atmospheric nitrogen gas (N2) into ammonia (NH3) which is absorbed into the vascular tissue of the root and transported away to the rest of the legume plant. The legume plant produces sugar (e. glucose) by photosynthesis, which the Rhizobium bacteria absorb and then respire to release energy. The bacteria also get a protective environment in which to replicate. This is termed a mutualistic relationship.
The enzyme in the Rhizobium that fixes N2 gas into NH3 is called nitrogenase. This enzyme is susceptible to high levels of oxygen (i.e. high O2 levels may inactivate nitrogenase). For this reason, the legume plant synthesises the protein haemoglobin which, when in the root nodule, can bind O2 preventing levels getting too high and therefore allowing nitrogenase to work efficiently. The presence of haemoglobin gives the root nodule a pink colour (see picture below).
The free-living Azotobacter do not have any haemoglobin, instead thy have a very high rate of metabolism (aerobic respiration) meaning oxygen is used up quickly, thus preventing oxygen from accumulating inside the bacterium and so ensuring nitrogenase can work effectively.
2. Putrefaction
Bacteria and fungi can decompose dead plants, dead animals, faeces and urine turning these organic nitrogen-compounds into ammonium ions (NH4+) which are released into the soil and dissolve in the soil water. This process is also called "ammonification".
3. Nitrification
The ammonia (NH3) or ammonium ions (NH4+) formed in putrefaction is converted by a process called nitrification first to nitrite ions (NO32-) and then to nitrate ions (NO3-). Various bacteria are involved. For example, ammonia/ammonium ions are converted to nitrite ions first by Nitrosomonas and the nitrite ions are converted to nitrate ions by Nitrobacter. These bacteria require aerobic conditions (the O2 gas from the atmosphere must be able to circulate in between the soil particles).
4. De-nitrification
Nitrogen is lost from ecosystems by denitrification. This is a particular problem in waterlogged soils with anaerobic conditions (lacking O2) where anaerobic bacteria, such as Pseudomonas, can reduce nitrates (NO3- ions) in the soil back to nitrogen gas (N2).
The root nodules
Root nodules on the roots of legume plants (top left and top right). The root nodule in the top left picture has been cut open to show the Rhizobium bacteria inside. These bacteria fix atmospheric nitrogen into ammonia/ammonium ions which is absorbed into the xylem vessels of the plant from the nodule. The rhizobium bacteria gain sugars from the plant for respiration. This is a mutualistic relationship. The diagram on the bottom shows how the rhizobia bacteria infect and eventually form root nodules in legume plants. The root nodules appear pink because the legume plant produces haemoglobin which binds oxygen thus preventing nitrogenase enzyme from being exposed to high O2 levels (which would reduce its effectiveness in fixing N2 gas into NH3).