Lectures 9 & 10 - Nitrogen Cycles I & II

Reduced Nitrogen

Dominant in anoxic water. Oxidized N is used up as a resource.

Oxidized Nitrogen

Dominant in Oxic water. Reduced N is used up as a resource.

N2 is the dominant form. Why?

It is the largest reservoir of nitrogen. Builds up due to large activation state caused by a triple bond. It lacks a dipole as well. Most of it is atmospheric or aqueous. It can be found in sediments as well. These reservoirs have very slow turnover times. Surface soil, marine biomass, and dissolved inorganic nitrogen have faster turnover times.

Anthropogenic effects on the N cycle

Fertilizer runoff introduces more N into bodies of water. This creates an excess of dissolved inorganic nitrogen. Bacteria respire more often and deplete oxygen. An anoxic environment is created (Eutrophication). This kills animals and other organisms that cannot handle the hypoxic conditions. Toxic algal blooms can also occur. Acid rain. N2O greenhouse gas depleting the ozone layer.

Understand the N and C cycle flowcharts and steps

N-cycle overview

Assimilatory Processes: 1. N2 fixation (oxic or anoxic environment), . 2. NH3, NO3- assimilation. Waste Processes: 3. Ammonification. Deaminase proteins remove amine. (occurs in oxic or anoxic environment). Dissimilatory Processes: 4. Chemolithotrophic processes - Nitrification. 5. Anammox: NH3 oxidation with NO2- as e- acceptor. Anaerobic Respiratory Processes: 6. Nitrate reduction. NO3- to NO2-, NO, N2O, N2, or NH3

N-Fixing Microorganisms

Diazotrophs. They include a variety of BAC and ARC.

N-Fixing by Diazotrophs

Nitrogenase and Nitrogenase reductase. 6e- and ~24 ATP per N2 reduced. Reduction takes place at FeMo cofactor in nitrogenase, which is O2 sensitive.

15N2 Assimilation

Incorporation for the 15N stable isotope into biomass. Better but requires isotope ratio Mass spectrometer.

Acetylene Reduction

C2H2 triple bond. Accidental reduction by dinitrogenase produces ethylene. Measured by gas chromatography-flame detection. (GC-FID)

Free-living Diazotrophs

Includes Chemoorganotrophs, chemolithoautotrophs, photoautotrophs, and photoheterotrophs. Some fix N at night. Aerobes have ways to protect nitrogenase enzyme. Heterocysts are used in Anabena. Slime layers are used in Azotobacter. Azo- typically used for N-Fixing Bacteria.

Symbiotic Diazotrophs

Mostly symbiotic with plant root nodules, very specific symbiosis. This allows plants to live in low Nitrogen environments. These pioneer species live in disturbed soils and naturally N-poor soils. Lupine. “Rhizobia” typically reserved for symbionts.

Sharing Carbon and Nitrogen

Bacterioids are a differentiated form of rhizobia that form within the root nodules. Plant tissues: fix CO2, produce O2. Organic acids transported to bacterioid. Bacterioid: Fix N using the energy from the organic acids. The fixed N is exported as glutamine and asparagine. The bacterioid is protected from O2 by leghemoglobin.

Nitrification 1st step

Chemolithotrophic Ammonia Oxidation: Aerobic process with NH3 as e- donor. Slower process, so nitrite does not build up

Nitrification 2nd step

Chemolithotrophic Nitrite Oxidation: Aerobic process with NO2- as e- donor. Much faster process than 1st step.

Ammonia-oxidizing BAC: Oxidation of ammonia to hydroxylamine

Ammonia monooxygenase (AmoA, B, and C) One atom of oxygen from O2 is incorporated using electrons from hydroxylamine oxidation. Oxygen is a reactant, not just TEA

Ammonia-oxidizing BAC: Oxidation of hydroxylamine to nitrite

Hydroxylamine oxidized by hydroxylamin oxidoreductase to nitrite. 2 e- used to activate ammonia oxidation and another 2 e- are used for e- transport.

Ammonia Oxidizing Bacteria

A few genera have classes of proteobacteria (Nitroso-). Autotrophic via Calvin cycle. Biomarker is amoA gene/transcript

Ammonia-Oxidizing Arachaea

dominant ammonia-oxidizing organisms in almost all environments. Detailed mechanism of ammonia oxidation not known. Biomarker is amoA (distinct from AOB gene) and special lipid called crenarchaeol.

Nitrogen-Oxidizing BAC

use nitrite oxidoreductase to reduce nitrite to nitrate each step.

Acetylene Block

C2H2 buildup inhibits nitrous oxidase reductase

Anammox

Chemolithic anaerobic ammonia oxidation. Ladderine lipid biomarker and 16S rRNA gene.