Nitrogen mineralization and assimilation at millimeter scales
David D Myrold1, Jennifer Pett-Ridge, Peter J Bottomley
1Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, USA.
Methods in Enzymology
|April 26, 2011
Summary
Microbial nitrogen (N) cycling involves N uptake and ammonium production. This review explores methods to measure these processes within soil microhabitats, crucial for understanding soil N dynamics.
Area of Science:
- Microbial ecology
- Soil science
- Biogeochemistry
Background:
- Microbial nitrogen (N) assimilation and ammonium production are key processes.
- These processes are regulated by microbial N and carbon (C) demands.
- Bulk measurements mask microhabitat variations in soil N cycling.
Purpose of the Study:
- To review methods for measuring N mineralization and immobilization at soil microhabitat scales.
- To highlight techniques applicable from micrometer to millimeter scales.
Main Methods:
- Adaptations of (15)N isotope pool dilution.
- Isotope Ratio Mass Spectrometry (IRMS).
- Secondary Ion Mass Spectrometry (SIMS).
Main Results:
- Specific methodologies allow for microhabitat-level analysis of N cycling.
- These techniques overcome limitations of bulk measurements.
- Provides a framework for studying spatial heterogeneity in soil N transformations.
Conclusions:
- Advanced isotopic techniques enable precise measurement of microscale N cycling.
- Understanding microhabitat N dynamics is essential for soil N budgets.
- This review facilitates research into the spatial variability of microbial N transformations in soils.
Related Concept Videos
01:22Inorganic Nitrogen Assimilation
Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme nitrate reductase...
01:25Microbial Mats
Microbial communities forming biofilms and mats represent complex, spatially structured ecosystems where metabolic processes are stratified according to light, oxygen, and nutrient gradients. Biofilms are initial colonization stages, only a few millimeters thick, while mature microbial mats can reach centimeter-scale thickness and display intricate vertical organization. Their structural and functional heterogeneity allows microorganisms to occupy distinct ecological niches within a few...
01:26Microbes and the Nitrogen Cycle
The nitrogen cycle is a complex biogeochemical process critical to maintaining the balance of nitrogenous compounds in ecosystems. This cycle involves multiple microbial-mediated transformations through which nitrogen changes oxidation states, supporting essential ecological functions and contributing to plant and microbial growth.Nitrogen Fixation and AmmonificationNitrogen fixation initiates the cycle by converting inert atmospheric nitrogen (N₂) into bioavailable ammonia (NH₃), a process...
01:20Overview of Nitrogen Metabolism
Nitrogen is a very important element for life because it is a major constituent of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds and stored in the form of ammonia, ammonium ions, nitrate, nitrite, or nitrogen gas by many metabolic processes. Many of these metabolic processes are carried out only by prokaryotes.
The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N2) from the air, but this nitrogen...
The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N2) from the air, but this nitrogen...
01:20Sulfur Assimilation
Sulfur is an essential element in biological systems, contributing to synthesizing key biomolecules, including amino acids such as cysteine and methionine, and cofactors such as coenzyme A and biotin. Microorganisms primarily assimilate sulfur as sulfate (SO₄²⁻) from the environment, which must undergo a series of biochemical transformations before it can be incorporated into cellular components. As sulfate is highly oxidized, it must undergo assimilatory sulfate reduction to become...
01:15Metabolism of Chemolithotrophs
Chemolithotrophs are microorganisms that obtain energy by oxidizing inorganic molecules such as hydrogen gas (H₂), ammonia (NH₃), reduced sulfur compounds (H₂S, S²⁻), and ferrous iron (Fe²⁺). Unlike heterotrophic organisms that rely on organic carbon, chemolithotrophs transfer electrons from these inorganic donors to the electron transport chain (ETC), generating a proton motive force (PMF) that drives ATP synthesis through oxidative phosphorylation. However, because inorganic electron donors...