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Related Concept Videos

Inorganic Nitrogen Assimilation01:22

Inorganic 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...
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Overview of Nitrogen Metabolism01:20

Overview 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...
Microbial Mats01:25

Microbial 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...
The Nitrogen Cycle01:49

The Nitrogen Cycle

Nitrogen atoms, present in all proteins and DNA, are recycled between abiotic and biotic components of the ecosystem. However, the primary form of nitrogen on Earth is nitrogen gas, which cannot be used by most animals and plants. Thus, nitrogen gas must first be converted into a usable form by nitrogen-fixing bacteria before it can be cycled through other living organisms. The use of nitrogen-containing fertilizers and animal waste products in human agriculture has greatly influenced the...
The Roles of Bacteria and Fungi in Plant Nutrition02:11

The Roles of Bacteria and Fungi in Plant Nutrition

Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.

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A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities
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Published on: December 25, 2015

Trait-based representation of biological nitrification: model development, testing, and predicted community

Nicholas J Bouskill1, Jinyun Tang, William J Riley

  • 1Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.

Frontiers in Microbiology
|October 23, 2012
PubMed
Summary

Trait-based microbial models like MicroTrait-N predict nitrification rates and nitrous oxide production. Environmental factors such as temperature and pH significantly influence microbial communities and nitrogen cycling processes.

Keywords:
biologicalgeochemistrymathematical modelingmodelsnitrificationnitrogen cycle

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Measurement of the Potential Rates of Dissimilatory Nitrate Reduction to Ammonium Based on 14NH4+/15NH4+ Analyses via Sequential Conversion to N2O
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Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

Area of Science:

  • Microbial ecology
  • Biogeochemistry
  • Computational biology

Background:

  • Trait-based microbial models offer a promising approach to understanding microbial diversity and activity across ecosystems.
  • These models use specific traits to represent organism fitness in different environments, capturing complexity across scales.

Purpose of the Study:

  • Introduce MicroTrait-N, a microbial community trait-based modeling framework for nitrification.
  • Represent ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB) using key traits.
  • Predict nitrifier diversity, ammonia oxidation rates, and nitrous oxide production under varying environmental conditions.

Main Methods:

  • Developed the MicroTrait-N model incorporating enzyme kinetics and physiological traits for AOB, AOA, and NOB.
  • Simulated microbial community responses across gradients of pH, temperature, and substrate availability.
  • Validated the model against field data from Alaska, assessing ammonia oxidation rates and AOA:AOB biomass ratios.

Main Results:

  • Nitrifier diversity was primarily driven by temperature and substrate availability, with pH influencing substrate levels.
  • Transient nitrous oxide (N(2)O) production peaked when AOB and NOB communities were uncoupled.
  • Cumulative N(2)O production over longer periods was maximized when AOB and NOB interactions were maintained, as uncoupling led to AOB instability and reduced activity.

Conclusions:

  • A limited set of traits can sufficiently characterize nitrifying community structure and function.
  • Climate and edaphic changes may alter nitrification rates in ways not currently accounted for by existing biogeochemical models.
  • The MicroTrait-N model accurately simulates ammonia oxidation and AOA:AOB ratios, demonstrating its utility in predicting microbial responses to environmental change.