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Overview of Nitrogen Metabolism01:20

Overview of Nitrogen Metabolism

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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...
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Inorganic Nitrogen Assimilation01:22

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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...
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Overview of Metabolism01:40

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Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
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The Nitrogen Cycle01:49

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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...
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The Roles of Bacteria and Fungi in Plant Nutrition02:11

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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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Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources
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DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.

Julian Damashek1, Cody S Sheik2,3, Caitlin Petro4

  • 1Department of Biology, Hamilton College, Clinton, New York, USA.

Microbiology Resource Announcements
|September 30, 2025
PubMed
Summary

Microbial nitrogen fixation is vital for ecosystems. The DiazoTIME database provides a unique resource for classifying nitrogen-fixing bacteria (diazotrophs) by both their taxonomic identity and metabolic functions.

Keywords:
biogeochemistrydiazotrophsgenomicsmetabolismmicrobial ecologynitrogen cycle enzymesnitrogen fixation

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Area of Science:

  • Microbiology
  • Ecology
  • Genomics

Background:

  • Microbial nitrogen fixation (diazotrophy) is a fundamental ecological process essential for nutrient cycling.
  • Understanding the diversity and metabolic capabilities of diazotrophs is crucial for ecological and agricultural applications.

Purpose of the Study:

  • To curate and present a comprehensive database of diazotroph genomes.
  • To provide detailed taxonomic annotation and metabolic predictions for diazotrophs.
  • To create a unique resource that resolves both taxonomy and metabolic functionality for diazotroph classification.

Main Methods:

  • Genome data curation for known and potential diazotrophs.
  • Bioinformatic analysis for taxonomic annotation.
  • Metabolic pathway prediction using computational tools.

Main Results:

  • Development of DiazoTIME, a comprehensive database of diazotroph genomes.
  • Inclusion of detailed taxonomic classifications for each organism.
  • Prediction of metabolic capabilities, including nitrogen fixation pathways.

Conclusions:

  • DiazoTIME offers a unique, integrated resource for studying diazotrophs.
  • The database facilitates research into the ecological roles and evolutionary history of nitrogen fixation.
  • This resource will advance our understanding of microbial contributions to global nitrogen cycling.