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Environmental microbiology
Mar, 2025;27 (3): e70060.

Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain.

Anna N Rasmussen, Bradley B Tolar, John R Bargar, Kristin Boye, Christopher A Francis
Author Information
  1. Anna N Rasmussen: Department of Earth System Science, Stanford University, Stanford, California, USA.
  2. Bradley B Tolar: Department of Earth System Science, Stanford University, Stanford, California, USA. ORCID
  3. John R Bargar: Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
  4. Kristin Boye: Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
  5. Christopher A Francis: Department of Earth System Science, Stanford University, Stanford, California, USA. ORCID
PMID: 40103293 DOI: 10.1111/1462-2920.70060

Abstract

Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

Keywords

ammonia���oxidising archaea comammox floodplain metagenome���assembled genome (MAG) nitrification river sediment

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Grants

  1. DE- AC02-76SF00515/SLAC Accelerator Laboratory, U.S. Department of Energy, Biological and Environmental Research
  2. /Watershed Function Science Focus Area

MeSH Term

Archaea
Bacteria
Geologic Sediments
Nitrification
Metagenome
Ammonia
Phylogeny
Rivers
Oxidation-Reduction
Nitrites
Genome, Bacterial

Chemicals

Ammonia
Nitrites
Journal Article
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Word Cloud

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