Metagenome‐Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Rasmussen, Anna N.; Tolar, Bradley B.; Bargar, John R.; Boye, Kristin; Francis, Christopher A.

doi:10.1111/1462-2920.70060

Metagenome‐Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Journal Article · Tue Mar 18 00:00:00 EDT 2025 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.70060· OSTI ID:2575492

Rasmussen, Anna N. ^[1]; ^[2]; Bargar, John R. ^[3]; Boye, Kristin ^[4]; ^[5]

Stanford Univ., CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Stanford Univ., CA (United States); University of North Carolina, Wilmington, NC (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Stanford Univ., CA (United States)

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. In conclusion, the SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 2575492

Alternate ID(s):: OSTI ID: 2555921

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 3 Vol. 27; ISSN 1462-2920; ISSN 1462-2912

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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