Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain

Abstract

Riparian ﬂoodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and comammox bacteria from Slate River (SR) ﬂoodplain sediments (Crested Bute, CO, US). Addi�onally, we explore MAGs from poten�al nitrite-oxidizing 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-oxidizing 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 puta�ve NOB. Nitrite oxida�on 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 harbor genes for using alterna�ve 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. 3 14622920, 2025, 3, Downloaded from https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.70060 by National Energy Technology Laboratory, Wiley Online Library on [11/08/2025]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License

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