Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil.

Yang Ouyang,Jeanette M Norton

doi:10.3389/fmicb.2020.01736

Yang Ouyang, Jeanette M Norton

Open Access

https://doi.org/10.3389/fmicb.2020.01736

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Abstract

Autotrophic nitrification is mediated by ammonia oxidizing bacteria (AOB) or ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB). Mounting studies have examined the impact of nitrogen (N) fertilization on the dynamic and diversity of AOA and AOB, while we have limited information on the response of the activity, abundance, and diversity of NOB to N fertilization. We investigated the influence of organic and inorganic N fertilizers on soil NOB in silage corn field plots that received contrasting nitrogen (N) treatments: control (no additional N), ammonium sulfate (AS 100 and 200 kg N ha−1), and compost (200 kg N ha−1). Nitrifying community was examined using a universal marker (16S rRNA gene), functional gene markers (AOB amoA and Nitrospira nxrB), and metagenomics. The overall nitrifying community was not altered after the first fertilization but was significantly shifted by 4-year repeated application of ammonium fertilizers. Nitrospira were the dominant NOB (>99.7%) in our agricultural soil. Both community compositions of AOB and Nitrospira were significantly changed by ammonium fertilizers but not by compost after 4 years of repeated applications. All nitrifiers, including comammox, were recovered in soil metagenomes based on a gene-targeted assembly, but their sequence counts were very low. Although N treatment did not affect the abundance of Nitrospira nxrB determined by real-time quantitative PCR, ammonium fertilizers significantly promoted rates of potential nitrite oxidation determined at 0.15 mM nitrite in soil slurries. Understanding the response of both ammonia oxidizers and nitrite oxidizers to N fertilization may initiate or improve strategies for mitigating potential environmental impacts of nitrate production in agricultural ecosystems.

Highlights

Nitrification, the oxidation of ammonium to nitrite and nitrate, mobilizes soil nitrogen (N), and promotes N loss through nitrate leaching and denitrification and, often reduces N use efficiency in agricultural ecosystems (Norton and Ouyang, 2019)
Recent studies showed that potential nitrite oxidation (PNO) was much higher than potential ammonia oxidation (Ke et al, 2013)
Compared to our nitrification potentials (NP), PNO rates were much lower than NPs in the same soil samples (Ouyang et al, 2017)

Summary

Introduction

Nitrification, the oxidation of ammonium to nitrite and nitrate, mobilizes soil nitrogen (N), and promotes N loss through nitrate leaching and denitrification and, often reduces N use efficiency in agricultural ecosystems (Norton and Ouyang, 2019). Since nitrifiers are generally slow growing and recalcitrant to isolation, culture-independent molecular techniques, targeting 16S ribosomal RNA (rRNA) or functional marker genes, have been primarily used to investigate the quantity and diversity of these organisms in natural and managed ecosystems (Rotthauwe et al, 1997; Purkhold et al, 2000; Leininger et al, 2006; Attard et al, 2010; Prosser, 2011; Pester et al, 2012, 2014). The genes encoding the alpha or beta subunit of nitrite oxidoreductase (nxrA or nxrB) have been developed to detect and quantify NOB in pure cultures and environmental samples (Poly et al, 2008; Pester et al, 2014). Functional marker genes of nitrifiers, such as amoA and nxrB, often provide a higher phylogenetic resolution than 16S rRNA for discriminating nitrifiers on the strain and species levels (Norton et al, 2002; Pester et al, 2014, Aigle et al, 2019)

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