Depth-related variation in the activity and community structure of nitrite- and nitrate-coupled anaerobic methanotrophs in freshwater lake sediment

Abstract

Nitrite- and nitrate-coupled anaerobic oxidation of methane (AOM), mediated by Candidatus Methylomirabilis-like bacteria and Methanoperedens-like archaea, respectively, are two recent additions of freshwater carbon and nitrogen cycles. However, the quantitative roles of the two AOM processes in CH₄ emission reduction in lakes have not yet been characterized. Here, we explored vertical (0–10, 10–20, and 20–30 cm) variation in nitrite- and nitrate-coupled AOM activity, as well as the abundance and community structure of Methylomirabilis- and Methanoperedens-like methanotrophs in freshwater lake sediment. The potential rates of nitrite- and nitrate-coupled AOM quantified via ¹³CH₄ isotopic experiments were 0.41–3.84 and 0.32–3.88 nmol CH₄/(g·d), respectively. The rates of AOM exhibited significant and consistent depth-related variation across different sampling sites, with both peaking in the 10–20 cm layer. The abundance of Methylomirabilis-like bacteria and Methanoperedens-like archaea quantified via quantitative PCR was 3.34 × 10⁵–9.17 × 10⁶ and 1.27 × 10⁶–9.46 × 10⁶ copies/g, respectively. There was no consistent depth-related variation in the abundance of bacteria or archaea. The community composition of both Methylomirabilis- and Methanoperedens-like methanotrophs remained relatively stable along the sediment profile, while the composition significantly changed across sampling sites. Sediment pH and the content of NH₄⁺ and organic carbon were key variables influencing the community structure of Methylomirabilis- and Methanoperedens-like methanotrophs. Overall, we characterized vertical variation in nitrite- and nitrate-coupled AOM processes in lake sediment, which helps quantify their role in CH₄ consumption in freshwater aquatic ecosystems.

Graphical abstract

Keywords

Nitrite- and nitrite-coupled AOM / Sediment depth / Methylomirabilis / Methanoperedens / Aquatic ecosystem

Highlight

	● Nitrite- and nitrate-coupled AOM activity both peaked at 10–20 cm sediment.
	● There was no consistent depth-related variation in abundance of the methanotrophs.
	● Community composition of methanotrophs remained relatively stable along the sediment.
	● Nitrite- and nitrate-coupled AOM showed equal importance in CH4 consumption.
	● Sediment pH, NH4+ and organic carbon contents were key factors affecting the AOM.

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