Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams

TL;DR

Cattle manure in farm dams increases methane and nitrous oxide emissions by altering microbial communities, but fencing can reduce these emissions.

Contribution

Identifies specific microbial mechanisms by which cattle manure increases greenhouse gas emissions in farm dams.

Findings

Fencing farm dams reduces methane and nitrous oxide emissions by promoting aerobic methanotrophs.

Manure increases greenhouse gas emissions by causing eutrophication and hypoxia, which stimulate denitrifiers and inhibit methanotrophs.

New methanotroph species were identified through metagenome-assembled genomes in fenced dams.

Abstract

Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.

We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.

Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-025-02314-4.

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