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<p>Nitrous oxide (N₂O) emission of fresh invertebrates has too long been neglected in eutrophic lakes, although the sediments these animals inhabit are presumably hot spots of N₂O emission. Thus, the experiment in this research was designed to gain insight into the influence of cyanobacteria<ins cite="mailto:lenovo" datetime="2014-09-24T20:23">l</ins> degradation on the N₂O emission by fresh water invertebrates<em> (Chironomus plumosus).</em><em> </em>The presence of decaying cyanobacteria in Lake Taihu decreased the N₂O emission rate of<em> Chironomus </em>plumosus larvae from the larvae body by almost 400% for the larvae as a whole. The N₂O emission rate decreased by 350% based on readings from studies of their gut, which was mostly due to stimulation of intestinal complete denitrification. The quantitative PCR results showed that intestinal gene abundance of <em>nirK</em>, <em>nosZ</em> (encoding the copper nitrite reductase and N₂O reductase, respectively) were significantly increased with the presence of decaying cyanobacteria. In contrast <em>nirS</em> (encoding the cytochrome cd₁heme nitrite reductase) and the total bacteria decreased. In the gut of <em>Chironomus plumosus</em><em>, </em>the diversity and richness of <em>nosZ</em> and <em>nirK</em> were lower with the cyanobacteria. Phylogenetic analysis of the intestinal function genes (<em>nosZ</em> and <em>nirK</em>) showed that the <em>nosZ</em>- and <em>nirK</em>-type denitrifying bacterial sequences were related to different phylotypes. Hence, additional cyanobacteria increased the abundance, but decreased the richness and diversity of intestinal nitrate-reducing bacteria, probably by providing more carbon source in the gut. The data obtained in this study elucidates that the decaying cyanobacteria decreased the emissions of N₂O by the aquatic invertebrates in freshwater sediment and could serve as a valuable resource for nitrogen removal affecting greenhouse gas emissions.</p>