Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO 2 g −1 (dry sediment) d − 1 , respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera ( M. oxyfera )-like bacteria and Candidatus Methanoperedens nitroreducens ( M. nitroreducens )-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 10 5 to 1.5 × 10 7 and 2.1 × 10 4 to 2.5 × 10 5 copies g − 1 dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera -like bacteria and M. nitroreducens -like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera -like bacteria and M. nitroreducens -like archaea are dominant.

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Summary Anaerobic ammonium oxidation (anammox) and nitrite‐dependent anaerobic methane oxidation (n‐damo) play important roles in nitrogen and carbon cycling in fresh waters but we do not know how these two processes compete for their common electron acceptor, nitrite. Here, we investigated the spatial distribution of anammox and n‐damo across a range of permeable riverbed sediments. Anammox activity and gene abundance were detected in both gravel and sandy riverbeds and showed a simple, common vertical distribution pattern, while the patterns in n‐damo were more complex and n‐damo activity was confined to the more reduced, sandy riverbeds. Anammox was most active in surficial sediment (0–2 cm), coincident with a peak in hzsA gene abundance and nitrite. In contrast, n‐damo activity peaked deeper down (4–8 cm) in the sandy riverbeds, coincident with a peak in n‐damo 16S rRNA gene abundance and higher methane concentration. Pore water nitrite, methane and oxygen were key factors influencing the distribution of these two processes in permeable riverbeds. Furthermore, both anammox‐ and n‐damo‐ activity were positively correlated with denitrification activity, suggesting a role for denitrification in supplying both processes with nitrite. Our data reveal spatial separation between anammox and n‐damo in permeable riverbed sediments that potentially avoids them competing for nitrite.

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The coupling between nitrification and N2 gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N2 gas. Here we show, in oxic riverbeds, that the pattern of N2 gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N2 gas that 20 years’ research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle.