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Background  Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH 4 ) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks.    Results  The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH 4  emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH 4  emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to  Methanobacterium, Methanocella ,  Methanothrix , and  Methanosarcina , possessed high linkages with the methane generation functional genes  mcrA ,  fwdB ,  mtbA,  and  mtbC . Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa.    Conclusions  These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions.Video abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s40168-020-00978-8.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies