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Loss of biodiversity is considered to be detrimental to ecosystem function but a mechanistic understanding, and theoretical support, of this process in soil is lacking. Our previous studies found that reductive dechlorination of organochlorine pollutants is usually accompanied by methanogenesis in flooded paddy soil. Here, taking a typical organochlorine pesticide hexachlorocyclohexane isomers lindane (γ-HCH), as an example disturbance, we artificially manipulated the soil microbiome by inoculating irradiated-sterile soil with a serially diluted soil suspension to address the impact of microbial diversity loss on both γ-HCH degradation and methanogenesis. The presence of γ-HCH delayed methanogenesis in all treatments but methanogenesis with increasing dilution levels showed increasing performance. Dilution had little negative effect on the degradation rate of γ-HCH. Dilution intensified the coupling between γ-HCH degradation and methanogenesis, as evidenced by co-occurrence network and RDA analysis. Relative functional redundancy index (rFRI), community assembly, community structure and functional diversity were all significantly affected by dilution, with the bacterial community showing a greater divergence than archaea. Null model analyses suggest the relative contribution of stochastic process increased in bacterial community re-assembly with dilution but decreased in archaea. Intensified coupling between methanogenesis and dechlorination was related to specific microbial taxa. The loss of soil microbial diversity could have an important impact on specialized soil functions such as pollution remediation and greenhouse gas emission, with function restoration regulated by the competitive and synergistically-mediated mechanism of co-occurring microorganisms and assembly processes. • Soil microbial diversity was manipulated by the dilution-to-extinction approach. • Loss of microbial diversity led increased CH 4 emission. • Functional redundancy may maintain the degradation of γ-HCH under diversity loss. • Dilution enhanced the coupling between dechlorination and methanogenesis. • Both stochastic and deterministic assembly of microbes regulated specialized soil function. [ABSTRACT FROM AUTHOR]