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Sulfur (S) metabolism is an important biogeochemical cycles in lowland rice. However, S biogeochemistry in rice soil is underestimated due to low standing pools of sulfate and unknown taxa of sulfur-reducing microorganisms. A whole-genome metagenomic study considering KEGG pathways and prevalence of enzymatic assay could provide an insight of dominating pathways of S-metabolism which are important in the context of S nutrition to plant and of mitigating GHGs emission in relation to climate change feedback. In this study, soil bacterial diversity and S-metabolism pathways were studied under ambient CO2 (a-CO2) and elevated CO2 + temperature (e-CO2T) in lowland rice. The assimilatory pathway was the dominant irrespective of atmospheric CO2 concentrations indicated higher influence of ecology than atmospheric condition. The phylum Proteobacteria and Firmicutes were dominant and showed an abundance of 54 and 12%, under a-CO2 and e-CO2T, respectively. Desulfovibrio was the most dominant genus. Desulfatibacillum, Desulfotomaculum, Desulfococcus, and Desulfitobacterium also showed higher abundance reads under e-CO2T. As a whole, total bacterial diversities were more under a-CO2, whereas, the activities of dominant bacteria were higher under e-CO2T. Shannon-Weaver and Simpson indices were higher under e-CO2T than a-CO2. The targeted gene-based quantification of bacteria responsible for S-metabolism is the future need.