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We studied the microbial functional and structure interactions between nitrate and selenate reductions in the H2 based membrane biofilm reactor (MBfR).When SeO42- was the only electron acceptor in Stage 1,40% of Se (Ⅵ) could be reduced to Se0 after 55 days of SeO42- addition,and 20% of influent total Se was transformed as Se (Ⅳ).In Stage 2,the Se removal was strongly inhibited by the addition of a higher concentration of NO3--N (10 mg/L),the NO3- reduction was inhibited by the presence of Se (80% removal).The Se reduction significantly increased since Stage 3 when the NO3- loading returned to zero,and maintained steady in Stage 4 and 5,when 1 and 5 mg/L of NO3--N were added respectively.However,through all stages,SeO42- could not be completely reduced to Se0.When SeO42- was the only input in Stage 1,the α-Proteobacteria counted about 30% of the total bacterial,the β-Proteobacteria represented about 55% of total bacterial in biofilm.When NO3- was introduced to the MBfR,the β-Proteobacteria became absolutely dominant phylotype,counted more than 90% in the biofilm.Even NO3- was removed from the influent in Stage 3,the microbial community structures were similar among stages 2,3,4 and 5.